THERAPEUTIC ANTIGEN-BINDING MOLECULE WITH A FcRn-BINDING DOMAIN THAT PROMOTES ANTIGEN CLEARANCE

• US 20140363428A1
• Filed: 09/28/2012
• Published: 12/11/2014
• Est. Priority Date: 09/30/2011
• Status: Active Grant

• Current Assignee: Chugai Seiyaku Kabushiki Kaisha (Roche Holding AG)
• Original Assignee: Chugai Seiyaku Kabushiki Kaisha (Roche Holding AG)
• Inventors: Igawa, Tomoyuki, Maeda, Atsuhiko, Mimoto, Futa, Kuramochi, Taichi
• Granted Patent: US 10,253,100 B2
• Time in Patent Office: Days
• US Class Current: 424/133.1
• CPC Class Codes: A61K 2039/505 comprising antibodies
• CPC Class Codes: A61P 19/02 for joint disorders, e.g. arthritis, arthrosis
• CPC Class Codes: A61P 29/00 Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• CPC Class Codes: A61P 37/00 Drugs for immunological or allergic disorders
• CPC Class Codes: A61P 37/06 Immunosuppressants, e.g. drugs for graft rejection
• CPC Class Codes: C07K 16/2812 against CD4
• CPC Class Codes: C07K 16/2866 against receptors for cytokines, lymphokines, interferons
• CPC Class Codes: C07K 2317/34 Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
• CPC Class Codes: C07K 2317/52 Constant or Fc region; Isotype
• CPC Class Codes: C07K 2317/524 CH2 domain
• CPC Class Codes: C07K 2317/526 CH3 domain
• CPC Class Codes: C07K 2317/94 Stability, e.g. half-life, pH, temperature or enzyme-resistance

Abstract

The present invention provides: a modified FcRn-binding domain having an enhanced affinity for the Fc Receptor neonatal (FcRn) at neutral pH; an antigen-binding molecule comprising said FcRn-binding domain, which has low immunogenicity, high stability and form only a few aggregates; a modified antigen-binding molecule having an increased FcRn-binding activity at neutral or acidic pH without an increased binding activity at neutral pH for a pre-existing anti-drug antibody; use of the antigen-binding molecules for improving antigen-binding molecule-mediated antigen uptake into cells; use of the antigen-binding molecules for reducing the plasma concentration of a specific antigen; use of the modified FcRn-binding domain for increasing the total number of antigens to which a single antigen-binding molecule can bind before its degradation; use of the modified FcRn-binding domain for improving pharmacokinetics of an antigen-binding molecule; methods for decreasing the binding activity for a pre-existing anti-drug antibody; and methods for producing said antigen-binding molecules.

Claims

1-61. -61. (canceled)

62. An antigen-binding molecule comprising a modified FcRn-binding domain, the amino acid sequence of which differs from the sequence of a native human IgG FcRn-binding domain at one or more positions, including an amino acid substitution at at least one of the following positions (EU numbering):

238, 250, 252, 254, 255, 258, 286, 307, 308, 309, 311, 315, 428, 433, 434, and 436.

63. The antigen-binding molecule of claim 62, wherein the at least one position that is substituted includes positions 252 and 434 and one or more of the following positions:

238, 250, 254, 255, 256, 258, 286, 387, 307, 308, 309, 311, 315, 428, 433, and 436 (all positions by EU numbering).

64. The antigen-binding molecule of claim 62, wherein at least one of the following positions in the modified FcRn-binding domain is occupied by the indicated amino acid (all positions by EU numbering):

aspartic acid at position 238;

valine at position 250;

tyrosine at position 252;

threonine at position 254;

leucine at position 255;

glutamic acid at position 256;

either aspartic acid or isoleucine at position 258;

glutamic acid at position 286;

glutamine at position 307;

proline at position 308;

glutamic acid at position 309;

either alanine or histidine at position 311;

aspartic acid at position 315;

isoleucine at position 428;

any one of alanine, lysine, proline, arginine, and serine at position 433;

either tyrosine or tryptophan at position 434;

any one of isoleucine, leucine, valine, threonine, and phenylalanine at position 436.

