WO2018104893A1 - Anticorps anti-alpha4-beta7 présentant une liaison à fcrn et/ou une demi-vie augmentées - Google Patents

Anticorps anti-alpha4-beta7 présentant une liaison à fcrn et/ou une demi-vie augmentées Download PDF

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WO2018104893A1
WO2018104893A1 PCT/IB2017/057710 IB2017057710W WO2018104893A1 WO 2018104893 A1 WO2018104893 A1 WO 2018104893A1 IB 2017057710 W IB2017057710 W IB 2017057710W WO 2018104893 A1 WO2018104893 A1 WO 2018104893A1
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seq
antibody
antigen binding
fcrn
human
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Zhi Hong
Brian Alvin Johns
Gerald Wayne Gough
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Glaxosmithkline Intellectual Property Development Limited
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2839—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the integrin superfamily
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/513—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim having oxo groups directly attached to the heterocyclic ring, e.g. cytosine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/535—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
    • A61K31/5365—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines ortho- or peri-condensed with heterocyclic ring systems
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/66—Phosphorus compounds
    • A61K31/675—Phosphorus compounds having nitrogen as a ring hetero atom, e.g. pyridoxal phosphate
    • 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
    • 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
    • A61P31/14—Antivirals for RNA viruses
    • A61P31/18—Antivirals for RNA viruses for HIV
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/52—Constant or Fc region; Isotype
    • C07K2317/524—CH2 domain
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/52—Constant or Fc region; Isotype
    • C07K2317/526—CH3 domain
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/72—Increased effector function due to an Fc-modification
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/94—Stability, e.g. half-life, pH, temperature or enzyme-resistance

Definitions

  • the present invention relates to modified ⁇ 4 ⁇ 7 binding proteins and methods for treating an HIV infection in a subject using said modified antigen binding proteins.
  • the modified antigen binding proteins are Fc region-containing antigen binding proteins that have altered effector function, such as increased affinity for FcRn, wherein the method for treating an HIV infection results in a functional cure of the HIV infection in a subject.
  • Antigen binding proteins are proteins which exhibit binding specificity to a specific antigen.
  • native antibodies are usually heterotetrameric glycoproteins of about 150,000 daltons, composed of two identical light (L) chains and two identical heavy (H) chains. Each light chain is linked to a heavy chain by one covalent disulfide bond, while the number of disulfide linkages varies between the heavy chains of different immunoglobulin isotypes.
  • Each heavy and light chain also has regularly spaced intrachain disulfide bridges.
  • Each heavy chain has at one end a variable domain (VH) followed by a number of constant domains.
  • VH variable domain
  • Each light chain has a variable domain at one end (VL) and a constant domain at its other end; the constant domain of the light chain is aligned with the first constant domain of the heavy chain, l and the light chain variable domain is aligned with the variable domain of the heavy chain. Particular amino acid residues are believed to form an interface between the light and heavy chain variable domains.
  • the constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions such as participation in antibody dependent cell-mediated cytotoxicity (ADCC), phagocytosis via binding to Fey receptor, half-life/clearance rate via neonatal Fc receptor (FcRn) and complement dependent cytotoxicity (CDC) via the C1 q component of the complement cascade.
  • ADCC antibody dependent cell-mediated cytotoxicity
  • FcRn neonatal Fc receptor
  • CDC complement dependent cytotoxicity
  • antibodies or immunoglobulins can be assigned to different classes. There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG and IgM, and these may be further divided into subclasses (isotypes), e.g.
  • the heavy chain constant regions that correspond to the different classes of immunoglobulins are called ⁇ , ⁇ , ⁇ , ⁇ , and ⁇ , respectively.
  • different isotypes of IgG antibodies are known to have varying degrees of effector function for example human lgG1 and lgG3 mediate antibody-dependent cell-mediated cytotoxicity (ADCC) more effectively than lgG2 and lgG4.
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • FIG. 1 A schematic representation of the native lgG1 structure is shown in Fig. 1 , where the various portions of the native antibody molecule are indicated.
  • Papain digestion of antibodies produces two identical antigen binding fragments, called Fab fragments, each with a single antigen binding site, and a residual "Fc" fragment, whose name reflects its ability to crystallize readily.
  • the crystal structure of the human IgG Fc region has been determined (Deisenhofer, Biochemistry 20:2361-2370 (1981).
  • the Fc region is generated by papain cleavage N-terminal to Cys 226.
  • the Fc region is central to the effector functions of antibodies.
  • effector functions mediated by the antibody Fc region can be divided into two categories: (1) effector functions that operate after the binding of antibody to an antigen (these functions involve the participation of the complement cascade or Fc receptor (FcR)-bearing cells); and (2) effector functions that operate independently of antigen binding (these functions confer persistence in the circulation and the ability to be transferred across cellular barriers by transcytosis). (Ward and Ghetie, Therapeutic Immunology 2:77-94 (1995)).
  • IgG immunoglobulin G
  • FcRn plays a key role in maintaining serum antibody levels by acting as a protective receptor that binds and salvages antibodies of the IgG isotype from degradation.
  • IgG molecules are endocytosed by endothelial cells, and if they bind to FcRn, are recycled out into circulation.
  • IgG molecules that do not bind to FcRn enter the cells and are targeted to the lysosomal pathway where they are degraded.
  • the neonatal FcRn receptor is believed to be involved in both antibody clearance and the transcytosis across tissues (Junghans R.P (1997) Immunol.Res 16. 29-57 and Ghetie et al (2000) Annu. Rev. Immunol. 18, 739-766).
  • the FcRn interaction site encompasses three spatially close loops comprised of sequences that are distal in the primary amino acid sequence.
  • the central role of Fc histidines in building this site accounts for the marked pH-dependence (binding at pH 6.0, release at pH 7.2-7.4) of the Fc-FcRn interaction (Rodewald and .Kraehenbuhl, 1984; Raghavan et al, 1995; Popov et al., 1996).
  • This pH dependence is essential for the release of FcRn bound IgG molecules when they come to the cell surface following intracellular recycling or transcytosis (Ghetie and Ward, 2000; Ober et al., 2004).
  • Fc fragments of IgGs with increased affinity for binding to FcRn have been engineered (Ghetie et al., 1997; Shields et al., 2001; Hinton et al., 2004) and these molecules have increased serum persistence in mice (Ghetie et al., 1997) or cynomologous monkeys (Hinton et al., 2004).
  • Immunoglobulin Fc domains are also of great interest for purposes of studying the mechanisms of antibody interactions with further molecules of the immune system. These include, depending on the class of antibody, interactions with complement, and binding to specific receptors on other cells, including macrophages, neutrophils and mast cells. More detailed knowledge of the biology of Fc regions is important in understanding various molecular processes of the immune system, such as phagocytosis, antibody-dependent cell mediated cytotoxicity and allergic reactions.
  • IgGs there are multiple situations in which increased clearance of IgGs from the circulation would be desirable, e.g., in autoimmune diseases such as systemic lupus erythematosus (SLE) where circulating autoreactive antibodies cause pathology, and in situations where toxins or drugs are to be cleared rapidly from the body using an antibody as a clearing agent.
  • Increased clearance of an antibody should be achievable by using a molecule, such as an engineered antibody, that binds to FcRn with high affinity and does not dissociate rapidly at near neutral pH (unlike naturally-occurring antibodies).
  • Such antibodies would not be released from cells, but would instead be predicted to remain bound to FcRn and block binding of other, lower affinity IgGs.
  • FcRn function would be blocked and endogenous or therapeutic IgGs would be directed into the lysosomal pathway for degradation (Ober et al., 2004).
  • the targeting of such 'blocking' antibodies to FcRn might also be useful in the prevention of transport of pathogenic (e.g., autoreactive) antibodies from mother to fetus during pregnancy.
  • pathogenic (e.g., autoreactive) antibodies from mother to fetus during pregnancy.
  • the long half-life of IgG antibodies is reported to be dependent on its binding to FcRn.
  • vedolizumab reduces trafficking of c ⁇ 7-expressing CD4 + T cells to GITs, which is the basis for vedolizumab's use in treating inflammatory bowel disease (IBD).
  • IBD inflammatory bowel disease
  • WO 9734631 discloses a composition comprising a mutant IgG molecule having increased serum half-life and at least one amino acid substitution in the Fc-hinge region. Amino acid substitution at one or more of the amino acids selected from number 252, 254, 256, 309, 31 1 or 315 in the CH2 domain or 433 or 434 in the CH3 domain is disclosed.
  • WO 00/42072 discloses a polypeptide comprising a variant Fc region with altered FcRn binding affinity, which polypeptide comprises an amino acid modification at any one or more of amino acid positions 238, 252, 253, 254, 255, 256, 265, 272, 286, 288, 303, 305, 307, 309, 31 1 , 312, 317, 340, 356, 360, 362, 376, 378, 380, 386,388, 400, 413, 415, 424,433, 434, 435, 436, 439, and 447 of the Fc region.
  • WO 02/060919 discloses a modified IgG comprising an IgG constant domain comprising amino acid modifications at one or more of positions 251 , 253, 255, 285-290, 308-314, 385-389, and 428-435.
  • WO 2004035752 discloses a modified antibody of class IgG wherein at least one amino acid residue from the heavy chain constant region selected from the group consisting of amino acid residues 250, 314, and 428 is different from that present in an unmodified class IgG antibody.
  • Dall'Acqua et al. (2002, J Immunol. ;169:5171 -80) described random mutagenesis and screening of human lgG1 hinge-Fc fragment phage display libraries against mouse FcRn. They disclosed random mutagenesis of positions 251 , 252, 254-256, 308, 309, 31 1 , 312, 314, 385- 387, 389, 428, 433, 434, and 436.
  • WO2006130834 discloses modified IgG comprising an IgG constant domain comprising amino acid modifications at one or more positions of 252, 254, 256, 433, 434 and 436.
  • antigen binding proteins as therapeutics requires injections with a prescribed frequency relating to the clearance and half-life characteristics of the protein and, as such, if dosage frequency is high or target antigen is abundant there is a further need to modify the half-life of an antigen binding protein to gain maximal antigen clearance.
  • the invention relates to novel antigen binding proteins which bind specifically to ⁇ 4 ⁇ 7.
  • the invention relates to novel variants of anti-a 4 7 antibodies, such as Vedolizumab, Etrolizumab and AMG181/MEDI7183, which show increased binding to the FcRn receptor and/or increased half-life as compared to Vedolizumab, Etrolizumab and AMG181/MEDI7183, respectively.
  • Vedolizumab is an IgG monoclonal antibody comprising the variable light chain sequence of SEQ ID No: 7 and the variable heavy chain sequence of SEQ ID No: 8 and is detailed fully in US 7,147,851 and CAS registry No. 943609-66-3.
  • Vedolizumab is a full-length, humanized lgG1 monoclonal antibody that recognizes the ⁇ 4 ⁇ 7 integrin receptor (LPAM-1 ) of human and selected other species. It is composed of the humanized variable domains of the heavy and the light chains of the ACT-1 mouse monoclonal antibody and the constant domains of human lgG1 heavy chain and human kappa light chain. The two identical light chains are approximately 24 kilodaltons (kDa) each and the two identical heavy chains are approximately 49 kDa each.
  • LPAM-1 ⁇ 4 ⁇ 7 integrin receptor
  • the invention relates to an antigen binding protein which specifically binds to ⁇ 4 ⁇ 7 comprising CDRH 1 (SEQ ID NO: 1 ), CDRH2 (SEQ ID NO: 2), CDRH3 (SEQ ID No: 3), CDRL1 (SEQ ID NO: 4), CDRL2 (SEQ ID NO: 5), and CDRL3 (SEQ ID NO: 6) or variants thereof; and a neonatal Fc receptor (FcRn) binding portion of a human lgG1 constant domain comprising one or more amino acid substitutions relative to the human lgG1 constant domain, wherein the antigen binding protein has an increased FcRn binding affinity at pH 6 and/or increased half-life as compared to an IgG comprising the light chain sequence of SEQ ID No: 9 and the heavy chain sequence of SEQ ID No:10.
  • CDRH 1 SEQ ID NO: 1
  • CDRH2 SEQ ID NO: 2
  • CDRH3 SEQ ID No: 3
  • CDRL1 SEQ ID NO:
  • the modified FcRn binding portion has modifications at one or more of amino acid residues 251-256, 285-290, 308- 314, 385-389, and 428-436 that increase the affinity of the FcRn binding portion thereof for FcRn.
  • modifications are at one or more surface exposed residues, and the modification is a substitution with a residue of similar charge, polarity or hydrophobicity to the residue being substituted.
  • human lgG1 constant domain encompasses all allotypes and variants thereof known to a person skilled in the art.
  • the invention relates to an antigen binding protein which specifically binds to ⁇ 4 ⁇ 7 comprising CDRH 1 (SEQ ID NO: 1 ), CDRH2 (SEQ ID NO: 2), CDRH3 (SEQ ID No: 3), CDRL1 (SEQ ID NO: 4), CDRL2 (SEQ ID NO: 5), and CDRL3 (SEQ ID NO: 6) or variants thereof; and a FcRn binding portion of a human lgG1 constant domain comprising one or more amino acid substitutions relative to the human lgG1 constant domain, wherein the antigen binding protein has an increased FcRn binding affinity at pH 6 and/or increased half-life as compared to an IgG comprising the light chain sequence of SEQ ID No: 9 and the heavy chain sequence of SEQ ID No: 10 and the antigen binding protein can be administered no more than once every other day, or once every week, or once every 2 weeks, once every 3 weeks, once every 4 weeks, once every 5 weeks, once every 6 weeks
  • the modified antigen binding protein comprises a variant CDR.
  • a variant CDR comprises 1 , 2 or 3 mutations in the CDR region relative to the unmodified CDR.
  • the modified antigen binding protein comprises only one variant CDR.
  • the variant CDR has one amino acid substitution.
  • this CDR variant is a substitution with a residue of similar charge, polarity or hydrophobicity to the residue being substituted.
