Patent Application
20240417437
This disclosure relates to the field of linker polypeptides comprising one or more targeting sequences. The linker polypeptides are useful, e.g., for targeting to certain types of extracellular environments.
It can be beneficial to target protein therapeutics and other polypeptides to particular extracellular environments. It can also be beneficial to modulate the activity and/or pharmacokinetics to limit systemic and/or adverse effects.
For example, various forms of active domains, including but not limited to immunoglobulin antigen-binding domains, such as an Fv, scFv, Fab, or VHH, and cytokines and chemokines, such as IL-2, IL-10, IL-15, TGF-β, CXCL9, CXCL10, and others, play a significant role in targeting diseased cells and/or sustaining an effective immune cell response. In some cases, however, systemic administration of such compounds can activate immune cells throughout the body. Systemic activation can lead to systemic toxicity and indiscriminate activation of immune cells, including immune cells that respond to a variety of epitopes, antigens, and stimuli. The therapeutic potential of such therapy can be affected by these severe toxicities.
Peptide, immunoglobulin, and cytokine therapies can also suffer from a short serum half-life, sometimes on the order of several minutes. Thus, the high doses thereof that can be necessary to achieve an optimal effect can contribute to severe toxicities.
Further, in a traditional antibody, the immunoglobulin antigen-binding domains are fixed to a pharmacokinetic modulator, such as an Fc region. As such, the Fc region's activity is tied to the immunoglobulin antigen-binding domains' activities, and these regions and domains cannot operate independently, even when these activities are needed at different locations and/or at different times, or have differing requirements for Fc function, such as when one region or domain is for target destruction and another region or domain is for immunostimulation.
Accordingly, polypeptides that overcome the hurdles of systemic or untargeted function, severe toxicity, poor pharmacokinetics, and inseparable activities, are needed. Additionally, cancer cells may be stimulated by the presence of certain growth factors. Interfering with such stimulation while also increasing an immune response against the cancer cells would be beneficial. The present disclosure aims to meet one or more of these needs, provide other benefits, or at least provide the public with a useful choice.
In some aspects, linker polypeptides are provided, which can be targeted to certain types of extracellular environments through the use of targeting sequences. In some embodiments, the linker polypeptides can include a first targeting sequence; a second targeting sequence; and a first linker between the first targeting sequence and the second targeting sequence, the linker comprising a protease-cleavable polypeptide sequence. In some embodiments, the linker polypeptide can include a first active domain; a second active domain; a pharmacokinetic modulator; and a first linker between the pharmacokinetic modulator and the first active domain, or between the first active domain and the second active domain, the first linker comprising a protease-cleavable polypeptide sequence. In some embodiments, the linker polypeptide can include a first active domain; an inhibitory polypeptide sequence capable of blocking an activity of the first active domain; a first linker between the first active domain and the inhibitory polypeptide sequence, the linker comprising a protease-cleavable polypeptide sequence; and a first targeting sequence.
In some embodiments, different functions of different components of a linker polypeptide can be decoupled from each other and/or activated when one or more protease-cleavable polypeptide sequences are cleaved by one or more proteases. For example, cleaving a protease-cleavable polypeptide can allow an inhibitory polypeptide sequence to dissociate from a cytokine polypeptide sequence, and/or can allow an active domain (e.g., which may have an immunostimulatory function) to disassociate from the remainder of the linker polypeptide (e.g., which may have a target-destroying function).
Many tumors and tumor microenvironments exhibit aberrant expression and activation of proteases. The present disclosure provides linker polypeptides with components that may be decoupled from each other and/or activated through proteolytic cleavage, such that they become active when they come in contact with proteases in a tumor or tumor microenvironment. In some cases, for example, this can lead to an increase in active domains (e.g., cytokines or immunoglobulin domains) in and around the tumor or tumor microenvironment relative to the rest of a subject's body or healthy tissue. One exemplary advantage that can result is the formation of gradients of the active domain. Such a gradient can form when a linker polypeptide is administered and selectively or preferentially becomes activated in the tumor or tumor microenvironment and subsequently diffuses out of these areas to the rest of the body. These gradients can, e.g., increase the trafficking of immune cells to the tumor and tumor microenvironment. Immune cells that traffic to the tumor can infiltrate the tumor. Infiltrating immune cells can mount an immune response against the cancer. Infiltrating immune cells can also secrete their own chemokines and cytokines. The cytokines can have either or both of autocrine and paracrine effects within the tumor and tumor microenvironment. In some cases, the immune cells include T cells, such as T effector cells or cytotoxic T cells, or NK cells.