65. The antigen-binding molecule of claim 62, wherein the at least one position that is substituted includes all members of a set of positions selected from any of sets (a)-(g):

(a) positions 252, 434, and 436;

(b) positions 252, 307, 311 and 434;

(c) positions 252, 315, and 434;

(d) positions 252, 308, and 434;

(e) positions 238, 252, and 434;

(f) positions 252, 434, 307, 311, and 436;

(g) positions 252, 387, and 434 (all positions by EU numbering).

66. The antigen-binding molecule of claim 62, wherein the modified FcRn-binding domain comprises one of the following combinations of amino acid residues at the indicated positions:

(a) tyrosine at position 252, aspartic acid at position 315, and tyrosine at position 434;

(b) tyrosine at position 252, tyrosine at position 434, and isoleucine at position 436;

(c) tyrosine at position 252, tyrosine at position 434, and leucine at position 436;

(d) tyrosine at position 252, tyrosine at position 434, and valine at position 436;

or

(e) tyrosine at position 252, threonine at position 254, tyrosine at position 434, and isoleucine at position 436 (all positions by EU numbering).

67. The antigen-binding molecule of claim 62, wherein the at least one position that is substituted includes all members of a set of positions selected from any of sets (a)-(h):

(a) positions 252, 434, 307, 311, and 286;

(b) positions 252, 434, 307, 311, 286, and 254;

(c) positions 252, 434, 307, 311, and 436;

(d) positions 252, 434, 307, 311, 436, and 254;

(e) positions 252, 434, 307, 311, 436, and 250;

(f) positions 252, 434, 308, and 250;

(g) positions 252, 434, 308, 250, and 436;

(h) positions 252, 434, 308, 250, 307, and 311 (all positions by EU numbering).

68. The antigen-binding molecule of claim 62, wherein the modified FcRn-binding domain comprises one of the following combinations of amino acid residues at the indicated positions:

(a) tyrosine at position 252, glutamic acid at position 286, glutamine at position 307, alanine at position 311, and tyrosine at position 434;

(b) tyrosine at position 252, threonine at position 254, glutamic acid at position 286, glutamine at position 307, alanine at position 311, and tyrosine at position 434;

(c) tyrosine at position 252, glutamine at position 307, alanine at position 311, tyrosine at position 434, and isoleucine at position 436;

(d) tyrosine at position 252, threonine at position 254, glutamic acid at position 286, glutamine at position 307, alanine at position 311, tyrosine at position 434, and isoleucine at position 436;

(e) valine at position 250, tyrosine at position 252, threonine at position 254, proline at position 308, tyrosine at position 434, and valine at position 436;

(f) valine at position 250, tyrosine at position 252, glutamine at position 307, alanine at position 311, tyrosine at position 434, and valine at position 436;

(g) tyrosine at position 252, glutamine at position 307, alanine at position 311, tyrosine at position 434, and valine at position 436;

(h) valine at position 250, tyrosine at position 252, proline at position 308, and tyrosine at position 434;

or

(i) valine at position 250, tyrosine at position 252, glutamine at position 307, proline at position 308, alanine at position 311, and tyrosine at position 434 (all positions by EU numbering).

69. The antigen-binding molecule of claim 62, wherein the at least one position that is substituted includes all members of a set of positions selected from any of sets (a)-(d):

(a) positions 252, 434, 307, 311, 436, and 286;

(b) positions 252, 434, 307, 311, 436, 250, and 308;

(c) positions 252, 434, 307, 311, 436, 250, 286, and 308;

(d) positions 252, 434, 307, 311, 436, 250, 286, 308, and 428 (all positions by EU numbering).