  • the invention relates to a modified antigen binding protein which specifically binds to ⁇ 4 ⁇ 7 comprising CDRH1 (SEQ ID NO: 1 ), CDRH2 (SEQ ID NO: 2), CDRH3 (SEQ ID No: 3), CDRL1 (SEQ ID NO: 4), CDRL2 (SEQ ID NO: 5), and CDRL3 (SEQ ID NO: 6) and variants thereof; and a FcRn binding portion of a human lgG1 constant domain comprising one of more amino acid substitutions relative to the human lgG1 constant domain, wherein the modified antigen binding protein has an increased FcRn binding affinity at pH 6 and/or increased half-life as compared to an IgG comprising the light chain sequence of SEQ ID No: 9 and the heavy chain sequence of SEQ ID No:10, wherein the modified antigen binding protein has an affinity for FcRn of 2 fold, or 3 fold, or 4 fold or 5 fold, or 6 fold or 8 fold or 12-fold or greater than
  • sequences described herein include sequences which are substantially identical, for example sequences which are at least 90% identical, for example which are at least 91 %, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97% or at least 98%, or at least 99% identical to the sequences described herein.
  • sequences which are at least 90% identical, for example which are at least 91 %, or at least 92%, or at least 93%, or at least 94%, or at least 95%, or at least 96%, or at least 97% or at least 98%, or at least 99% identical to the sequences described herein.
  • leader sequences for example, it will be appreciated that certain sequences are provided with leader sequences.
  • the invention relates to a modified antigen binding protein which is a variant of an IgG comprising the light chain sequence of SEQ ID No: 9 and the heavy chain sequence of SEQ ID No: 10, wherein the modified antigen binding protein comprises one or more substitutions in the FcRn binding portion of the IgG constant domain to increase the half- life of the modified antigen binding protein compared with the IgG without such substitutions, wherein when the modified antigen binding protein is administered to patients at a single dose of 20 to 30 mg every other day, weekly, once every other week, once every three weeks, once every 4 weeks, once every 5 weeks, once every 6 weeks, once every 7 weeks, to once every 8 weeks intervals, and wherein the mean steady-state trough concentration in the patient population does not fall below 9 ⁇ g mL to 15 ⁇ g mL, or does not fall below 20 ⁇ g mL to 30 ⁇ g mL, or does not fall below 35 ⁇ g /mL to 40 ⁇ g mL between do
  • the mean serum trough modified antigen binding protein concentration in the patient population does not fall below 40 ⁇ g mL between dosing intervals when the modified antigen binding protein is administered to patients at a single dose of 50 mg/kg every other day.
  • the mean serum trough modified antibody binding protein concentration in the patient population does not fall below 30 ⁇ g /mL between dosing intervals whilst still providing the optimal efficacy when the modified antibody binding protein is administered to patients at a single dose of 50 mg/kg at a weekly interval.
  • the mean serum trough modified antibody binding protein concentration in the patient population does not fall below 20 ⁇ g/mL between dosing intervals whilst still providing the optimal efficacy when the modified antibody binding protein is administered to patients at a single dose of 50 mg/kg mg at an interval of every 3 weeks.
  • the mean serum trough modified antibody binding protein concentration in the patient population does not fall below 15 ⁇ g/mL between dosing intervals whilst still providing the optimal efficacy when the modified antibody binding protein is administered to patients at a single dose of 50 mg/kg at an interval of every 4 weeks.
  • the mean serum trough modified antibody binding protein concentration in the patient population does not fall below 10 ⁇ g /mL between dosing intervals whilst still providing the optimal efficacy when the modified antibody binding protein is administered to patients at a single dose of 50 mg/kg at an interval of every 5 weeks, every 6 weeks, every 7 weeks or every 8 weeks.
  • the invention relates to a method of treating a patient with a disease, the method comprising administering an antigen binding protein according to the invention.
  • the antigen binding protein is administered in combination with an antiretroviral agent.
  • a therapeutically effective amount of one or more antiretroviral compounds is administered in combination with the antigen binding protein of the present invention.
  • the antiretroviral agent is one of the antiretroviral compounds listed in Figure 4 (Anti-Retroviral Therapy - ART) and wherein administration of the ART and the modified IgG polypeptide or modified IgG ⁇ 4 ⁇ 7 antibody is done together or separately, and may be administered concurrently, overlapping, or serially, in any order.
  • the ART regimen consists of raltegravir, tenofovir and emtricitabine, or the ART consists of dolutegravir, and the modified IgG ⁇ 4 ⁇ 7 antibody is modified vedolizumab, such that the method results in sustained virologic control of the HIV infection, achieving a "functional cure" of the HIV infection in the subject.
  • HIV persists in patients despite long-term ART such that, once ART is withdrawn, virus invariably rebounds. Therefore, there is a current unmet need for improved methods for treating subjects with HIV that will result in virologic control, and ultimately a cure or a "functional cure”.
  • a method of treating an HIV infection in a subject susceptible to or suffering from an HIV infection comprising administering to the subject a therapeutically effective amount of an antiretroviral agent as disclosed herein, and concurrently, sequentially, or in a staggered regimen administering a modified vedolizumab, wherein the modified vedolizumab constant domain or fragment thereof has higher affinity for FcRn at pH 6.0 than at pH 7.4, and may also alter (i.e., increase or decrease) the bioavailability (e.g., transport to mucosal surfaces, or other target tissues) of the modified vedolizumab.
  • the invention relates to a nucleic acid sequence encoding the antigen binding protein according to the invention, or a part thereof such as a heavy or light chain. In one aspect, the invention relates to an expression vector encoding the antigen binding protein according to the invention, or a part thereof such as a heavy or light chain.
  • the invention relates to a host cell comprising the nucleic acid sequence encoding the antigen binding protein according to the invention.
  • the invention relates to an antigen binding protein according to the invention for use in the treatment of Human Immunodeficiency virus (HIV).
  • HIV Human Immunodeficiency virus
  • the invention relates to a kit comprising the antigen binding protein according to the invention, and optionally comprising an antiretroviral agent for concomitant delivery.
  • the invention relates to an antigen binding protein as disclosed herein for treatment of HIV in an individual who is already being treated with an antiretroviral agent, and to an antigen binding protein in combination with an antiretroviral agent for treatment of HIV, wherein the combination is delivered simultaneously, substantially simultaneously, or sequentially.
  • Figure 1 is a schematic representation of a native IgG. Disulfide bonds are represented by heavy lines between CH1 and CL domains and the two CH2 domains. V is variable domain; C is constant domain; L stands for light chain and H stands for heavy chain.
  • Figure 2 shows the amino acid sequence (SEQ ID NO: 1 1) of the human lgG1 hinge-Fc region containing a hinge region, CH2 domain, and CH3 domain.
  • Figure 3 shows the relative positions of sites of three amino acid modifications (M252Y, S254T, T256E), in the Fc region of human igG1 , wherein modification at these sites in an Fc region is referred to as ⁇ " technology or a YTE variant.
  • Figure 4 is a list of anti-retroviral therapy (ART) suitable for use in methods of treating an HIV infection in a subject, in combination with a modified IgG antibody, such as a modified ⁇ 4 ⁇ 7 binding protein including a modified vedolizumab.
  • ART anti-retroviral therapy
  • Figure 5 shows a schematic for a treatment regimen, consistent with the methods of treating HIV in a subject as described herein, for achieving a functional cure for HIV.
  • antigen binding protein or " ⁇ 4 ⁇ 7 binding protein” as used herein refers to antibodies and other protein constructs, such as domains, which are capable of binding to ⁇ 4 ⁇ 7.
  • Modified antigen binding protein and " ⁇ 4 ⁇ 7 binding protein” means antibodies that specifically bind to ⁇ 4 ⁇ 7 and have been modified in the fc region by substitution, deletion, addition or other modification such as mutation in the binding protein sequence, particularly in the fc region of the binding protein sequence.
  • antibody is used herein in the broadest sense to refer to molecules with an immunoglobulin-like domain (for example IgG, IgM, IgA, IgD or IgE) and includes monoclonal, recombinant, polyclonal, chimeric, human, humanised, multispecific antibodies, including bispecific antibodies, and heteroconjugate antibodies; a single variable domain (e.g., VH, VHH, VL, domain antibody (dAbTM)), antigen binding antibody fragments, Fab, F(ab')2, Fv, disulphide linked Fv, single chain Fv, disulphide-linked scFv, diabodies, TANDABSTM, etc. and modified versions of any of the foregoing.
  • immunoglobulin-like domain for example IgG, IgM, IgA, IgD or IgE
  • a single variable domain e.g., VH, VHH, VL, domain antibody (dAbTM)
  • Fab fragment antigen binding antibody fragments
  • domain refers to a folded protein structure which retains its tertiary structure independent of the rest of the protein. Generally, domains are responsible for discrete functional properties of proteins and in many cases may be added, removed or transferred to other proteins without loss of function of the remainder of the protein and/or of the domain.
  • single variable domain refers to a folded polypeptide domain comprising sequences characteristic of antibody variable domains. It therefore includes complete antibody variable domains such as VH, VHH and VL and modified antibody variable domains, for example, in which one or more loops have been replaced by sequences which are not characteristic of antibody variable domains, or antibody variable domains which have been truncated or comprise N- or C-terminal extensions, as well as folded fragments of variable domains which retain at least the binding activity and specificity of the full-length domain.
  • a single variable domain is capable of binding an antigen or epitope independently of a different variable region or domain.
  • a single variable domain may be a human single variable domain, but also includes single variable domains from other species such as rodent nurse shark and Camelid VHH.
  • Camelid VHH are immunoglobulin single variable domain polypeptides that are derived from species including camel, llama, alpaca, dromedary, and guanaco, which produce heavy chain antibodies naturally devoid of light chains.
  • Such VHH domains may be humanised according to standard techniques available in the art, and such domains are considered to be "single variable domains".
  • VH includes camelid VHH domains.
  • An antigen binding fragment may be provided by means of arrangement of one or more CDRs on non-antibody protein scaffolds.
  • Protein Scaffold as used herein includes but is not limited to an immunoglobulin (Ig) scaffold, for example an IgG scaffold, which may be a four chain or two chain antibody, or which may comprise only the Fc region of an antibody, or which may comprise one or more constant regions from an antibody, which constant regions may be of human or primate origin, or which may be an artificial chimera of human and primate constant regions.
  • Ig immunoglobulin
  • the protein scaffold may be an Ig scaffold, for example an IgG, or IgA scaffold.
  • the IgG scaffold may comprise some or all the domains of an antibody (i.e. CH1 , CH2, CH3, VH, VL).
  • the antigen binding protein may comprise an IgG scaffold selected from IgG 1 , lgG2, lgG3, lgG4 or lgG4PE.
  • the scaffold may be lgG1.
  • the scaffold may consist of, or comprise, the Fc region of an antibody, or is a part thereof.
  • Antigen binding site or " a 4b 7 binding site” as used herein refers to a site on an antigen binding protein which is capable of specifically binding to an antigen, this may be a single variable domain, or it may be paired VH VL domains as can be found on a standard antibody.
  • Single-chain Fv (ScFv) domains can also provide antigen-binding sites.
  • a4b7 antigen binding site refers to a site on an a 4 7antigen binding protein - which is capable of specifically binding to an ⁇ 4 ⁇ 7 antigen.
  • epitope epitope independently of a different domain.
  • antigen binding proteins of the present disclosure show cross- reactivity between human a ⁇ 7 and a ⁇ from another species, such as cynomolgus monkey (cyno) ⁇ 4 ⁇ 7.
  • the antigen binding proteins of the invention specifically bind human and cyno ⁇ 4 ⁇ 7 This is particularly useful, since drug development typically requires testing of lead drug candidates in other systems before the drug is tested in humans. The provision of a drug that can bind human and cynomolgus species allows one to test results in these system and make side-by-side comparisons of data using the same drug.
  • the binding affinity of the antigen binding protein for at least cyno ⁇ ⁇ 7 and the binding affinity for human ⁇ ⁇ 7 differ by no more than a factor of 2, 5, 10, 50 or 100.
  • Affinity is the strength of binding of one molecule, e.g. an antigen binding protein of the invention, to another, e.g. its target antigen, at a single binding site.
  • the binding affinity of an antigen binding protein to its target may be determined by equilibrium methods (e.g. enzyme-linked immunoabsorbent assay (ELISA) or radioimmunoassay (RIA)), or kinetics (e.g. BiacoreTM analysis).
  • ELISA enzyme-linked immunoabsorbent assay
  • RIA radioimmunoassay
  • BiacoreTM analysis e.g. BiacoreTM analysis.
  • the BiacoreTM methods described in Examples 3 and 4 may be used to measure binding affinity.
  • IgG Fc region refers the portion of an IgG molecule that correlates to a crystallizable fragment obtained by papain digestion of an IgG molecule.
  • the Fc region consists of the C-terminal half of the two heavy chains of an IgG
  • the Fc fragment contains the entire second constant domain CH2 (residues 231 -340 of human lgG1 , according to the Kabat numbering system) (e.g., SEQ ID NO:80 of WO 02/060919) and the third constant domain CH3 (residues 341 -447) (e.g., SEQ ID NO:81 of WO 02/060919).
  • IgG hinge-Fc region or "hinge-Fc fragment” as used herein refers
  • the term "constant domain” refers to the portion of an immunoglobulin molecule having a more conserved amino acid sequence relative to the other portion of the
  • variable domain which contains the antigen binding site.
  • the constant domain contains the CHI, CH2 and CH3 domains of the heavy chain and the CHL domain of the light chain.
  • FcRn receptor or “FcRn” as used herein refers to an Fc receptor ("n" indicates neonatal) which is known to be involved in transfer of maternal IgGs to a fetus through the human or primate placenta, or yolk sac (rabbits) and to a neonate from the colostrum through the small intestine. It is also known that FcRn is involved in the maintenance of constant serum IgG levels by binding the IgG molecules and recycling them into the serum. The binding of FcRn to IgG molecules is strictly pH-dependent with optimum binding at pH 6.0.
  • FcRn comprises a heterodimer of two polypeptides, whose molecular weights are approximately 50 kD and 15 kD, respectively.
  • the extracellular domains of the 50 kD polypeptide are related to major histocompatibility complex (MHC) class I a-chains and the 15 kD polypeptide was shown to be the non-polymorphic ⁇ 2 microglobulin ( ⁇ 2- ⁇ ).