Also described herein are methods of treatment and methods of administrating the linker polypeptides described herein. Such administration can be systemic or local. In some embodiments, a linker polypeptide described herein is administered systemically or locally to treat a cancer.
The following embodiments are encompassed.
Embodiment 1 is a linker polypeptide, comprising:
Embodiment 2 is the linker polypeptide of the immediately preceding embodiment, further comprising a first active domain, optionally wherein the first active domain is proximal to the first targeting sequence relative to the second targeting sequence.
Embodiment 3 is the linker polypeptide of the immediately preceding embodiment, further comprising an additional domain, optionally wherein the additional domain comprises an inhibitory polypeptide sequence capable of blocking an activity of the first active domain, a pharmacokinetic modulator, and/or a second active domain, and optionally wherein the additional domain is proximal to the second targeting sequence relative to the first targeting sequence.
Embodiment 4 is the linker polypeptide of the immediately preceding embodiment, comprising sequentially, from the N-terminus to the C-terminus or from the C-terminus to the N-terminus, the first active domain, the first targeting sequence, the first linker, the second targeting sequence, and the additional domain.
Embodiment 5 is a linker polypeptide, comprising
Embodiment 6 is the linker polypeptide of embodiment 5, further comprising a first targeting sequence.
Embodiment 7 is a linker polypeptide, comprising:
Embodiment 8 is the linker polypeptide of the immediately preceding embodiment, comprising a pharmacokinetic modulator.
Embodiment 9 is a linker polypeptide, comprising:
Embodiment 10 is a linker polypeptide, comprising:
Embodiment 11 is the linker polypeptide of embodiment 9 or 10, wherein the inhibitory polypeptide sequence is C-terminal to the second domain of the pharmacokinetic modulator.
Embodiment 12 is the linker polypeptide of embodiment 9 or 10, wherein the inhibitory polypeptide sequence is N-terminal to the second domain of the pharmacokinetic modulator.
Embodiment 13 is the linker polypeptide of any one of embodiments 9-12, wherein the targeting sequence is between the protease-cleavable polypeptide sequence and the first domain of the pharmacokinetic modulator.
Embodiment 14 is the linker polypeptide of any one of embodiments 9-12, wherein the targeting sequence is between the protease-cleavable polypeptide sequence and the first active domain.
Embodiment 15 is the linker polypeptide of any one of embodiments 9-12, wherein the targeting sequence is C-terminal to the first active domain.
Embodiment 16 is the linker polypeptide of any one of embodiments 9-12, wherein the targeting sequence is N-terminal to the first active domain.
Embodiment 17 is the linker polypeptide of any one of embodiments 9-12, wherein the targeting sequence is C-terminal to the inhibitory polypeptide sequence.
Embodiment 18 is the linker polypeptide of any one of embodiments 9-12, wherein the targeting sequence is N-terminal to the inhibitory polypeptide sequence.
Embodiment 19 is the linker polypeptide of any one of embodiments 9-12, wherein the targeting sequence is between the inhibitory polypeptide sequence and the second domain of the pharmacokinetic modulator.
Embodiment 20 is the linker polypeptide of any one of embodiments 9-19, wherein the targeting sequence binds heparin, optionally wherein the targeting sequence comprises SEQ ID NO: 664.
Embodiment 21 is the linker polypeptide of any one of embodiments 9-19, wherein the targeting sequence binds collagen IV, optionally wherein the targeting sequence comprises SEQ ID NO: 200.
Embodiment 22 is the linker polypeptide of any one of embodiments 9-19, wherein the targeting sequence binds collagen I, optionally wherein the targeting sequence comprises SEQ ID NO: 188.
Embodiment 23 is the linker polypeptide of any one of embodiments 9-19, wherein the targeting sequence binds fibronectin, optionally wherein the targeting sequence comprises SEQ ID NO: 653.
Embodiment 24 is the linker polypeptide of any one of embodiments 9-23, wherein the targeting sequence is a first targeting sequence and the linker polypeptide further comprises a second targeting sequence.