70. The antigen-binding molecule of claim 62, wherein the modified FcRn-binding domain comprises one of the following combinations of amino acid residues at the indicated positions:

(a) tyrosine at position 252, glutamic acid at position 286, glutamine at position 307, alanine at position 311, tyrosine at position 434, and valine at position 436;

(b) valine at position 250, tyrosine at position 252, glutamine at position 307, proline at position 308, alanine at position 311, tyrosine at position 434, and valine at position 436;

(c) valine at position 250, tyrosine at position 252, glutamic acid at position 286, glutamine at position 307, proline at position 308, alanine at position 311, tyrosine at position 434, and valine at position 436;

or

(d) valine at position 250, tyrosine at position 252, glutamic acid at position 286, glutamine at position 307, proline at position 308, alanine at position 311, tyrosine at position 434, and valine at position 436 (all positions by EU numbering).

71. The antigen-binding molecule of claim 62, wherein the at least one position that is substituted includes all members of a set of positions selected from any of sets (a)-(c):

(a) positions 434, 307, and 311;

(b) positions 434, 307, 309, and 311;

(c) positions 434, 250, 252, and 436 (all positions by EU numbering).

72. The antigen-binding molecule of claim 62, wherein the modified FcRn-binding domain comprises one of the following combinations of amino acid residues at the indicated positions:

(a) glutamine at position 307, histidine at position 311, and tyrosine at position 434;

(b) glutamine at position 307, glutamic acid at position 309, alanine at position 311, and tyrosine at position 434;

(c) glutamine at position 307, glutamic acid at position 309, histidine at position 311, and tyrosine at position 434;

or

(d) valine at position 250, tyrosine at position 252, tyrosine at position 434, and valine at position 436 (all positions by EU numbering).

73. The antigen-binding molecule of claim 62, wherein the antigen-binding molecule comprises an antigen-binding domain whose antigen-binding activity is lower at pH 5.8 than at pH 7.4.

74. The antigen-binding molecule of claim 62, wherein the antigen-binding molecule comprises an antigen-binding domain whose antigen-binding activity is lower at a first calcium concentration that is between 0.1 μ

M to 30 μ

M than at a second calcium concentration that is between 100 μ

M to 10 mM.

75. The antigen-binding molecule of claim 62, wherein the antigen-binding molecule has an FcRn receptor-binding affinity of 50-150 nM at pH 7.0, a melting temperature (Tm) above 63.0°

C., and an Epibase score lower than 250.

76. The antigen-binding molecule of claim 62, wherein the antigen-binding molecule has an FcRn receptor binding affinity of 15-50 nM at pH 7.0, a Tm above 60°

C., and an Epibase score lower than 500.

77. The antigen-binding molecule of claim 62, wherein the antigen-binding molecule has an FcRn receptor binding affinity stronger than 15 nM at pH 7.0, a Tm higher than 57.5°

C., and an Epibase score lower than 500.

78. The antigen-binding molecule of claim 62, wherein the at least one position that is substituted includes (a) one or more of positions 238, 255, and 258;

and (b) three or more additional positions, wherein the three or more additional positions are a combination of positions selected from any of the combinations listed in any of Tables 4 to 7 (all positions by EU numbering).

79. The antigen-binding molecule of claim 62, wherein the amino acid at position 257 (EU numbering) of the modified FcRn-binding domain is not alanine, valine, isoleucine, leucine, or threonine.

80. The antigen-binding molecule of claim 62, wherein the amino acid at position 252 (EU numbering) of the modified FcRn-binding domain is not tryptophan.

81. The antigen-binding molecule of claim 62, wherein a rheumatoid factor (RF) antibody'"'"'s binding affinity for the modified FcRn-binding domain is the same or decreased compared to the binding affinity of the RF antibody for a native human IgG FcRn-binding domain of a control IgG antibody.

82. The antigen-binding molecule of claim 81, wherein the difference between the sequence of the modified FcRn-binding domain and the sequence of the native human IgG FcRn-binding domain also includes a substitution at one or more of the following positions (by EU numbering):

387, 422, 424, 426, 433, 436, 438 and 440.