  • MHC major histocompatibility complex
  • ⁇ 2- ⁇ non-polymorphic ⁇ 2 microglobulin
  • FcRn is also expressed in various tissues across species as well as various types of endothelial cell lines.
  • in vivo half-life refers to a biological half-life of a particular type of IgG molecule or its fragments containing FcRn-binding sites in the circulation of a given animal and is represented by a time required for half the quantity administered in the animal to be cleared from the circulation and/or other tissues in the animal.
  • the curve is usually biphasic with a rapid a-phase which represents an equilibration of the injected IgG molecules between the intra- and extra- vascular space and which is, in part, determined by the size of molecules, and a longer ⁇ -phase which represents the catabolism of the IgG molecules in the intravascular space.
  • the term "in vivo half-life" practically corresponds to the half life of the IgG molecules in the ⁇ -phase.
  • an "isolated” or “purified” antibody or fusion protein is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the protein is derived, or substantially free of chemical precursors or other chemicals when chemically synthesized.
  • the language “substantially free of cellular material” includes preparations of an antibody or a fusion protein in which the antibody or the fusion protein is separated from cellular components of the cells from which it is isolated or recombinantly produced.
  • an antibody or a fusion protein that is substantially free of cellular material includes preparations of antibody or fusion protein having less than about 30%, 20%, 10%, or 5% (by dry weight) of contaminating protein.
  • the antibody or the fusion protein When the antibody or the fusion protein is recombinantly produced, it is also preferably substantially free of culture medium, i. e., culture medium represents less than about 20%, 10%, or 5% of the volume of the protein preparation.
  • culture medium represents less than about 20%, 10%, or 5% of the volume of the protein preparation.
  • the antibody or the fusion protein When the antibody or the fusion protein is produced by chemical synthesis, it is preferably substantially free of chemical precursors or other chemicals, i. e., it is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein. Accordingly such preparations of the antibody or the fusion protein have less than about 30%, 20%, 10%, 5% (by dry weight) of chemical precursors or compounds other than the antibody or antibody fragment of interest.
  • antibodies are isolated or purified.
  • fusion proteins are isolated or purified.
  • an "isolated" nucleic acid molecule is one which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid molecule. Moreover, an "isolated" nucleic acid molecule, such as a cDNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. An “isolated” nucleic acid molecule does not include cDNA molecules within a cDNA library.
  • host cell refers to the particular subject cell transfected with a nucleic acid molecule or infected with phagemid or bacteriophage and the progeny or potential progeny of such a cell. Progeny of such a cell may not be identical to the parent cell transfected with the nucleic acid molecule due to mutations or environmental influences that may occur in succeeding generations or integration of the nucleic acid molecule into the host cell genome.
  • the equilibrium dissociation constant (KD) of the antigen binding protein- ⁇ 4 ⁇ 7 interaction is 100 nM or less, 10 nM or less, 2 nM or less or 1 nM or less.
  • the KD may be between 5 and 10 nM; or between 1 and 2 nM.
  • the KD may be between 1 pM and 500 pM; or between 500 pM and 1 nM.
  • the reciprocal of KD i.e. 1/KD
  • KA equilibrium association constant having units M-1.
  • KA equilibrium association constant
  • the dissociation rate constant (kd) or "off-rate” describes the stability of the antigen binding protein- ⁇ 4 ⁇ 7 complex, i.e. the fraction of complexes that decay per second. For example, a kd of 0.01 s-1 equates to 1 % of the complexes decaying per second.
  • the dissociation rate constant (kd) is 1x10-3 s-1 or less, 1x10-4 s-1 or less, 1x10-5 s-1 or less, or 1x10-6 s-1 or less.
  • the kd may be between 1x10-5 s-1 and 1x10-4 s-1 ; or between 1x10-4 s-1 and 1x10-3 s-1.
  • neutralises as used throughout the present specification means that the biological activity of ⁇ 4 ⁇ 7 is reduced in the presence of an antigen binding protein as described herein in comparison to the activity of ⁇ 4 ⁇ 7. in the absence of the antigen binding protein, in vitro or in vivo. Neutralisation may be due to one or more of blocking ⁇ 4 ⁇ 7 binding to its receptor, preventing ⁇ ⁇ 7 from activating its receptor, down regulating ⁇ ⁇ 7 or its receptor, or affecting effector functionality.
  • CDRs are defined as the complementarity determining region amino acid sequences of an antigen binding protein. These are the hypervariable regions of immunoglobulin heavy and light chains. There are three heavy chain and three light chain CDRs (or CDR regions) in the variable portion of an immunoglobulin. Thus, “CDRs” as used herein refers to all three heavy chain CDRs, all three light chain CDRs, all heavy and light chain CDRs, or at least two CDRs.
  • CDR CDR
  • CDRL1 CDRL2
  • CDRL3 CDRH1
  • CDRH2 CDRH3
  • the minimum overlapping region using at least two of the Kabat, Chothia, AbM and contact methods can be determined to provide the "minimum binding unit".
  • the minimum binding unit may be a sub- portion of a CDR.
  • Table 1 represents one definition using each numbering convention for each CDR or binding unit.
  • the Kabat numbering scheme is used in Table 1 to number the variable domain amino acid sequence. It should be noted that some of the CDR definitions may vary depending on the individual publication used.
  • an antigen binding protein which comprises any one or a combination of the following CDRs:
  • CDRL1 of SEQ ID NO: 4 RSSQSLAKSYGNTYLS
  • CDRs or minimum binding units may be modified by at least one amino acid substitution, deletion or addition, wherein the variant antigen binding protein substantially retains the biological characteristics of the unmodified protein, such as Vedolizumab.
  • each of CDR H1 , H2, H3, L1 , L2, L3 may be modified alone or in combination with any other CDR, in any permutation or combination.
  • a CDR is modified by the substitution, deletion or addition of up to 3 amino acids, for example 1 or 2 amino acids, for example 1 amino acid.
  • the modification is a substitution, particularly a conservative substitution, for example as shown in Table 2 below.
  • amino acid residues of the minimum binding unit may remain the same, but the flanking residues that comprise the CDR as part of the Kabat or
  • Chothia definition(s) may be substituted with a conservative amino acid residue.
  • Such antigen binding proteins comprising modified CDRs or minimum binding units as described above may be referred to herein as "functional CDR variants” or “functional binding unit variants”.
  • epitope refers to that portion of the antigen that makes contact with a particular binding domain of the antigen binding protein.
  • An epitope may be linear or conformational/discontinuous.
  • a conformational or discontinuous epitope comprises amino acid residues that are separated by other sequences, i.e. not in a continuous sequence in the antigen's primary sequence. Although the residues may be from different regions of the peptide chain, they are in close proximity in the three dimensional structure of the antigen.
  • a conformational or discontinuous epitope may include residues from different peptide chains. Particular residues comprised within an epitope can be determined through computer modelling programs or via three-dimensional structures obtained through methods known in the art, such as X-ray crystallography.
  • competition between the antigen binding protein and a reference antibody may be determined by competition ELISA, FMAT or Biacore analysis. There are several possible reasons for this competition: the two proteins may bind to the same or overlapping epitopes, there may be steric inhibition of binding, or binding of the first protein may induce a
  • a neutralising antigen binding protein may neutralise the activity of c ⁇ by at least 20%, 30% 40%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 82%, 84%, 86%, 88%, 90%, 92%, 94%, 95%, 96%, 97%, 98%, 99% or 100% relative to ⁇ antigen> activity in the absence of the antigen binding protein.
  • Neutralisation may be determined or measured using one or more assays known to the skilled person or as described herein.
  • the CDRs L1 , L2, L3, H1 and H2 tend to structurally exhibit one of a finite number of main chain conformations.
  • the particular canonical structure class of a CDR is defined by both the length of the CDR and by the loop packing, determined by residues located at key positions in both the CDRs and the framework regions (structurally determining residues or SDRs).
  • Martin and Thornton (1996; J Mol Biol 263:800-815) have generated an automatic method to define the "key residue" canonical templates.
  • Cluster analysis is used to define the canonical classes for sets of CDRs, and canonical templates are then identified by analysing buried hydrophobics, hydrogen-bonding residues, and conserved glycines and prolines.
  • the CDRs of antibody sequences can be assigned to canonical classes by comparing the sequences to the key residue templates and scoring each template using identity or similarity matrices.
  • the particular canonical structure class of a CDR is defined by both the length of the CDR and by the loop packing, determined by residues located at key positions in both the CDRs and the framework regions.
  • Percent identity between a query amino acid sequence and a subject amino acid sequence is the "Identities" value, expressed as a percentage, that is calculated by the BLASTP algorithm when a subject amino acid sequence has 100% query coverage with a query amino acid sequence after a pair-wise BLASTP alignment is performed.
  • Such pair-wise BLASTP alignments between a query amino acid sequence and a subject amino acid sequence are performed by using the default settings of the BLASTP algorithm available on the National Center for Biotechnology Institute's website with the filter for low complexity regions turned off.
  • a query amino acid sequence may be described by an amino acid sequence identified in one or more claims herein.
  • the query sequence may be 100% identical to the subject sequence, or it may include up to a certain integer number of amino acid or nucleotide alterations as compared to the subject sequence such that the % identity is less than 100%.
  • the query sequence is at least 50, 60, 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99% identical to the subject sequence.
  • Such alterations include at least one amino acid deletion, substitution (including conservative and non-conservative substitution), or insertion, and wherein said alterations may occur at the amino- or carboxy-terminal positions of the query sequence or anywhere between those terminal positions, interspersed either individually among the amino acids or nucleotides in the query sequence or in one or more contiguous groups within the query sequence.
  • the % identity may be determined across the entire length of the query sequence, including the CDR(s). Alternatively, the % identity may exclude the CDR(s), for example the CDR(s) is 100% identical to the subject sequence and the % identity variation is in the remaining portion of the query sequence, so that the CDR sequence is fixed/intact.
  • the modified ⁇ 4 ⁇ 7 binding protein sequence substantially retains the biological characteristics of the unmodified antigen binding protein, such as vedolizumab
  • VH or VL sequence may be a variant sequence with up to 10 amino acid substitutions, additions or deletions.
  • the variant sequence may have up to 9, 8, 7, 6, 5, 4, 3, 2 or 1 amino acid substitution(s), addition(s) or deletion(s).
  • the HC sequence may be a variant sequence with up to 10 amino acid substitutions, additions or deletions.
  • the LC sequence may be a variant sequence with up to amino acid substitutions, additions or deletions.
  • the sequence variation may exclude the CDR(s), for example the CDR(s) is the same as the VH or VL (or HC or LC) sequence and the variation is in the remaining portion of the VH or VL (or HC or LC) sequence, so that the CDR sequence is fixed/intact.
  • the variation is a substitution, particularly a conservative substitution, for example as shown in Table 2 above.
  • the variant sequence substantially retains the biological characteristics of the unmodified protein, such as vedolizumab
  • the sequences are aligned for optimal comparison purposes (e. g. , gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino acid or nucleic acid sequence).
  • the amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position.
  • the determination of percent identity between two sequences can also be accomplished using a mathematical algorithm.
  • a preferred, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul, 1990, Proc. Natl. Acad. Sci. US.A. 87:2264-2268, modified as in Karlin and Altschul, 1993, Proc. Nat!. Acad. Sci. US.A. 90:5873-5877. Such an algorithm is incorporated into the N BLAST and XBLAST programs of Altschul et a!., 1990, 1. Mol. Biol. 215 :403.
  • Gapped BLAST can be utilized as described in Altschul et al. , 1997, Nucleic Acids Res. 25:3389-3402.
  • PSI-BLAST can be used to perform an iterated search which detects distant relationships between molecules (Id.).
  • the default parameters of the respective programs e.g., of XBLAST and N BLAST
  • Another preferred, non- limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, 1988, CAB/OS 4: 1 1 -17.
  • Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package.
  • ALIGN program version 2.0
  • the percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted.
  • cure indicates the eradication, cessation, stoppage, halt or end of the human immunodeficiency virus or symptoms, such as the HIV virus or symptoms, or the progression of the symptoms or virus, for a prescribed period.
  • cure means a therapeutic administration or a combination of
  • the term "functional cure” is used herein to indicate the goal of clearing the virus from the blood of the HIV infected subject and eliminating any negative effects.
  • “functional cure” of HIV means a subject infected with HIV will never develop AIDS (Acquired Immuno Deficiency Syndrome) or other signs of HIV disease, including premature aging, various cancers associated with immunodeficiency, pneumonias and any other infectious disease or other condition associated with a compromised immune system.
  • a functional cure of HIV in a subject is a practical one, and involves achieving sustained virologic control such that levels of HIV in the subject's blood remain undetectable, the subject's immune system functions well and remains robust, and the subject does not progress to AIDS.
  • Antibody drugs show unique complex pharmacokinetics, see for example, Wang (2008).
  • [00126] refers to the time required for the concentration of the antigen binding protein to reach half of its original value.
  • the serum half-life of proteins can be measured by standard pharmacokinetic studies, for example, using radiolabelled proteins administered via intravenous injection. Other methods for pharmacokinetic analysis and determination of the half-life of a molecule will be familiar to those skilled in the art. Reference is also made to Wang (2008). which describes pharmacokinetic parameters of relevance to antibody drugs.
  • Css steady state concentration
  • Microgram/ml "Mean steady-state trough concentration” refers to the mean of the trough level across the patient population at a given time.
  • Comparable mean steady-state trough concentration for the antigen binding proteins of the invention may be considered to be those mean steady-state trough concentrations that are 0.8 to 1 .25 times the mean steady-state trough concentration achieved with an IgG comprising the light chain sequence of SEQ ID No. 9 and the heavy chain sequence of SEQ ID No. 10.
  • Half lives and AUC can be determined from a curve of serum concentration of drug (for example the antigen binding protein of the present invention) against time.
  • Half life may be determined through compartmental or non-compartmental analysis.
  • the WINNONLINTM analysis package (available from Pharsight Corp., Mountain View, CA94040, USA) can be used, for example, to model the curve.
  • "half life" refers to the terminal half life.
  • the curve may be modelled to a 2-compartmental model.
  • the t alpha (t a) half life is the half life of the first phase and the t beta (t ⁇ ) half life is the half life of the second, in this case, terminal, phase i.e the terminal half life.