Embodiment 25 is the linker polypeptide of the immediately preceding embodiment, wherein the first targeting sequence is part of the first polypeptide chain and the second targeting sequence is part of the second polypeptide chain.
Embodiment 26 is the linker polypeptide of the immediately preceding embodiment, wherein the first targeting sequence is C-terminal to the first active domain and the second targeting sequence is C-terminal to the inhibitory polypeptide sequence.
Embodiment 27 is the linker polypeptide of any one of embodiments 24-26, wherein the second targeting sequence binds heparin, optionally wherein the targeting sequence comprises SEQ ID NO: 664.
Embodiment 28 is the linker polypeptide of any one of embodiments 24-26, wherein the second targeting sequence binds collagen IV, optionally wherein the targeting sequence comprises SEQ ID NO: 200.
Embodiment 29 is the linker polypeptide of any one of embodiments 24-26, wherein the second targeting sequence binds collagen I, optionally wherein the targeting sequence comprises SEQ ID NO: 188.
Embodiment 30 is the linker polypeptide of any one of embodiments 24-26, wherein the second targeting sequence binds fibronectin, optionally wherein the targeting sequence comprises SEQ ID NO: 653.
Embodiment 31 is the linker polypeptide of any one of embodiments 9-30, further comprising a second active domain, optionally wherein the second active domain is part of the second polypeptide chain.
Embodiment 32 is the linker polypeptide of any one of embodiments 9-31, wherein the inhibitory polypeptide sequence is a first inhibitory polypeptide sequence, and the linker polypeptide further comprises a second inhibitory polypeptide sequence.
Embodiment 33 is the linker polypeptide of the immediately preceding embodiment, wherein the second inhibitory polypeptide sequence is part of the second polypeptide chain.
Embodiment 34 is the linker polypeptide of the immediately preceding embodiment, wherein the second inhibitory polypeptide sequence is C-terminal to the first inhibitory polypeptide sequence.
Embodiment 35 is the linker polypeptide of any one of embodiments 32-34, wherein the second inhibitory polypeptide sequence is an immunoglobulin inhibitory polypeptide sequence.
Embodiment 36 is the linker polypeptide of the immediately preceding embodiment, wherein the first inhibitory polypeptide sequence is an immunoglobulin inhibitory polypeptide sequence.
Embodiment 37 is the linker polypeptide of embodiment 35 or 36, wherein one or each of the immunoglobulin inhibitory polypeptide sequences is a VHH.
Embodiment 38 is the linker polypeptide of any one of embodiments 8-37, wherein the pharmacokinetic modulator comprises a heterodimeric Fc or heterodimeric CH3 domains.
Embodiment 39 is the linker polypeptide of the immediately preceding embodiment, wherein the heterodimeric Fc or heterodimeric CH3 domains comprise a knob CH3 domain and a hole CH3 domain.
Embodiment 40 is the linker polypeptide of the immediately preceding embodiment, wherein the first domain of the pharmacokinetic modulator is a knob CH3 domain and the second domain of the pharmacokinetic modulator is a hole CH3 domain.
Embodiment 41 is the linker polypeptide of embodiment 39, wherein the first domain of the pharmacokinetic modulator is a hole CH3 domain and the second domain of the pharmacokinetic modulator is a knob CH3 domain.
Embodiment 42 is the linker polypeptide of any one of embodiments 38-41, wherein the pharmacokinetic modulator comprises the sequence of SEQ ID NO: 75.
Embodiment 43 is the linker polypeptide of any one of embodiments 38-41, wherein the pharmacokinetic modulator comprises the sequence of SEQ ID NO: 76.
Embodiment 44 is the linker polypeptide of any one of embodiments 38-41, wherein the pharmacokinetic modulator comprises the sequence of SEQ ID NO: 756.
Embodiment 45 is the linker polypeptide of any one of embodiments 38-44, wherein the pharmacokinetic modulator comprises the sequence of SEQ ID NO: 77.
Embodiment 46 is the linker polypeptide of any one of embodiments 38-44, wherein the pharmacokinetic modulator comprises the sequence of SEQ ID NO: 78.
Embodiment 47 is the linker polypeptide of any one of embodiments 38-44, wherein the pharmacokinetic modulator comprises the sequence of SEQ ID NO: 757.