83. The antigen-binding molecule of claim 82, wherein one or more of the following positions (EU numbering) in the modified FcRn-binding domain is occupied by the indicated amino acid:

arginine at position 387,

any one of glutamic acid, arginine, serine, aspartic acid, lysine, threonine and glutamine at position 422;

any one of glutamic acid, arginine, lysine, and asparagine at position 424;

any one of aspartic acid, glutamine, alanine, and tyrosine at position 426;

aspartic acid at position 433;

threonine at position 436;

any one of glutamic acid, arginine, serine, and lysine at position 438; and

any one of glutamic acid, aspartic acid and glutamine at position 440.

84. The antigen-binding molecule of claim 62, wherein the modified FcRn-binding domain differs from the native human IgG FcRn-binding domain by substitutions comprising a combination of substitutions selected from the combinations of three or more substitutions listed in Tables 12 and 13.

85. The antigen-binding molecule of claim 62, wherein the modified FcRn-binding domain differs from the native human IgG FcRn-binding domain by substitutions comprising a combination of substitutions selected from the combinations listed in Tables 14 and 15.

86. The antigen-binding molecule of claim 82, wherein the modified FcRn-binding domain comprises any one of the following sets of amino acids at the indicated positions (all positions by EU numbering):

(a) tyrosine at position 252, arginine at position 387, tyrosine at position 434, and valine at position 436;

or

(b) tyrosine at position 252, glutamic acid at position 422, tyrosine at position 434, and valine at position 436;

or

(c) tyrosine at position 252, arginine at position 422, tyrosine at position 434, and valine at position 436;

or

(d) tyrosine at position 252, serine at position 422, tyrosine at position 434, and valine at position 436;

or

(e) tyrosine at position 252, glutamic acid at position 424, tyrosine at position 434, and valine at position 436;

or

(f) tyrosine at position 252, arginine at position 424, tyrosine at position 434, and valine at position 436;

or

(g) tyrosine at position 252, tyrosine at position 434, valine at position 436, and glutamic acid at position 438;

or

(h) tyrosine at position 252, tyrosine at position 434, valine at position 436, and arginine at position 438;

or

(i) tyrosine at position 252, tyrosine at position 434, valine at position 436, and serine at position 438;

or

(j) tyrosine at position 252, tyrosine at position 434, valine at position 436, and glutamic acid at position 440.

87. The antigen-binding molecule of claim 62, wherein the antigen-binding molecule is an antibody.

88. A composition comprising the antigen-binding molecule of claim 87, wherein at least 98% of the antigen-binding molecule in the composition is in the form of antibody monomers containing two heavy chains and two light chains.

89. A method for reducing plasma concentration of an antigen in a subject, the method comprising administering to the subject the antigen-binding molecule of claim 62, wherein the antigen-binding molecule binds to the antigen.

90. A method of producing the molecule of claim 62, the method comprising:

identifying a nucleotide sequence encoding a first polypeptide comprising a first FcRn-binding domain;

generating a DNA comprising a second nucleotide sequence encoding a second polypeptide comprising a modified FcRn-binding domain, wherein the amino acid sequence of the modified FcRn-binding domain differs from the amino acid sequence of the first FcRn-binding domain, and from the amino acid sequence of a native human IgG FcRn-binding domain, at one or more positions, including an amino acid substitution at at least one of the following positions (EU numbering);

238, 250, 252, 254, 255, 258, 286, 307, 308, 309, 311, 315, 428, 433, 434, and 436;

expressing the DNA, thereby producing the second polypeptide; and

collecting the second polypeptide.

91. The method of claim 90, wherein the second polypeptide further comprises an antigen-binding domain that binds antigen in a pH-dependent or calcium ion concentration-dependent manner.

92. The method of claim 90, further comprises

identifying a parent antigen-binding domain;

generating a nucleotide sequence encoding a mutant antigen-binding domain identical to the parent antigen-binding domain except for one or more amino acid substitutions that alter the pH dependence of antigen binding; and

incorporating the nucleotide sequence encoding the mutant antigen-binding domain into the second nucleotide sequence, so that the second polypeptide comprises both the mutant antigen-binding domain and the modified FcRn-binding domain.