  • the curve may be modelled to a 3- compartmental model.
  • the terminal phase is the t gamma (t ⁇ ) half-life i.e. terminal half life.
  • a first phase (the alpha phase) of either a 2- or 3-compartmental distribution
  • the antigen binding protein is undergoing mainly distribution in the patient, along with
  • the present disclosure provides an antigen binding protein or a composition comprising an antigen binding protein according to the disclosure having a t alpha half life in the range of 15 minutes or more.
  • the lower end of the range is 30 minutes, 45 minutes, 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 10 hours, 1 1 hours or 12 hours.
  • an antigen binding protein or composition according to the disclosure will have a t alpha half life in the range of up to and including 12 hours.
  • the upper end of the range is 1 1 , 10, 9, 8, 7, 6 or 5 hours.
  • An example of a suitable range is 1 to 6 hours, 2 to 5 hours or 3 to 4 hours.
  • the terminal phase is when the antigen binding protein has been distributed and the serum concentration is decreasing as the ligand is cleared from the patient. Terminal half life can also be determined from non-compartmental analysis.
  • the present disclosure provides an antigen binding protein or a composition comprising an antigen binding protein according to the disclosure having a terminal half-life in the range of about 2.5 hours or more.
  • the lower end of the range is about 3 hours, about 4 hours, about 5 hours, about 6 hours, about 7 hours, about 10 hours, about 1 1 hours, or about 12 hours.
  • an antigen binding protein composition according to the disclosure has a terminal half life in the range of up to and including 21 days.
  • the upper end of the range is about 12 hours, about 24 hours, about 2 days, about 3 days, about 5 days, about 10 days, about 15 days or about 20 days.
  • an antigen binding protein or composition according to the disclosure will have a terminal half life in the range about 12 to about 60 hours. In a further embodiment, it will be in the range about 12 to about 48 hours. In a further embodiment still, it will be in the range about 12 to about 26 hours.
  • the present disclosure provides an antigen binding protein or a composition comprising an antigen binding protein according to the disclosure having an AUC value (area under the curve) in the range of about 1 mg « min/mL or more.
  • the lower end of the range is about 5, about 10, about 15, about 20, about 30, about 100, about 200 or about 300 mg « min/mL.
  • an antigen binding protein or composition according to the disclosure has an AUC in the range of up to about 600 mg « min/mL.
  • the upper end of the range is about 500, about 400, about 300, about 200, about 150, about 100, about 75 or about 50 mg « min/mL.
  • an antigen binding protein according to the disclosure will have a AUC in the range selected from the group consisting of the following: about 15 to about 150 mg « min/mL about 15 to about 100 mg « min/mL, about 15 to about 75 mg « min/mL, and about 15 to about
  • an antigen binding protein is increased if its concentration and/or functional activity persists, in vivo, for a longer period than a similar antigen binding protein which is not bound to or does not bind a half-life increasing molecule.
  • an antigen binding protein which comprises a half-life increasing molecule, or a moiety specific for a half life increasing molecule, and a moiety specific for a target molecule is compared with the same antigen binding protein wherein half-life increasing moiety is not present.
  • an antigen binding protein which comprises a moiety specific for serum albumin and a moiety specific for a target molecule is compared with the same antigen binding protein wherein the moiety with specificity to serum albumin is not present.
  • the antigen binding protein for comparison may lack a moiety specific for serum albumin and/or may comprise a "dummy dAbTM", i.e. a non-binding dAbTM, instead of the moiety specific for serum albumin.
  • the half-life is increased by 10%, 20%, 30%, 40%, 50% or more. Increases in the range of 2x, 3x, 4x, 5x, 10x, 20x, 30x, 40x, 50x or more of the half-life are possible. Alternatively, or in addition, increases in the range of up to 30x, 40x, 50x, 60x, 70x, 80x, 90x, 100x, 150x of the half life are possible.
  • the clearance rate in ⁇ -phase is calculated and compared with that of the unmodified IgG.
  • Antigen binding protein as described herein may be incorporated into
  • the pharmaceutical composition for use in the treatment of the human diseases described herein.
  • the pharmaceutical composition comprises an antigen binding protein optionally in combination with one or more pharmaceutically acceptable carriers and/or excipients.
  • compositions comprise a pharmaceutically acceptable carrier as known and called for by acceptable pharmaceutical practice.
  • compositions may be administered by injection or continuous infusion (examples include, but are not limited to, intravenous, intraperitoneal, intradermal, subcutaneous, intramuscular and intraportal).
  • the composition is suitable for parenteral administration.
  • Pharmaceutical compositions may be suitable for topical administration (which includes, but is not limited to, epicutaneous, inhaled, intranasal or ocular administration) or enteral administration (which includes, but is not limited to, oral or rectal administration).
  • compositions may comprise between 1 mg to 10g of antigen binding protein, for example between 5 mg and 1 g of antigen binding protein.
  • the composition may comprise between 5 mg and 500 mg, for example between 5 mg and 50 mg.
  • Effective doses and treatment regimes for administering the antigen binding protein may be dependent on factors such as the age, weight and health status of the patient and disease to be treated. Such factors are within the purview of the attending physician.
  • the pharmaceutical composition may comprise a kit of parts of the antigen binding protein together with other medicaments, optionally with instructions for use.
  • the kit may comprise the reagents in predetermined amounts with instructions for use.
  • the terms "individual”, “subject” and “patient” are used herein interchangeably.
  • the subject is a mammal, such as a primate, for example a marmoset or monkey.
  • the subject is a human.
  • the antigen binding protein described herein may also be used in methods of treatment.
  • Treatment can be therapeutic, prophylactic or preventative. Treatment encompasses alleviation, reduction, or prevention of at least one aspect or symptom of a disease and encompasses prevention or cure of the diseases described herein.
  • the antigen binding protein described herein is used in an effective amount for therapeutic, prophylactic or preventative treatment.
  • a therapeutically effective amount of the antigen binding protein described herein is an amount effective to ameliorate or reduce one or more symptoms of, or to prevent or cure, the disease.
  • disease includes syndromes and conditions associated with or resulting from a viral infection, such as an HIV infection.
  • disease includes the HIV infection itself, and the acquired immunodefiniciency syndrome - i.e. AIDS - that may result from an HIV infection.
  • Antigen binding proteins may be prepared by any of a number of conventional techniques. For example, antigen binding proteins may purified from cells that naturally express them (e.g., an antibody can be purified from a hybridoma that produces it), or produced in recombinant expression systems.
  • a number of different expression systems and purification regimes can be used to generate the antigen binding protein of the invention.
  • host cells are transformed with a recombinant expression vector encoding the desired antigen binding protein.
  • a wide range of host cells can be employed, including Prokaryotes (including Gram negative or Gram positive bacteria, for example Escherichia coli, Bacilli sp., Pseudomonas sp., Co ryne bacterium sp.), Eukaryotes including yeast (for example Saccharomyces cerevisiae, Pichia pastoris), fungi (for example Aspergilus sp.), or higher Eukaryotes including insect cells and cell lines of mammalian origin (for example, CHO, Perc6, HEK293, HeLa).
  • the host cell may be an isolated host cell.
  • the host cell is usually not part of a multicellular organism (e.g., plant or animal).
  • the host cell may be a non-human host cell.
  • Appropriate cloning and expression vectors for use with bacterial, fungal, yeast, and mammalian cellular hosts and methods of cloning are known in the art.
  • the cells can be cultured under conditions that promote expression of the antigen binding protein, and the polypeptide recovered by conventional protein purification procedures.
  • the antigen binding proteins contemplated for use herein include substantially homogeneous antigen binding proteins substantially free of contaminating materials.
  • the present invention encompasses the use of antibodies which have been subjected to, or have undergone, one or more post-translational modifications.
  • the modification may occur in a CDR, the variable framework region, or the constant region.
  • the modification may result in a change in charge of the molecule.
  • the modification typically does not result in a change in antigen binding, function, bioactivity, nor does it impact the PK/PD.
  • ADCC Antibody dependent cell mediated cytotoxic activity
  • CDC Complement-dependent cytotoxic activity
  • ADCP antibody dependent cellular phagocytosis
  • FcR Fc receptors
  • FcR Fc receptors
  • FcR Fc receptors
  • FcR Fc receptors
  • Significant biological effects can be a consequence of effector functionality.
  • the ability to mediate effector function requires binding of the antigen binding protein to an antigen and not all antigen binding proteins will mediate every effector function.
  • Effector function can be measured in a number of ways including for example via binding of the FCYRI I I to Natural Killer cells or via FcvRI to monocytes/macrophages to measure for ADCC effector function.
  • an antigen binding protein of the present invention can be assessed for ADCC effector function in a Natural Killer cell assay. Practical approaches to evaluate ADCC and /or CDC function can be found in Kellner (2013).
  • novel modified antigen binding proteins of the invention have an increased binding to the FcRn receptor and/or increased half-life and/or increased Mean Residence Time and/or decreased Clearance. It is considered that binding to FcRn results in longer serum retention in vivo. In order to increase the retention of the Fc proteins in vivo, the increase in binding affinity is observed around pH 6. In one aspect, the present invention therefore provides a modified antigen binding protein with optimized binding to FcRn.
  • the invention relates to an antigen binding protein which specifically binds to ⁇ 4 ⁇ 7 comprising CDRH 1 (SEQ ID NO: 1 ), CDRH2 (SEQ ID NO: 2), CDRH3 (SEQ ID No: 3), CDRL1 (SEQ ID NO: 4), CDRL2 (SEQ ID NO: 5), and CDRL3 (SEQ ID NO: 6), or a CDR variant(s) thereof; and a neonatal FcRn binding portion of a human lgG1 constant domain comprising one or more amino acid substitutions relative to the human lgG 1 constant domain, wherein the antigen binding protein has an increased FcRn binding affinity at pH 6 and/or increased half-life as compared to an IgG comprising the light chain sequence of SEQ ID No: 9 and the heavy chain sequence of SEQ ID No: 10.
  • a variant CDR comprises 1 , 2 or 3 mutations in one or more of the CDR regions. In a further embodiment this variant is in only one of the CDR's. In one particular embodiment the variant has one amino acid substitution. In a further embodiment this variant is a substitution with a residue of similar charge, polarity or hydrophobicity to the residue being substituted.
  • the modified FcRn binding portion has modifications at one or more of amino acid residue positions 251 -256, 285-290, 308-314,385-389, and 428-436 that increase the affinity of the FcRn binding portion thereof for FcRn.
  • the present invention therefore provides a modified ⁇ 4 ⁇ 7 binding protein with optimized binding to FcRn.
  • the modified ⁇ 4 ⁇ 7 binding protein comprises at least one amino acid modification in the Fc region of said a p 7 antigen binding protein, wherein said modification occurs at a position selected from the group consisting of 226, 227, 228, 230, 231 , 233, 234, 239, 241 , 243, 246, 250, 252, 256, 259, 264, 265, 267, 269, 270, 276, 284, 285, 288, 289, 290, 291 , 292, 294, 297, 298, 299, 301 , 302, 303, 305, 307, 308, 309, 31 1 , 315, 317, 320, 322, 325, 327, 330, 332, 334, 335, 338, 340, 342, 343, 345, 347, 350, 352, 354, 355, 356, 359, 360, 361
  • the one or more amino acid substitution in the FcRn binding portion of the human lgG1 heavy chain constant domain of the modified antigen binding protein is at amino acid residue positions 252, 254 and 256 numbered according to EU index of Kabat.
  • the amino acid substitution at position 252 is a substitution of M (Met) with Y (Tyr), F (Phe), S (Ser), W (Trp) or T (Thr);
  • the amino acid substitution at position 254 is a substitution of S (Ser) with T (Thr);
  • the amino acid substitution at position 256 is a substitution of T (Thr) with S (Ser), R (Arg), Q (Gin), E (Glu), D (Asp), A (Ala), N(Asn) or T (Thr).
  • the amino acid substitution at position 252 is a substitution with tyr;
  • the antigen binding proteins of the present invention comprise modifications at one or more of Tyr252, Thr254 and Glu256; specifically Tyr252 and Thr254; Tyr252 and Glu256; Thr254 and Glu256; or Tyr252, Thr254 and Glu256.
  • the substitutions present in the modified antigen binding protein are M252Y or S254T or T256E, i.e the ⁇ " modification.
  • the antigen binding proteins of the present invention comprise modifications at positions His433Lys or Asn434Phe or Tyr436 (to any amino acid).
  • the modifications present are Lys433 and Phe434.
  • the modifications present are Lys433, Phe434 and Tyr436.
  • the invention relates to an ⁇ 4 ⁇ 7 binding protein comprising CDRH1 (SEQ ID NO: 1 ), CDRH2 (SEQ ID NO: 2), CDRH3 (SEQ ID No: 3), CDRL1 (SEQ ID NO: 4), CDRL2 (SEQ ID NO: 5), and CDRL3 (SEQ ID NO: 6), or a variant(s) thereof; and a FcRn binding portion of a human lgG1 constant domain comprising modifications His433Lys and Asn434Phe relative to the human lgG1 constant domain, wherein the a 4 7binding protein has an increased FcRn binding affinity at pH 6 and/or increased half-life as compared to an IgG comprising the light chain sequence of SEQ ID No. 9 and the heavy chain sequence of SEQ ID No. 10.
  • the invention relates to an a 4 7binding protein comprising CDRH1 (SEQ ID NO: 1 ), CDRH2 (SEQ ID NO: 2), CDRH3 (SEQ ID No: 3), CDRL1 (SEQ ID NO: 4), CDRL2 (SEQ ID NO: 5), and CDRL3 (SEQ ID NO: 6) or variants thereof; and a FcRn binding portion of a human lgG1 constant domain comprising modifications His433Lys and Asn434Phe relative to the human lgG1 constant domain, wherein the a 4 7binding protein has an increased FcRn binding affinity at pH 6 and/ or increased half-life as compared to an IgG comprising the light chain sequence of SEQ ID No. 9 and the heavy chain sequence of SEQ ID No.10.
  • the human IgGI molecule show a ⁇ 6-fold higher binding affinity for human FcRn relative to wild-type. Importantly, it retains pH-dependent binding to FcRn.