Embodiment 48 is the linker polypeptide of any one of the preceding embodiments, wherein the first active domain comprises a first immunoglobulin antigen-binding domain.
Embodiment 49 is the linker polypeptide of any one of the preceding embodiments, wherein the second active domain comprises a second immunoglobulin antigen-binding domain.
Embodiment 50 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a VH region and a VL region.
Embodiment 51 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises an Fv, scFv, Fab, or VHH.
Embodiment 52 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently is humanized or fully human.
Embodiment 53 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently is configured to bind to one or more sequences selected from a cancer cell surface antigen sequence, a growth factor sequence, and a growth factor receptor sequence.
Embodiment 54 is the linker polypeptide of the immediately preceding embodiment, wherein one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently is configured to bind to a HER2 sequence, an EGFR extracellular domain sequence, a PD-1 extracellular domain sequence, a PD-L1 extracellular domain sequence, or a CD3 extracellular domain sequence.
Embodiment 55 is the linker polypeptide of any one of the preceding embodiments, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain is configured to bind to a HER2 sequence.
Embodiment 56 is the linker polypeptide of the immediately preceding embodiment, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a VH region comprising hypervariable regions (HVRs) HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of SEQ ID NO: 910, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of SEQ ID NO: 909.
Embodiment 57 is the linker polypeptide of the immediately preceding embodiment, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a VH region comprising the amino acid sequence of SEQ ID NO: 910; and a VL region comprising the amino acid sequence of SEQ ID NO: 909.
Embodiment 58 is the linker polypeptide of embodiment 55 or 56, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 909 or 910.
Embodiment 59 is the linker polypeptide of embodiment 55, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain is an antigen-binding domain of trastuzumab.
Embodiment 60 is the linker polypeptide of any one of the preceding embodiments, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain is configured to bind to an EGFR extracellular domain sequence.
Embodiment 61 is the linker polypeptide of the immediately preceding embodiment, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of SEQ ID NO: 914, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of SEQ ID NO: 913.
Embodiment 62 is the linker polypeptide of the immediately preceding embodiment, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a VH region comprising the amino acid sequence of SEQ ID NO: 914; and a VL region comprising the amino acid sequence of SEQ ID NO: 913.
Embodiment 63 is the linker polypeptide of embodiment 60 or 61, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 913 or 914.
Embodiment 64 is the linker polypeptide of embodiment 60, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain is an antigen-binding domain of cetuximab.
Embodiment 65 is the linker polypeptide of any one of the preceding embodiments, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain is configured to bind to a PD-1 extracellular domain sequence.
Embodiment 66 is the linker polypeptide of the immediately preceding embodiment, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of SEQ ID NO: 917, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of SEQ ID NO: 918.
Embodiment 67 is the linker polypeptide of the immediately preceding embodiment, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a VH region comprising the amino acid sequence of SEQ ID NO: 917; and a VL region comprising the amino acid sequence of SEQ ID NO: 918.
Embodiment 68 is the linker polypeptide of embodiment 65 or 66, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 917 or 918.
Embodiment 69 is the linker polypeptide of embodiment 65, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain is an antigen-binding domain of nivolumab.
Embodiment 70 is the linker polypeptide of any one of the preceding embodiments, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain is configured to bind to a PD-L1 extracellular domain sequence.
Embodiment 71 is the linker polypeptide of the immediately preceding embodiment, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of SEQ ID NO: 921, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of SEQ ID NO: 922.
Embodiment 72 is the linker polypeptide of the immediately preceding embodiment, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a VH region comprising the amino acid sequence of SEQ ID NO: 921; and a VL region comprising the amino acid sequence of SEQ ID NO: 922.
Embodiment 73 is the linker polypeptide of embodiment 70 or 71, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 921 or 922.
Embodiment 74 is the linker polypeptide of embodiment 70, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain is an antigen-binding domain of atezolizumab.
Embodiment 75 is the linker polypeptide of any one of the preceding embodiments, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain is configured to bind to a CD3 extracellular domain sequence.
Embodiment 76 is the linker polypeptide of the immediately preceding embodiment, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of any one of SEQ ID NOs: 925, 929, 933, and 937, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of any one of SEQ ID NOs: 926, 930, 934, and 938.