93. The method of claim 90, further comprises

identifying a parent antigen-binding domain;

generating a nucleotide sequence encoding a mutant antigen-binding domain identical to the parent antigen-binding domain except for one or more amino acid substitutions that alter the calcium ion concentration dependence of antigen binding; and

incorporating the nucleotide sequence encoding the mutant antigen-binding domain into the second nucleotide sequence, so that the second polypeptide comprises both the mutant antigen-binding domain and the modified FcRn-binding domain.

94. The method of claim 91, further comprising conducting one or more assays to confirm that the second polypeptide has one or more of the following properties compared to a polypeptide comprising the antigen-binding domain and the first FcRn-binding domain:

(1) increased plasma retention time in vivo,

(2) delayed elimination in vivo,

(3) increased rate of eliminating the antigen from a subject'"'"'s plasma,

(4) increased binding affinity for a human FcRn receptor at a first pH between 4.0-6.5 and at a second pH between 6.7-10.0.

95. An antigen-binding molecule comprising a modified FcRn-binding domain that contains at least one amino acid substitution compared to a native human IgG FcRn-binding domain, including a substitution at one or more of the following positions (by EU numbering):

387, 422, 424, 426, 433, 436, 438 and 440,

wherein a rheumatoid factor (RF) antibody'"'"'s binding affinity for the modified FcRn-binding domain at pH 7 is the same or decreased compared to the binding affinity of the RF antibody for the native human IgG FcRn-binding domain at pH 7.

96. The antigen-binding molecule of claim 95, wherein (a) the antigen-binding molecule'"'"'s binding affinity for a human FcRn receptor at a first pH between 4.0-6.5 is increased compared to the binding affinity of a control antibody for the human FcRn receptor at the first pH, or (b) the antigen-binding molecule'"'"'s binding affinity for the human FcRn receptor at a second pH between 6.7-10.0 is increased compared to the binding affinity of the control antibody for the human FcRn receptor at the second pH, wherein the control antibody comprises the native human IgG FcRn-binding domain.

97. The antigen-binding molecule of claim 95, wherein one or more of the following positions (EU numbering) in the modified FcRn-binding domain is occupied by the indicated amino acid:

arginine at position 387;

any one of glutamic acid, arginine, serine, aspartic acid, lysine, threonine, and glutamine at position 422;

any one of glutamic acid, arginine, lysine, and asparagine at position 424;

any one of aspartic acid, glutamine, alanine, and tyrosine at position 426;

aspartic acid at position 433;

threonine at position 436;

any one of glutamic acid, arginine, serine, and lysine at position 438; and

any one of glutamic acid, aspartic acid, and glutamine at position 440.

98. The antigen-binding molecule of claim 95, wherein the at least one substitution includes substitution at one of the positions or combinations of positions listed in Table 10.

99. The antigen-binding molecule of claim 95, wherein the at least one substitution includes a substitution or combination of substitutions listed in Table 11.

100. The antigen-binding molecule of claim 95, wherein the at least one substitution further comprises a substitution at one or more of the following positions (EU numbering):

238, 250, 252, 254, 255, 256, 258, 286, 307, 308, 309, 311, 315, 428, 434, and 436; and

wherein (a) the antigen-binding molecule'"'"'s binding affinity for a human FcRn receptor at a first pH between 4.0-6.5 is increased compared to the binding affinity of a control antibody for the human FcRn receptor at the first pH, or (b) the antigen-binding molecule'"'"'s binding affinity for the human FcRn receptor at a second pH between 6.7-10.0 is increased compared to the binding affinity of the control antibody for the human FcRn receptor at the second pH, the control antibody comprising the native human IgG FcRn-binding domain.

101. The antigen-binding molecule of claim 95, wherein the at least one substitution also includes substitutions at:

(i) either

(a) positions 438 and 440, or

(b) position 424; and

(ii) any one of the following sets of positions;

(c) position 434,

(d) positions 252, 254, and 256,

(e) positions 428 and 434,

(f) positions 250 and 428

(all positions by EU numbering).