  • Using an ex vivo placental transport model it shows increased transport across the placental barrier, and is predicted to have improved serum persistence. It would also be expected to be transported more efficiently across cells that express FcRn, such as bronchial or intestinal epithelia (Spiekerman et ai, 2002; Dickinson et ai, 1999; Yoshida et ai, 2004).
  • the one or more amino acid substitution in the FcRn binding portion of the human lgG1 constant domain is at amino acid residues 259 or 308 numbered according to EU index of Kabat.
  • the substitution at residue 259 is a substitution of Val with lie and the aa substitution at residue 308 is a substitution of val with phe.
  • the one or more amino acid substitution in the FcRn binding portion of the human lgG1 heavy chain constant domain is at amino acid residues 257 and 434 numbered according to EU index of Kabat.
  • the one or more amino acid substitution in the FcRn binding portion of the human lgG1 heavy chain constant domain is at amino acid residues 433 and 434 numbered according to EU index of Kabat for example the residues are H433K and N434F.
  • the antigen binding proteins of the present invention comprise modifications at positions Met428Leu or Asn434Ser or Asn434Phe. [00183] In a further embodiment the modifications present are Met428Leu and
  • the antigen binding protein is an antibody.
  • the antibody is humanized, chimeric or human. In a further embodiment it is humanized. In yet a further embodiment the antibody is a monoclonal antibody.
  • substitutions in the constant region are able to significantly improve the functions of therapeutic IgG antibodies, substitutions in the strictly conserved constant region have the risk of immunogenicity in human (Presta, supra, 2008; De Groot and Martin, Clin Immunol 131: 189-201, 2009) and substitution in the highly diverse variable region sequence might be less immunogenic.
  • variable region reports concerned with the variable region include engineering the CDR residues to improve binding affinity to the antigen (Rothe et al., Expert Opin Bioi Ther 6: 177-187,2006; Bostrom et a I., Methods Mol Bioi 525: 353-376,2009; Thie et a I., Methods Mol Bioi 525: 309-322, 2009) and engineering the CDR and framework residues to improve stability ⁇ Worn and Pluckthun, J Mol Bioi 305: 989-1010, 2001; Ewert et al., Methods 34: 184-199, 2004) and decrease immunogenicity risk (De Groot and Martin, supra, 2009; Jones et al., Methods Mol Bio 525: 405-423, xiv, 2009).
  • improved affinity to the antigen can be achieved by affinity maturation using the phage or ribosome display of a randomized library.
  • Improved stability can be rationally obtained from sequence- and structure-based rational design.
  • Decreased immunogenicity risk can be accomplished by various humanization methodologies and the removal of T-cell epitopes, which can be predicted using in silico technologies or determined by in vitro assays. Additionally, variable regions have been engineered to lower pi. A longer half-life was observed for these antibodies as compared to wild type antibodies despite comparable FcRn binding.
  • Engineering or selecting antibodies with pH dependent antigen binding to modify antibody and/or antigen half-life eg lgG2 antibody half-life can be shortened if antigen-mediated clearance mechanisms normally degrade the antibody when bound to the antigen.
  • the antigen:antibody complex can impact the half-life of the antigen, either extending half-life by protecting the antigen from the typical degradation processes, or shortening the half-life via antibody-mediated degradation.
  • One embodiment relates to antibodies with higher affinity for antigen at pH 7.4 as compared to endosomal pH (i.e., pH 5.5-6.0) such that the KD ratio at pH5.5/ pH 7.4 or at pH 6.0/ pH 7.4 is 2 or more.
  • PK pharmacokinetic
  • PD pharmacodynamic
  • the half-life of the antigen binding protein of the present invention is increased 2 to 6 fold, such as 2 fold, 3 fold, 4 fold, 5 fold or 6 fold as compared to an IgG comprising the light chain sequence of SEQ ID No. 9 and heavy chain sequence of SEQ ID No.10.
  • the half-life of the antigen binding protein of the invention is increased 2 fold 3 fold, 4 fold, or more compared to an IgG comprising the light chain sequence of SEQ ID No. 9 and heavy chain sequence of SEQ ID No.10.
  • an antigen binding protein of the present invention shows a half life of about 30 to 60 days.
  • the antigen binding protein of the invention can be administered once every 2, 3, 4, 5, 6, 7 or 8 weeks to achieve comparable mean steady- state trough concentrations as those achieved by vedolizumab, when administered once every two weeks at the same dose.
  • the antigen binding protein of the invention can be administered once every 3 or 4 weeks.
  • the antigen binding protein of the invention can be administered once every 5 or 6 weeks.
  • the antigen binding protein of the invention can be administered once every 7 or 8 weeks.
  • the invention relates to a method of treating a human patient with a disease, the method comprising administering an antigen binding protein according to the invention.
  • the invention also relates to an antigen binding protein as disclosed herein for the treatment of disease in a human.
  • the invention also relates to use of an antigen binding protein as disclosed herein in the manufacture of a medicament for the treatment of disease, and an antigen binding protein as disclosed herein for use in treatment of disease.
  • the disease to be treated by the antigen binding protein of the invention is HIV.
  • the present invention provides a method of treating an HIV infection in a subject susceptible to or suffering from an HIV infection, comprising administering to the subject a therapeutically effective amount of an antiretroviral agent as disclosed herein, and concurrently, sequentially, or in a staggered regimen administering an antigen binding protein according to the invention as herein described.
  • the invention also provides a polynucleotide sequence encoding any amino acid sequence disclosed herein, including a heavy chain of any of the antigen binding constructs described herein, and a polynucleotide encoding a light chain of any of the antigen binding constructs described herein.
  • polynucleotides represent the coding sequence which corresponds to the equivalent polypeptide sequences, however it will be understood that such polynucleotide sequences could be cloned into an expression vector along with a start codon, an appropriate signal sequence and a stop codon.
  • the polynucleotide may be DNA or RNA.
  • the invention also provides a host cell, for example a recombinant, transformed or transfected cell, comprising one or more polynucleotides encoding a heavy chain and/or a light chain of any of the antigen binding constructs described herein.
  • a host cell for example a recombinant, transformed or transfected cell, comprising one or more polynucleotides encoding a heavy chain and/or a light chain of any of the antigen binding constructs described herein.
  • the invention further provides a pharmaceutical composition comprising an antigen binding construct as described herein a pharmaceutically acceptable carrier.
  • the invention further provides a method for the production of any of the antigen binding constructs described herein which method comprises the step of culturing a host cell comprising a first and second vector, said first vector comprising a polynucleotide encoding a heavy chain of any of the antigen binding constructs described herein and said second vector comprising a polynucleotide encoding a light chain of any of the antigen binding constructs described herein, in a serum- free / chemically defined / animal derived component free culture media.
  • a method may comprise culturing a host cell comprising a vector comprising a polynucleotide encoding a heavy chain of any of the antigen binding constructs described herein and a polynucleotide encoding a light chain of any of the antigen binding constructs described herein, suitably in a serum- free / chemically defined / animal derived component free culture media.
  • the invention includes a method of increasing the half- life of an antibody by modifying an Fc according to the modifications described herein.
  • the invention includes an antigen binding protein as described herein with enhanced FcRn binding and having one or more additional substitutions, deletions or insertions that modulate another property of the effector function.
  • the antigen binding protein of the invention is then examined for in vitro activity by use of an appropriate assay.
  • an appropriate assay Presently conventional ELISA and Biacore assay formats are employed to assess qualitative and quantitative binding of the antigen binding construct to its target. Additionally, other in vitro assays may also be used to verify neutralizing efficacy prior to subsequent human clinical studies performed to evaluate the persistence of the antigen binding protein in the body despite the usual clearance mechanisms.
  • the dose and duration of treatment relates to the relative duration of the molecules of the present invention in the human circulation, and can be adjusted by one of skill in the art depending upon the condition being treated and the general health of the patient based on the information provided herein. It is envisaged that repeated dosing (e.g. once every 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks or 8 weeks) over an extended time period (e.g. four to six months or 9 to 12 months) maybe required to achieve maximal therapeutic efficacy.
  • repeated dosing e.g. once every 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks or 8 weeks
  • an extended time period e.g. four to six months or 9 to 12 months
  • the mode of administration of the therapeutic agent of the invention may be any suitable route which delivers the agent to the host.
  • the antigen binding proteins, and pharmaceutical compositions of the invention are particularly useful for parenteral
  • antigen binding proteins and pharmaceutical compositions of the invention are administered via a subcutaneous auto injector pen or a subcutaneous pre-filled syringe.
  • Antigen binding proteins of the invention may be prepared as pharmaceutical compositions containing an effective amount of the antigen binding protein of the invention as an active ingredient in a pharmaceutically acceptable carrier.
  • a pharmaceutically acceptable carrier preferably an aqueous carrier.
  • a variety of aqueous carriers may be employed, e.g., 0.9% saline, 0.3% glycine, and the like. These solutions may be made sterile and generally free of particulate matter.
  • compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, etc.
  • concentration of the antigen binding protein of the invention in such pharmaceutical formulation can vary widely, i.e., from less than about 0.5%, usually at or at least about 1 % to as much as 15 or 20% by weight and will be selected primarily based on fluid volumes, viscosities, etc., according to the particular mode of administration selected.
  • inventions provide a method of treating an HIV infection in a subject susceptible to or suffering from an HIV infection, comprising administering to the subject a therapeutically effective amount of an a nti retroviral agent as disclosed herein, and concurrently, sequentially, or in a staggered regimen administering a modified vedolizumab, wherein the modified vedolizumab has an IgG constant domain or fragment thereof (preferably, Fc or hinge-Fc domain) (preferably human), having amino acid modifications at one or more of positions 251 , 252, 254, 255, 256, 428, 433 and 434 more specifically, having substitutions at one or more of these positions.
  • IgG constant domain or fragment thereof preferably, Fc or hinge-Fc domain
  • residue 251 is substituted with leucine or arginine
  • residue 252 is substituted with tyrosine, phenylalanine, serine, tryptophan or threonine
  • residue 254 is substituted with threonine or serine
  • residue 255 is substituted with leucine, glycine, isoleucine or arginine
  • residue 256 is substituted with serine, arginine, glutamine, glutamic acid, aspartic acid, alanine, asparagines or threonine.
  • residue 251 is substituted with leucine
  • residue 252 is substituted with tyrosine
  • residue 254 is substituted with threonine or serine
  • residue 255 is substituted with arginine
  • residue 252 is substituted with phenylalanine and/or residue 256 is substituted with aspartic acid.
  • residue 251 is substituted with leucine
  • residue 252 is substituted with tyrosine
  • residue 254 is substituted with threonine or serine
  • residue 255 is substituted with arginine.
  • the invention further relates to methods of treating an HIV infection in a subject susceptible to or suffering from an HIV infection as described, wherein the modified vedolizumab constant domain or fragment thereof has any combination of these amino acid substitutions.
  • Still other embodiments of the invention provide a method of treating an HIV infection in a subject susceptible to or suffering from an HIV infection, comprising administering to the subject a therapeutically effective amount of an a nti retroviral agent as disclosed herein, and concurrently, sequentially, or in a staggered regimen administering a modified vedolizumab, wherein the modified vedolizumab has an lgG1 constant domain, or FcRn-binding fragment thereof (preferably, Fc or hinge-Fc domain) (preferably human), having amino acid modifications at one or more of positions 428, 433, 434, and 436, more specifically, having substitutions at one or more of these positions.
  • residue 428 is substituted with methionine, threonine, leucine, phenylalanine, or serine
  • residue 433 is substituted with lysine, arginine, serine, isoleucine, proline, glutamine, or histidine
  • residue 434 is substituted with phenylalanine, tyrosine, or histidine
  • residue 436 is substituted with histidine, asparagine, arginine, threonine, lysine, methionine, or threonine.
  • residues at one or more positions 433, 434, and 436 are substituted with lysine, phenylalanine, and histidine, respectively.
  • residue 428 is substituted with methionine and/or residue 434 is substituted with tyrosine.
  • Still other embodiments of the invention provide a method of treating an HIV infection in a subject susceptible to or suffering from an HIV infection, comprising administering to the subject a therapeutically effective amount of an a nti retroviral agent as disclosed herein, and concurrently, sequentially, or in a staggered regimen administering a modified vedolizumab, wherein the modified vedolizumab has an lgG1 constant domain, or FcRn-binding fragment thereof (preferably, Fc or hinge-Fc domain) (preferably human), having amino acid modifications at one or more positions 385,386,387, and 389, more specifically, having substitutions at one or more of these positions.
  • residue 385 is substituted with arginine, aspartic acid, serine, threonine, histidine, lysine, or alanine
  • residue 386 is substituted with threonine, proline, aspartic acid, serine, lysine, arginine, isoleucine, or methionine
  • residue 387 is substituted with arginine, histidine, serine, threonine, alanine, or proline
  • residue 389 is substituted with proline or serine.
  • residues at one or more positions 385, 386, 387, and 389 are substituted with arginine, threonine, arginine, and proline, respectively.
  • residues at one or more positions 385, 386, and 389 are substituted with aspartic acid, proline, and serine, respectively.
  • Still other embodiments of the invention provide a method of treating an HIV infection in a subject susceptible to or suffering from an HIV infection, comprising administering to the subject a therapeutically effective amount of an a nti retroviral agent as disclosed herein, and concurrently, sequentially, or in a staggered regimen administering a modified vedolizumab, wherein the modified vedolizumab has an lgG1 constant domain, or FcRn-binding fragment thereof (preferably, Fc or hinge-Fc domain) (preferably human), having amino acid modifications that include any combination of the above-described substitutions at one or more of residues 251 , 252, 254, 255, 256, 308, 309, 31 1 , 312, 385, 386, 387, 389, 428, 433, 434, and/or 436.
  • the modified vedolizumab for use in methods of the invention contains a Fc region, or FcRn-binding domain thereof, having one or more of the following substitutions: leucine at residue 251 , tyrosine at residue 252, threonine or serine at residue 254, arginine at residue 255, threonine at residue 308, proline at residue 309, serine at residue 31 1 , aspartic acid at residue 312, leucine at residue 314, arginine at residue 385, threonine at residue 386, arginine at residue 387, proline at residue 389, methionine at residue 428, and/or tyrosine at residue 434.
  • Still other embodiments of the invention provide a method of treating an HIV infection in a subject susceptible to or suffering from an HIV infection, comprising administering to the subject a therapeutically effective amount of antiretroviral agent as described herein, and concurrently, sequentially, or in a staggered regimen administering a modified vedolizumab having a modified IgG constant domain, or FcRn binding domain or fragment thereof
  • vedolizumab (preferably, Fc or hinge-Fc domain) (preferably human) as described herein, wherein the vedolizumab before modification is as described in W09624673, WO9806248, US7147851 , W012151247 or W012151248, each of which is hereby incorporated by reference herein in its entirety.
  • a method of treating a mammal with an immunodeficiency virus infection comprising administering to the mammal with the immunodeficiency virus infection a therapeutic amount of an antiretroviral agent combined with administration of a therapeutic monoclonal ⁇ 4 ⁇ 7 antibody.
  • the antiretroviral agent is any one or more of zidovudine, didanosine, lamivudine, zalcitabine, abacavir, stavudine, adefovir, adefovir dipivoxil, fozivudine, todoxil, emtricitabine, alovudine, amdoxovir, elvucitabine, nevirapine, delavirdine, efavirenz, loviride, immunocal, oltipraz, capravirine, lersivirine, GSK2248761 (fosdevirine), TMC-278 (rilpivirine), TMC-125 (etravirine), saquinavir, ritonavir, indinavir, nelfinavir, amprenavir, fosamprenavir, brecanavir, darunavir, atazanavir, tipranavir, palinavir, la
  • administration of the antiretroviral agent comprises administering a combination, concomitantly or serially, of raltegravir, tenofovir and emtricitabine. In still more particular embodiments, administration of the antiretroviral agent comprises administering dolutegravir.
  • Such antiretroviral agents may be may be administered together or separately and, when administered separately, administration may occur simultaneously or sequentially, in any order.
  • administration of the monoclonal ⁇ 4 ⁇ 7 antibody, e.g. vedolizumab may occur together or separately from the administration of the antiretroviral agent and, when administered separately from the antiretroviral agent, administration may occur simultaneously or sequentially, in any order.
  • a method of treating a subject with an HIV infection comprising administering to the subject with the HIV infection: therapeutic amounts of raltegravir, tenofovir and emtricitabine; and a therapeutic amount of a monoclonal ⁇ 4 ⁇ 7 antibody having a modified IgG binding domain or modified FcR binding domain or a fragment thereof compared to unmodified monoclonal antibody, wherein the monoclonal antibody with the modified IgG binding domain or modified FcR binding domain or fragment there is modified vedolizumab.
  • antiretroviral agent(s) will be administered to the subject for a set period of time, for example 30 days, 60 days, 90 days, or longer, before administration of vedolizumab.
  • Vedolizumab administration may be concurrent with some or all of the duration of administration of antiretroviral agent. More particularly, vedolizumab administration may begin at the time administration of antiretroviral agent begins, or administration of vedolizumab infusion may begin after administration of antiretroviral agent begins.
  • vedolizumab administration may continue after cessation of administration of the antiretroviral agent(s), or administration of vedolizumab may begin after cessation of administration of the antiretroviral agent(s).
  • administration of antiretroviral agent and vedolizumab is staggered, starting with antiretroviral agent administration alone, and ending with administration of vedolizumab alone, with a period of overlap in between, wherein both antiretroviral agent and vedolizumab are administered concurrently to the subject.
  • antiretroviral agent is administered daily for a total of 90 days; administration of vedolizumab infusion begins at day 60, and continues once every 3 weeks for 21 weeks, for 8 infusions of vedolizumab total.
  • daily administration of antiretroviral agent(s) ends on day 90, and administration of vedolizumab every 3 weeks continues until completion of the 8 infusions.
  • Sustained virologic control will be evidenced by a sustained reduction in viral antigens in the subject over a period of 1 month, 2 months, 3 months, 4 months, 5 months, 6 months and up to one year, two years, three years or longer post administration with ART, as determined by: (i) flow-cytometry measurement of total plasma viremia levels wherein a sustained (post-treatment) decrease in viremia levels in plasma indicates successful treatment and achievement of virological control; and/or (ii) measurement of plasma CD4+ T cells during and after treatment, wherein a sustained increase in CD4+ T cells in plasma indicates successful treatment and virological control; and/or (iii) measurement of proviral DNA levels in GITs during and after treatment, wherein a sustained decrease in proviral DNA levels in GITs indicates successful treatment and virological control.
  • Antigen binding polypeptides suitable for use in the methods of the present invention as described herein may have amino acid modifications that increase the affinity of the constant domain or fragment thereof for FcRn. Increasing the half-life of therapeutic and diagnostic IgG polypeptides and other bioactive molecules has many benefits including reducing the amount and/or frequency of dosing of these molecules.
  • an antigen binding polypeptide according to the invention provided herein (or a fusion protein) comprising all or a portion (an FcRn binding portion) of an IgG constant domain having one or more amino acid modification as described herein, and a non-lgG protein or nonprotein molecule conjugated to such a modified IgG constant domain, wherein the presence of the modified IgG constant domain increases the in vivo half life of the antigen binding protein.
  • FcRn Fc receptor neonate
  • Human lgG1 residues determined to interact directly with human FcRn include Ile253, Ser254, Lys288, Thr307, Gln31 1 , Asn434 and His435. Switches at any of these positions described in this section may enable increased serum half-life and/or altered effector properties of antigen binding proteins of the invention.
  • PCT Publication No. WO 00/42072 discloses a polypeptide comprising a variant Fc region with altered FcRn binding affinity, which polypeptide comprises an amino acid modification at any one or more of amino acid positions 238, 252, 253, 254, 255, 256, 265, 272, 286, 288, 303, 305, 307, 309, 31 1 , 312, 317, 340, 356, 360, 362, 376, 378, 380, 386,388, 400, 413, 415, 424,433, 434,435, 436, 439, and 447 of the Fc region, wherein the numbering of the residues in the Fc region is that of the EU index (Kabat et al).
  • PCT Publication No. WO 02/060919 discloses a modified IgG comprising an IgG constant domain comprising one or more amino acid modifications relative to a wild-type IgG constant domain, wherein the modified IgG has an increased half-life compared to the half-life of an IgG having the wild-type IgG constant domain, and wherein the one or more amino acid modifications are at one or more of positions 251 , 253, 255, 285-290, 308-314, 385-389, and 428-435.
  • the antigen binding protein of the invention comprises the E380A/N434A mutations and has increased binding to FcRn.
  • Dall'Acqua et al. (2002, J Immunol. ; 169:5171 -80) described random mutagenesis and screening of human lgG1 hinge-Fc fragment phage display libraries against mouse FcRn. They disclosed random mutagenesis of positions 251 , 252, 254-256, 308, 309, 31 1 , 312, 314, 385-387, 389, 428, 433, 434, and 436.
  • the major improvements in lgG1 -human FcRn complex stability occur in substituting residues located in a band across the Fc-FcRn interface (M252,
  • H433K/N434F/Y436H mutations and exhibited a 57-fold increase in affinity relative to the wild- type lgG1 .
  • the in vivo behaviour of such a mutated human lgG1 exhibited a nearly 4-fold increase in serum half-life in cynomolgous monkey as compared to wild-type lgG1 .
  • the present invention therefore provides a variant of an antigen binding protein with optimized binding to FcRn.
  • the said variant of an antigen binding protein comprises at least one amino acid modification in the Fc region of said antigen binding protein, wherein said modification is selected from the group consisting of 226, 227, 228, 230, 231 , 233, 234, 239, 241 , 243, 246, 250, 252, 256, 259, 264, 265, 267, 269, 270, 276, 284, 285, 288, 289, 290, 291 , 292, 294, 297, 298, 299, 301 , 302, 303, 305, 307, 308, 309, 31 1 , 315, 317, 320, 322, 325, 327, 330, 332, 334, 335, 338, 340, 342, 343, 345, 347, 350, 352, 354, 355, 356, 359, 360, 361 , 362, 369, 370, 3
  • a method of increasing IgG clearance rates in a subject comprising providing to said subject a modified lgG1 molecule comprising a modified Fc region that has increased affinity for FcyR relative to unmodified lgG1 antibody, concurrently with complete, partial or no overlap with administration of a region of ART comprising one or more a nti retroviral agents listed in Figure 4.
  • a pharmaceutical composition comprising: a therapeutic amount of one or more antiretroviral agents and a pharmaceutically acceptable diluent; and a therapeutically effective amount of a modified vedolizumab as described herein for administration as an infusion.
  • the pharmaceutical composition for use in the methods of treating a subject with an HIV infection comprises a therapeutic amount of one or more antiretroviral agents and a pharmaceutically acceptable diluent for oral administration; and comprises a therapeutically effective amount of a modified vedolizumab as described herein for administration as an intravenous infusion.
  • the composition of the one or more antiretroviral agents is formulated as a long-acting parenteral formulation.
  • the formulation of the one or more antiretroviral agents is a nano-particle formulation.
  • the one or more antiretroviral agents for use with a modified vedolizumab therapeutic antibody in the methods of treating a subject having an HIV infection as described herein are formulated for oral administration and can be administered as a conventional preparation, for example, as any dosage form of a solid agent such as tablets, powders, granules, capsules and the like; an aqueous agent; an oily suspension; or a liquid agent such as syrup and elixir.
  • the one or more antiretroviral agents for use with a modified vedolizumab for treating a subject with an HIV infection are formulated for parenteral administration and can be administered as an aqueous or oily suspension injectable, or a nasal drop.
  • a parenteral formulation with one or more antiretroviral agents as described herein such agent(s) may be formulated with additional non-therapeutic components including conventional excipients, binders, lubricants, aqueous solvents, oily solvents, emulsifiers, suspending agents, preservatives, stabilizers and the like.
  • the one or more antiretroviral agents for use in treating a subject having an HIV infection according to the invention are particularly and preferably formulated as an oral agent.
  • a preparation of a therapeutic amount of an antiretroviral agent as described herein, for use in treating a subject having HIV as described herein may be prepared by combining (e.g. mixing) a therapeutically effective amount of one or more antiretroviral agents with a pharmaceutically acceptable carrier or diluent.
  • compositions adapted for oral administration in the methods of the invention described herein may be presented as discrete units such as capsules or tablets; powders or granules; solutions or suspensions in aqueous or non-aqueous liquids; edible foams or whips; or oil-in-water liquid emulsions or water-in-oil liquid emulsions.
  • the one or more antiretroviral agent can be combined with an oral, non-toxic pharmaceutically acceptable inert carrier such as ethanol, glycerol, water and the like.
  • an oral, non-toxic pharmaceutically acceptable inert carrier such as ethanol, glycerol, water and the like.
  • Powders are prepared by comminuting the one or more antiretroviral agent to a suitable fine size and mixing with a similarly comminuted pharmaceutical carrier such as an edible carbohydrate, as, for example, starch or mannitol. Flavoring, preservative, dispersing and coloring agent can also be present.
  • Capsules are made by preparing a powder mixture, as described above, and filling formed gelatin sheaths.
  • Glidants and lubricants such as colloidal silica, talc, magnesium stearate, calcium stearate or solid polyethylene glycol can be added to the powder mixture before the filling operation.
  • a disintegrating or solubilizing agent such as agar-agar, calcium carbonate or sodium carbonate can also be added to improve the availability of the medicament when the capsule is ingested.
  • suitable binders include starch, gelatin, natural sugars such as glucose or beta-lactose, corn sweeteners, natural and synthetic gums such as acacia, tragacanth or sodium alginate, carboxymethylcellulose, polyethylene glycol, waxes and the like.
  • Lubricants used in these dosage forms include sodium oleate, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate, sodium chloride and the like.
  • Disintegrators include, without limitation, starch, methyl cellulose, agar, bentonite, xanthan gum and the like.
  • Tablets are formulated, for example, by preparing a powder mixture, granulating or slugging, adding a lubricant and disintegrant and pressing into tablets.
  • a powder mixture is prepared by mixing the compound, suitably comminuted, with a diluent or base as described above, and optionally, with a binder such as carboxymethylcellulose, an aliginate, gelatin, or polyvinyl pyrrolidone, a solution retardant such as paraffin, a resorption accelerator such as a quaternary salt and/or an absorption agent such as bentonite, kaolin or dicalcium phosphate.
  • a binder such as carboxymethylcellulose, an aliginate, gelatin, or polyvinyl pyrrolidone
  • a solution retardant such as paraffin
  • a resorption accelerator such as a quaternary salt
  • an absorption agent such as bentonite, kaolin or dicalcium phosphate.
  • the powder mixture can be granulated by wetting with a binder such as syrup, starch paste, acadia mucilage or solutions of cellulosic or polymeric materials and forcing through a screen.
  • a binder such as syrup, starch paste, acadia mucilage or solutions of cellulosic or polymeric materials and forcing through a screen.
  • the powder mixture can be run through the tablet machine and the result is imperfectly formed slugs broken into granules.
  • the granules can be lubricated to prevent sticking to the tablet forming dies by means of the addition of stearic acid, a stearate salt, talc or mineral oil. The lubricated mixture is then compressed into tablets.
  • the antiretroviral agents described herein, for use with a modified vedolizumab having an extended in vivo half-life, for treating an HIV infection in a subject can also be combined with a free flowing inert carrier and compressed into tablets directly without going through the granulating or slugging steps.
  • a clear or opaque protective coating consisting of a sealing coat of shellac, a coating of sugar or polymeric material and a polish coating of wax can be provided.
  • Dyestuffs can be added to these coatings to distinguish different unit dosages.
  • Oral fluids such as solutions, syrups and elixirs can be prepared in dosage unit form so that a given quantity contains a predetermined amount of the compound.
  • Syrups can be prepared by dissolving the compound in a suitably flavored aqueous solution, while elixirs are prepared through the use of a non-toxic alcoholic vehicle.
  • Suspensions can be formulated by dispersing the compound in a non-toxic vehicle.
  • Solubilizers and emulsifiers such as ethoxylated isostearyl alcohols and polyoxy ethylene sorbitol ethers, preservatives, flavor additive such as peppermint oil or natural sweeteners or saccharin or other artificial sweeteners, and the like can also be added.