102. The antigen-binding molecule of claim 101, wherein the at least one substitution includes:

(i) either

(a) arginine at position 438 and glutamic acid at position 440, or

(b) asparagine at position 424; and

(ii) any one of the following sets of substitutions (c)-(f);

(c) histidine at position 434,

(d) tyrosine at position 252, threonine at position 254, and glutamic acid at position 256,

(e) leucine at position 428 and serine at position 434, or

(f) glutamine at position 250 and leucine at position 428

(all positions by EU numbering).

103. The antigen-binding molecule of claim 101, wherein the at least one substitution includes a combination of substitutions listed in Table 13 or 15.

104. The antigen-binding molecule of claim 96, wherein the at least one substitution includes both (a) and (b):

(a) substitution at one or more of the following positions;

387, 422, 424, 438, 440, 433; and

(b) any one of the combinations of substitutions listed in Table 9

(all positions by EU numbering).

105. The antigen-binding molecule of claim 96, wherein the at least one substitution includes both (a) and (b):

(a) substitutions at either

(i) positions 422 and 424, or

(ii) positions 438 and 440; and

(b) any one of the combinations of substitutions listed in Table 9

(all positions by EU numbering).

106. The antigen-binding molecule of claim 104, wherein the at least one substitution includes one of the combinations of three or more substitutions listed in Table 12 or 14.

107. The antigen-binding molecule of claim 96, wherein the antigen-binding molecule comprises an antigen-binding domain that binds antigen in a pH-dependent manner.

108. The antigen-binding molecule of claim 96, wherein the antigen-binding molecule comprises an antigen-binding domain that binds antigen in a calcium ion concentration-dependent manner.

109. A method of producing the molecule of claim 96, the method comprising:

identifying a nucleotide sequence encoding a first polypeptide comprising a first FcRn-binding domain, wherein the first FcRn-binding domain (a) is a mutated form of a native human IgG FcRn-binding domain, (b) has greater binding affinity for a human FcRn at either a first pH in the range of 4.0 to 6.5 or a second pH in the range of 7.0 to 9.0 than does the native FcRn-binding domain at the same pH, and (c) has greater binding affinity for a RF antibody at pH 7 than does the native FcRn-binding domain at pH 7;

generating a DNA comprising a second nucleotide sequence encoding a second polypeptide comprising a second FcRn-binding domain and an antigen-binding domain, wherein the amino acid sequence of the second FcRn-binding domain differs from the amino acid sequence of the first FcRn-binding domain, and from the amino acid sequence of the native human IgG FcRn-binding domain, by substitutions at one or more positions, including an amino acid substitution at at least one of the following positions (EU numbering);

387, 422, 424, 426, 433, 436, 438, and 440, and wherein the antigen-binding domain binds to antigen in a pH-dependent or calcium ion-dependent manner;

expressing the DNA, thereby producing the second polypeptide; and

collecting the second polypeptide,

wherein the second polypeptide (i) has greater binding affinity for the human FcRn at either the first pH or the second pH than does the native FcRn-binding domain at the same pH, and (ii) has decreased binding affinity for a RF antibody at pH 7 than does the first FcRn-binding domain at pH 7.

110. The method of claim 109, wherein the first FcRn-binding domain differs from the native human IgG FcRn-binding domain by substitution at one or more of the following positions (EU numbering):

238, 250, 252, 254, 255, 256, 258, 286, 307, 308, 309, 311, 315, 428, 433, 434, 436.

111. The method of claim 109, wherein the substitutions at one or more positions include substitutions at one of the positions or combinations of positions listed in Table 10.

112. A method for reducing plasma concentration of an antigen in a subject, the method comprising administering to the subject the antigen-binding molecule of claim 95, wherein the antigen-binding molecule binds the antigen.

113. A pharmaceutical composition comprising the antigen-binding molecule of claim 95 and a pharmaceutically acceptable carrier.