  • dosage unit formulations for oral administration can be microencapsulated.
  • the one or more antiretroviral agents for use in the methods described herein can also be prepared to prolong or sustain the release of the compound, as for example by coating or embedding particulate material in polymers, wax or the like.
  • antiretroviral agents as described herein may also be delivered by the use of monoclonal antibodies as individual carriers to which the antiretroviral agents are coupled.
  • compositions of the one or more antiretroviral agents described herein for use in the methods of treating an HIV infection in a subject, adapted for parenteral administration, include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents and thickening agents.
  • the formulations may be presented in unit- dose or multi-dose containers, for example sealed ampoules and vials, and may be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example water for injections, immediately prior to use.
  • sterile liquid carrier for example water for injections, immediately prior to use.
  • Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules and tablets.
  • formulations described herein may include other agents conventional in the art having regard to the type of formulation in question, for example those suitable for oral administration may include flavouring agents.
  • a therapeutically effective amount of the one or more antiretroviral agents for use with a modified vedolizumab having an IgG constant region modified to bind the FcRn with higher affinity than non-modified vedolizumab, in the methods of treating an HIV infection in a subject as described herein, will depend upon a number of factors including, for example, the age and weight of the human or other animal, the precise condition requiring treatment and its severity, the nature of the formulation, and the route of administration, and will ultimately be at the discretion of the attendant physician or veterinarian.
  • An effective amount of a salt or hydrate thereof may be determined as a proportion of the effective amount of the antiretroviral agents or salts, thereof per se.
  • modified vedolizumab may be by infusion, over 30 minutes or longer.
  • the modified vedolizumab infusion may be formulated as 300 mg in 250 mL of a 0.9% sodium chloride solution, as a typical dose.
  • the dosage of modified vedolizumab may be 20 mg per kg of body weight, administered over 20, 30, 40, 50 or 60 minutes every two weeks or every three weeks as an intravenous infusion in 1 % saline solution.
  • the infusion may be prepared from white lyophilized cake or powder (300 mg) for reconstitution with saline solution (5 mL) to a final concentration of 60 mg per mL.
  • Administration of modified vedolizumab infusion for treating HIV infection in a subject may occur at weeks zero, three, six and nine weeks and then every 8 weeks thereafter for a total of 6, 7, 7, 9, 10 or more infusions, as appropriate based, on monitoring of CD4+ T cell levels, and/or proviral DNA levels and/or total viremia levels.
  • ART immunodeficiency virus susceptible to antiretroviral therapy
  • modified vedolizumab having a variant Fc binding region having increased affinity for FcRN compared to non-modified vedolizumab comprising administering to said mammal a therapeutically effective amount of one or more antiretroviral agents as listed in Figure 4 or a pharmaceutically acceptable salt thereof for a first proscribed period, and administering an infusion of modified vedolizumab over a second proscribed period, wherein the first and second proscribed periods may run concurrently for all, some or none of the first and second proscribed periods.
  • the immunodeficiency virus is selected from HIV, SIV and FIV. In one embodiment, the immunodeficiency virus is HIV. In one embodiment, the immunodeficiency virus is SIV. In one embodiment, the immunodeficiency virus is FIV.
  • the antiretroviral agents of the present invention and the modified vedolizumab having increased affinity for FcRn compared to unmodified vedolizumab may be administered together or separately and, when administered separately, administration may occur simultaneously or sequentially, in any order.
  • the amounts of the antiretroviral agents and modified vedolizumab for use in treating an immunodeficiency virus, e.g. HIV, SIV, FIV as described herein, and the relative timings of administration, will be selected in order to achieve the desired combined therapeutic effect.
  • the combination of one or more antiretroviral agents listed in Figure 4, with modified vedolizumab having an extended in vivo half-life compared to unmodified vedolizumab may be administered in combination by administration concomitantly in a unitary pharmaceutical composition including both the one or more antiretroviral agent and the modified vedolizumab; administered concomitantly in separate pharmaceutical compositions and formulations wherein the one or more antiretroviral agents selected from the list in Figure 4 is formulated for oral administration and the modified vedolizumab having an in vivo extended half- life is formulated for administration as an infusion.
  • the combination of one or more antiretroviral agents listed in Figure 4, with modified vedolizumab having an extended in vivo half-life compared to unmodified vedolizumab may be administered separately in a sequential manner wherein the one or more antiretroviral agent is administered first and the modified vedolizumab is administered second, or vice versa. Such sequential administration may be close in time or remote in time.
  • the amounts of the antiretroviral agents or salts thereof and the modified vedolizumab, and the relative timings of administration of each, will be selected in order to achieve the desired combined therapeutic effect.
  • a method of treating an immunodeficiency virus infection in a subject suffering from the virus infection comprising administering to the subject one or more antiretroviral agents wherein the antiretroviral agent is a selected from the list of agents in Figure 4, and administering to the subject a modified vedolizumab having an IgG constant domain, or FcRn binding domain that has been modified to have (i) an increased in vivo half-life relative to non-modified vedolizumab; (ii) an increased binding affinity for FcRn relative to unmodified vedolizumab; (iii) higher affinity for FcRn at pH 6.0 than at pH 7.41 and may increased bioavailability (e. g., transport to mucosal surfaces, or other target tissues) of the modified vedolizumab compared to unmodified vedolizumab.
  • the antiretroviral agent is a selected from the list of agents in Figure 4
  • the one or more antiretroviral agents is a combination of raltegravir, tenofovir and emtricitabine; or the one or more antiretroviral agent is dolutegravir.
  • the antiretroviral agents listed in Figure 4 in combination with modified vedolizumab as described herein are useful for treating viral infections in a subject where the infection is caused by an immunodeficiency virus, including HIV, SIV and FIV.
  • Example 1 Mutagenesis and Construction of Yeast Display Libraries
  • An initial library of molecules comprising variant Fc regions is produced using any random based mutagenesis techniques known in the art. It will be appreciated by one of skill in the art that amino acid sequence variants of Fc regions may be obtained by any mutagenesis technique known to those skilled in the art. Some of these techniques are briefly described herein, however, it will be recognized that alternative procedures may produce an equivalent result.
  • molecules of the invention comprising variant Fc regions are prepared by error-prone PCR as exemplified in Example 6, infra (See Leung et al. , 1989, Technique, 1:1 1 ). It is especially preferred to have error rates of 2-3 bp/Kb for use in the methods of the invention. In one embodiment, using error prone PCR a mutation frequency of 2- 3 mutations/kb is obtained.
  • Mutagenesis may be performed in accordance with any of the techniques known in the art including, but not limited to synthesizing an oligonucleotide having one or more modifications within the sequence of a polypeptide comprising an Fc region (e.g. the CH2 or CH3 domain), or the Fc region of an IgG antibody, such as vedolizumab, to be modified.
  • Site- specific mutagenesis allows the production of mutants through the use of specific
  • oligonucleotide sequence which encode the DNA sequence of the desired mutation, as well as a sufficient number of adjacent nucleotides, to provide a primer sequence of sufficient size and sequence complexity to form a stable duplex on both sides of the deletion junction being traversed.
  • a primer of about 30 to about 45 nucleotides or more in length is preferred with about 10 to about 25 or more residues on both sides of the junction of the sequence being altered.
  • a number of such primers introducing a variety of different mutations are one or more positions may be used to generate a library of mutants.
  • site-directed mutagenesis is performed by first obtaining a single-stranded vector or melting apart two strands of a double-stranded vector which includes its sequence a DNA sequence which encodes a desired peptide.
  • An oligonucleotide primer bearing the desired mutated sequence is prepared, generally synthetically.
  • This primer is then annealed with the single-stranded vector, and subjected to DNA polymerizing enzymes such as T7 DNA polymerase, in order to complete the synthesis of the mutation-bearing strand.
  • DNA polymerizing enzymes such as T7 DNA polymerase
  • This heteroduplex vector is then used to transform or transfect appropriate cells, such as E. coli cells, and clones are selected which include recombinant vectors bearing the mutated sequence arrangement.
  • the technique typically employs a phage vector which exists in both a single stranded and double stranded form.
  • Typical vectors useful in site- directed mutagenesis include vectors such as the M13 phage. These phage are readily commercially available and their use is generally well known to those skilled in the art. Double stranded plasmids are also routinely employed in site directed mutagenesis which eliminates the step of transferring the gene of interest from a plasmid to a phage.
  • thermostable enzymes such as Taq DNA polymerase may be used to incorporate a mutagenic
  • oligonucleotide primer into an amplified DNA fragment that can then be cloned into an appropriate cloning or expression vector. See, e.g., Tomic et al. , Nucleic Acids Res. ,
  • PCRTM employing a thermostable ligase in addition to a thermostable polymerase may also be used to incorporate a phosphorylated mutagenic oligonucleotide into an amplified DNA fragment that may then be cloned into an appropriate cloning or expression vector (see e.g., Michael, Biotechniques, 16(3):410-2, 1994, which is hereby incorporated by reference in its entirety)
  • Another method for preparing variants for use in the invention is cassette mutagenesis based on the technique described by Wells et al.
  • the starting material is the plasmid comprising the desired DNA encoding the protein to be mutated (e.g., the DNA encoding a polypeptide comprising an Fc region).
  • the codon(s) in the DNA sequence to be mutated are identified; there must be a unique restriction endonuclease site on each side of the identified mutations site(s). If no such restriction site exits, it may be generated by
  • oligonucleotide directed mutagenesis After the restriction sites have been introduced into the plasmid, the plasmid is cut at these sites and linearized. A double-stranded oligonucleotide encoding the sequence of the DNA between the restriction sites but containing the mutation is synthesized using standard procedures known to those skilled in the art. The double stranded oligonucleotide is referred to as the cassette. This cassette is designed to have 3' and 5' ends that are compatible with the ends of the linearized plasmid, such that it can be directly ligated to the plasmid.
  • sequence variants of the Fc region of an antibody or polypeptides comprising an Fc region can be used.
  • recombinant vectors encoding the amino acid sequence of the constant domain of an antibody or a fragment thereof may be treated with mutagenic agents, such as hydroxylamine, to obtain sequence variants.
  • the mutagenized library is transformed into a yeast strain, preferably EBY100 (Invitrogen), MATa ura3-52 trpl leu2A1 his3A 200 pep4::HIS3 prblA1 .6R canl GAL:: GAL-AGA1 using a standard lithium acetate transformation protocol known to those skilled in the art.
  • EBY100 Invitrogen
  • MATa ura3-52 trpl leu2A1 his3A 200 pep4::HIS3 prblA1 .6R canl GAL:: GAL-AGA1 using a standard lithium acetate transformation protocol known to those skilled in the art.
  • polypeptides with desired binding properties e.g., polypeptides with variant Fc regions with at least one amino acid modification, which modification enhances the affinity of the variant Fc region for Fc RIIIA relative to a comparable molecule, comprising a wild-type Fc region
  • modified therapeutic antibodies such as modified vedolizumab
  • An Fc R-Fc binding assay as described in US Patent No. 9,028,815, which is hereby incorporated by reference herein, can be used to select polypeptides having increased affinity to FcyR, which allows detection and quantitation of the interaction between the Fc binding domain (region) of the polypeptide and FcyR, despite the weak affinity of FcyR for its ligand (the Fc region of the polypeptide).
  • the affinity of Fc R for the IgG constant domain e.g. the Fc binding domain
  • the affinity of Fc R for the IgG constant domain is in the micromolar range for FcyRIIB and FcyRIIIA.
  • a preferred molecular complex is a tetrameric immune complex, comprising: (a) the soluble region of FcyP (e.g., the soluble region of FcyRIIIA, FcyRIIA or FcyRIIB); (b) a fusion protein comprising a biotinylated 15 amino acid AVITAG sequence (AVITAG) operably linked to the C-terminus of the soluble region of Fc R (e.g., the soluble region of FcyRIIIA, FcyRIIA or FcyRIIB); and (c) streptavidin- phycoerythrin (SA-PE); in a molar ratio to form a tetrameric FcyR complex (preferably in a 5:l molar ratio).
  • AVITAG biotinylated 15 amino acid AVITAG sequence
  • the fusion protein may be biotinylated enzymatically, using for example, the E. coli Bir A enzyme, a biotin ligase which specifically biotinylates a lysine residue in the 15 amino acid AVITAG sequence. Ideally, 75-85% of the fusion protein will be biotinylated, as determined by standard methods known to those of skill in the art, including but limited to streptavidin shift assay.
  • the biotinylated soluble FcyR proteins are then mixed with the SA-PE in a 1xSA-PE:5x biotinylated soluble FcyR molar ratio to form a tetrameric FcyR complex.
  • Polypeptides having an Fc region will bind the tetrameric FcyR complexes, and can be selected to have at least an 8- fold higher affinity than monomeric uncomplexed FcyR.
  • the binding of polypeptides comprising an Fc region to the tetrameric FcyR complexes may be determined using standard techniques known to those of skill in the art, such as for example, fluorescence activated cell sorting (FACS), radioimmunoassay, ELISA assays, etc.
  • FACS fluorescence activated cell sorting
  • ELISA assays ELISA assays
  • FcyRIIIA affinity and/or FcyRIIA such as the yeast surface display technology (for review see Boder and Wittrup, 2000, Methods in Enzymology, 328: 430-444, which is incorporated herein by reference in its entirety) which addresses the deficiency in the prior art for screening binding interactions of extracellular post-translationally modified proteins.
  • the yeast surface display is a genetic method whereby polypeptides comprising Fc mutants are expressed on the yeast cell wall in a form accessible for interacting with Fc7R.
  • Yeast surface display of the mutant Fc containing polypeptides of the invention may be performed in accordance with any of the techniques known to those skilled in the art. See U.S.Pat. No s. 6,423,538; 6, 1 14, 147; and 6,300, 065, all of which are incorporated herein by reference in their entirety. See Boder et al.,1997 Nat. Biotechnol., 15:553-7; Boder et al.,1998 Biotechnol.
  • modified vedolizumab having altered FcyR affinity i.e. enhanced FcyRIIIA affinity and/or Fc RIIA
  • FcyR affinity i.e. enhanced FcyRIIIA affinity and/or Fc RIIA
  • Example 3 (see Table 3) - binding to FcRn
  • the antibodies were diluted to 50 ⁇ g mL in sodium acetate buffer pH5.0 and directly immobilised onto a CM5 chip by primary amine coupling and human and cynomolgus monkey recombinant soluble FcRn (reagent generated in house) passed over the chip at 2048nM, 512nM, 128nM, 32nM, and 8nM for 300 seconds at 30ul/min, followed by a dissociation step of 300 seconds.
  • a OnM i.e. buffer alone
  • Regeneration of the chip surface between interactions was carried out using HBS-EP pH9.0.
  • the assay was run at 25 C in HBS-EP pH7.4 buffer and repeated in HBS-EP pH6.0 buffer. Affinities were calculated using the steady state binding model, inherent to the Biacore 4000 evaluation software and are shown in Table 3.
  • Example 4 (see Table 4A and Table 4B) - Binding to FcgRs
  • Binding to recombinant soluble human and cynomolgus monkey Fc-gamma receptors was assessed using the Biacore 4000 (GE Healthcare) surface plasmon resonance instrument.
  • a murine anti-poly-histidine IgG was immobilised on a CM5 biosensor chip by primary amine coupling.
  • Human and cynomolgus poly-histidine tagged Fc gamma receptors were diluted to 10pg/mL and captured on the murine anti-poly-histidine IgG surface.
  • Fey receptor proteins were generated in house, except human FcyR1 which was purchased from R&D Systems.
  • the antibodies were passed over the coated chip surface at 1024nM, 256nM, 64nM, 16nM and 4nM for 240 seconds at 30 ⁇ _/ ⁇ " ⁇ followed by a 400 second dissociation step.
  • a OnM i.e. buffer alone
  • the murine anti-poly-histidine IgG surface was regenerated with 100mM phosphoric acid between interactions.
  • the run was carried out at 25°C using HBS-EP as the running buffer. Data was analysed for each receptor separately, setting a global R-max and using the equilibrium model inherent to the Biacore analysis software for calculation of KD values, which can be found in Table 4A and Table 4B.
  • Example 5 (see Table 5) - Binding to ⁇ 4 ⁇ 7 and recovery from serum
  • Antibodies were diluted to 12C ⁇ g/ml_ in pooled human AB serum, rat serum and cynomolgus monkey serum. A Time 0 reference sample was immediately taken and frozen at - 20°C, remaining samples were incubated at 37°C with humidification and 5% C0 2 for six weeks. Following incubation, the amount of spiked antibody was measured using an immunoassay and interpolated against a standard curve of the corresponding antibody not incubated in serum.
  • Table 5 Six-week serum stability study. Anti- a 4 p 7 -parent and anti- ⁇ 4 ⁇ 7- ⁇ incubated in rat, human and cynomolgus monkey serum. Table shows % recoveries of antibody normalised to the concentration obtained in the TO reference samples.
  • PK assessment can be performed on cynomolgus serum samples for up to, for example, 5376 hours I32 weeks). Analysis is expected to show that anti- ⁇ 4 ⁇ 7- ⁇ has a 2-30 fold reduction in serum clearance rate compared to vedolizumab and an improved half-life between 2-fold and 10-fold longer than what is seen for vedolizumab (SEQ ID NO. 1 1 ).
  • SEQ ID NO. 1 1 ab
  • Example 7 Treating a subject infected with HIV with ART (raltegravir, tenofovir and emtricitabine) in combination with modified vedolizumab for an functional cure
  • ART raltegravir, tenofovir and emtricitabine
  • ART antiretroviral therapy
  • ART consists of tenofovir (or tenofovir alafenamide) at a dose of active drug ranging from10 mg/kg through 30 mg/kg and a nucleoside reverse transcriptase inhibitor such as emtricitabine at a dose ranging from 10 mg/kg through 30 mg/kg, each of tenofovir and emtricitabine to be administered subcutaneously, and an integrase inhibitor such as raltegravir at a total daily dose ranging from 50 through 500 mg to be administered orally 1x or 2x daily in approximate 6mg/kg doses.
  • Plasma viral loads are determined at time zero, prior to ART initiation, and again at 9 weeks post infection (4 weeks after initiation of ART) when there is undetectable plasma viremia, with subjects divided into 2 groups.
  • Group I consists of subjects that are administered 50 mg/kg of a recombinant modified vedolizumab (modified ⁇ 4 ⁇ 7 monoclonal antibody) by intravenous infusion
  • group II consists of subjects that are administered 50 mg/kg of recombinant human IgG by intravenous infusion as a control.
  • the HIV-positive subjects are administered the modified vedolizumab (modified ⁇ 4 ⁇ 7 mAb) or administered the human IgG every 3 weeks starting at week 9, continuing until week 32 post infection, for a total of 8 infusions.
  • Blood and gastro-intestinal tissue (GIT) biopsies are studied for viral loads. Values obtained following cessation of ART at week 18 are expected to represent the result of ART withdrawal but influenced by modified vedolizumab (modified ⁇ 4 ⁇ 7 mAb), as compared with IgG infusions.
  • the values obtained following cessation of ⁇ 4 ⁇ 7 mAb or IgG infusions at week 32 are expected to reflect the effects of ART + antibody infusion withdrawal on an HIV+ subject.
  • Example 8 Treating a subject infected with HIV with ART (raltegravir, tenofovir and emtricitabine) in combination with modified vedolizumab for an functional cure
  • ART antiregroviral therapy
  • ART consists of tenofovir (or tenofovir alafenamide) at a dose of active drug ranging froml O mg/kg through 30 mg/kg and a nucleoside reverse transcriptase inhibitor such as emtricitabine at a dose ranging from 10 mg/kg through 30 mg/kg, each of tenofovir and emtricitabine to be administered subcutaneously, and an integrase inhibitor such as raltegravir at a total daily dose ranging from 50 through 500 mg to be administered orally 1x or 2x daily in approximate 6mg/kg doses.
  • Plasma viral loads are determined at time zero, prior to ART initiation, and again at 9 weeks post infection (4 weeks after initiation of ART) when there is undetectable plasma viremia, with subjects divided into 2 groups.
  • Group I consists of subjects that are administered 50 mg/kg of a recombinant modified vedolizumab (modified ⁇ 4 ⁇ 7 monoclonal antibody) by intravenous infusion
  • group II consists of subjects that are administered 50 mg/kg of recombinant human IgG by intravenous infusion as a control.
  • the HIV-positive subjects are administered the modified vedolizumab (modified ⁇ 4 ⁇ 7 mAb) or administered the human IgG every 3 weeks starting at week 9, continuing until week 32 post infection, for a total of 8 infusions.
  • Blood and gastro-intestinal tissue (GIT) biopsies are studied for viral loads. Values obtained following cessation of ART at week 18 are expected to represent the result of ART withdrawal but influenced by modified vedolizumab (modified ⁇ 4 ⁇ 7 mAb), as compared with IgG infusions.
  • the values obtained following cessation of ⁇ 4 ⁇ 7 mAb or IgG infusions at week 32 are expected to reflect the effects of ART + antibody infusion withdrawal on an HIV+ subject.
  • Plasma is isolated from EDTA treated blood samples and is obtained from each subject at weekly intervals for 4 weeks, bi-weekly for 8 weeks and monthly thereafter subjects are monitored for levels of viremia as described in Wang, X. et al., "Monitoring alpha4beta7 integrin expression on circulating CD4+ T cells as a surrogate marker for tracking intestinal CD4+ T-cell loss in SIV infection.” Mucosal Immunol. 2, 518-526 (2009). Data is expressed as the number of viral copies/mL of plasma and the sensitivity of the assay is ⁇ 50 copies/mL of plasma.
  • GIT Gl tissue
  • biopsy obtains mononuclear cells, and DNA is isolated from a fixed number of cells and subjected to PCR analysis as described elsewhere for macaques (Byrareddy, S.N; et al, "Targeting ⁇ ⁇ 7 integrin reduces mucosal transmission of simian immunodeficiency virus and protects gut-associated lymphoid tissue from infection", Nat.Med. 20, 1397-1400 (2014); and Ansari, A.A.
  • PBMCs are isolated from blood samples and colorectal biopsy specimens from subjects, as described previously for macaques (Byrareddy, S.N; et al, "Targeting ⁇ 4 ⁇ 7 integrin reduces mucosal transmission of simian immunodeficiency virus and protects gut associated lymphoid tissue from infection", Nat.Med. 20, 1397-1400 (2014)).
  • EDTA blood samples are obtained and mononuclear cells are isolated using ficoll-hypaque gradient centrifugation. The cell viability should always be >95%.
  • PBMCs are isolated from blood samples and colorectal biopsy specimens from subjects, as described previously for macaques (Byrareddy, S.N; et al, "Targeting ⁇ 4 ⁇ 7 integrin reduces mucosal transmission of simian immunodeficiency virus and protects gut-associated lymphoid tissue from infection", Nat.Med. 20, 1397-1400 (2014)).
  • EDTA blood samples are obtained and mononuclear cells are isolated using ficoll-hypaque gradient centrifugation. The cell viability should always be >95%.
  • TH17/TH22 and NKp44 cells The frequencies of TH 17 and TH22 cells can be expressed as the percentage of CD4+ T-cells that produce IL-17 and IL-22 following in vitro stimulation with PMA & lonomycin.
  • PBMC and GIT derived mononuclear cells are re-suspended at 2 ⁇ 106 cells/mL in complete RPMI 1640 medium containing PMA/lonomycin and Golgi stop at 37°C for 4 hrs. The cells are then washed and stained with an appropriate panel of cell surface markers in the dark at room temperature which is followed by fixation and permeabilization. After permeabilization, cells are washed and are stained intra-cellularly with the anti-IL-17 or anti-IL-22 antibodies for 1 hour in the dark at room temperature.
  • NKp44+ cells an aliquot of the PBMC or GIT derived mononuclear cells were stained with CD3, HLA-DR, CD8a, CD16, CD56 and NKp44 antibodies. The gated population of CD3-, NKG2a-, HLA-DR+, CD16- cells were then screened for the frequencies of NK-44+ cells defined. In the case of GIT biopsy procured mononuclear samples, data for each lineage of lymphoid cells was expressed as the frequency of the gated population of CD45+ cells.
  • a significant decrease in the frequency of cells that bind to the anti-a4 integrin in the test sample as compared to the frequency that binds to the same anti-a4 integrin in the baseline sample is reasoned to reflect the absence of the ⁇ 4 ⁇ 7 expressing cells (secondary to either depletion or redistribution).
  • HIV-positive or "HIV+”
  • ART antiretroviral therapy
  • dolutegravir administered to dolutegravir
  • modified vedolizumab as described herein, similar to what is done in Example 7.
  • ART consists of oral dolutegravir in tablet form, at a dose of active drug ranging from 20 mg/kg through 100mg/kg once daily.
  • ART antiretroviral therapy
  • dolutegravir in tablet form, at a dose of active drug ranging from 20 mg/kg through 100mg/kg once daily.
  • Plasma viral loads are determined at time zero, prior to ART initiation, and again at 9 weeks post infection (4 weeks after initiation of ART) when there is undetectable plasma viremia, with subjects divided into 2 groups.
  • Group I consists of subjects that are administered 50 mg/kg of a recombinant modified vedolizumab (modified ⁇ 4 ⁇ 7 monoclonal antibody) by intravenous infusion
  • group II consists of subjects that are administered 50 mg/kg of recombinant human IgG by intravenous infusion as a control.
  • the HIV-positive subjects are administered the modified vedolizumab (modified ⁇ 4 ⁇ 7 mAb) or administered the human IgG every 3 weeks starting at week 9, continuing until week 32 post infection, for a total of 8 infusions.
  • Blood and gastro-intestinal tissue (GIT) biopsies are studied for viral loads. Values obtained following cessation of ART at week 18 are expected to represent the result of ART withdrawal but influenced by modified vedolizumab (modified ⁇ 4 ⁇ 7 mAb), as compared with IgG infusions.
  • the values obtained following cessation of ⁇ 4 ⁇ 7 mAb or IgG infusions at week 32 are expected to reflect the effects of ART + antibody infusion withdrawal on an HIV+ subject.
  • SEQ ID NO: !1 Human lgG1 hinge, CH2 and CH3 region (Fig 2)
  • SEQ ID NO 12 Vedolizumab heavy chain, LS variant
  • SEQ ID NO 13 Vedolizumab heavy chain, HN variant
  • SEQ ID NO !4 Vedolizumab heavy chain, YTE variant QVQLVQSGAEVKKPGASVKVSCKGSGYTFTSYWMHWVRQAPGQRLEW1GEIDPSESNTNYN

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Abstract

L'invention concerne de nouvelles protéines de liaison à l'antigène α4β7. En particulier, l'invention concerne des protéines de liaison à l'antigène modifiées qui sont de nouveaux variants d'anticorps anti-α4β7, tels que le védolizumab, qui présentent une liaison augmentée au récepteur FcRn et/ou une demi-vie augmentée par rapport au védolizumab. Le védolizumab est un anticorps monoclonal anti-IgG1 comprenant la séquence de chaîne légère de séquence SEQ ID NO : 7 et la séquence de chaîne lourde de séquence SEQ ID NO : 8. Les procédés selon l'invention comprennent l'administration d'un TAR (traitement antirétroviral) à l'aide des composés divulgués dans la figure 4 et l'administration d'une protéine de liaison à un antigène modifiée, par exemple un anticorps anti-IgG α4β7 modifié, tel qu'un védolizumab modifié, présentant une région Fc de variant présentant une affinité accrue vis-à-vis de FcRn par rapport à un anticorps non modifié, ce qui entraîne une élimination virologique prolongée de l'infection par le VIH chez le sujet, c'est-à-dire ce qui entraîne une guérison ou une guérison fonctionnelle d'une infection par le VIH chez le sujet.
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WO2020252072A1 (fr) * 2019-06-10 2020-12-17 Millennium Pharmaceuticals, Inc. Procédés de purification d'anticorps et compositions associées
WO2022016198A1 (fr) * 2020-07-16 2022-01-20 Abbvie Inc. Anticorps anti-αlpha-4-βeta-7

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