Embodiment 77 is the linker polypeptide of the immediately preceding embodiment, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a VH region comprising the amino acid sequence of any one of SEQ ID NOs: 925, 929, 933, and 937; and a VL region comprising the amino acid sequence of any one of SEQ ID NOs: 926, 930, 934, and 938.
Embodiment 78 is the linker polypeptide of embodiment 75 or 76, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 925, 926, 929, 930, 933, 934, 937, and 938.
Embodiment 79 is the linker polypeptide of embodiment 75, wherein one of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain is an antigen-binding domain of teplizumab, muromonab, otelixizumab, or visilizumab.
Embodiment 80 is the linker polypeptide of any one of the preceding embodiments, wherein the first active domain comprises a receptor-binding domain.
Embodiment 81 is the linker polypeptide of the immediately preceding embodiment, wherein the receptor-binding domain comprises a cytokine polypeptide sequence.
Embodiment 82 is the linker polypeptide of any one of embodiments 80-81, wherein the receptor-binding domain comprises a modification to prevent disulfide bond formation, and optionally otherwise comprises wild-type sequence.
Embodiment 83 is the linker polypeptide of any one of embodiments 80-82, wherein the receptor-binding domain has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a wild-type receptor-binding domain or to a receptor-binding domain in Table 1.
Embodiment 84 is the linker polypeptide of the immediately preceding embodiment, wherein the receptor-binding domain is a wild-type receptor-binding domain.
Embodiment 85 is the linker polypeptide of any one of embodiments 80-84, wherein the receptor-binding domain is a monomeric cytokine, or wherein the receptor-binding domain is a dimeric receptor-binding domain comprising monomers that are associated covalently (optionally via a polypeptide linker) or noncovalently.
Embodiment 86 is the linker polypeptide of any one of embodiments 80-85, further comprising
Embodiment 87 is the linker polypeptide of any one of embodiments 80-86 insofar as they depend from any one of embodiments 9-24, wherein the inhibitory polypeptide sequence comprises a cytokine-binding domain.
Embodiment 88 is the linker polypeptide of any one of embodiments 9-47 or 86-87, wherein the inhibitory polypeptide sequence comprises a cytokine-binding domain.
Embodiment 89 is the linker polypeptide of embodiment 87 or 88, wherein the cytokine-binding domain is a cytokine-binding domain of a cytokine receptor or a cytokine-binding domain of a fibronectin.
Embodiment 90 is the linker polypeptide of the immediately preceding embodiment, wherein the cytokine-binding domain is an immunoglobulin cytokine-binding domain.
Embodiment 91 is the linker polypeptide of the immediately preceding embodiment, wherein the immunoglobulin cytokine-binding domain comprises a VL region and a VH region that bind the cytokine.
Embodiment 92 is the linker polypeptide of embodiment 90 or 91, wherein the immunoglobulin cytokine-binding domain is an Fv, scFv, Fab, or VHH.
Embodiment 93 is the linker polypeptide of any one of embodiments 80-92, comprising a targeting sequence, wherein the targeting sequence is between the receptor-binding domain and the protease-cleavable polypeptide sequence or one of the protease-cleavable polypeptide sequences.
Embodiment 94 is the linker polypeptide of any one of embodiments 80-93, wherein the receptor-binding domain is an interleukin polypeptide sequence.
Embodiment 95 is the linker polypeptide of any one of embodiments 80-94, wherein the receptor-binding domain is capable of binding a receptor comprising CD132.
Embodiment 96 is the linker polypeptide of any one of embodiments 80-95, wherein the receptor-binding domain is capable of binding a receptor comprising CD122.
Embodiment 97 is the linker polypeptide of any one of embodiments 80-96, wherein the receptor-binding domain is capable of binding a receptor comprising CD25.
Embodiment 98 is the linker polypeptide of any one of embodiments 80-97, wherein the receptor-binding domain is capable of binding a receptor comprising IL-10R.
Embodiment 99 is the linker polypeptide of any one of embodiments 80-98, wherein the receptor-binding domain is capable of binding a receptor comprising IL-15R.
Embodiment 100 is the linker polypeptide of any one of embodiments 80-99, wherein the receptor-binding domain is capable of binding a receptor comprising CXCR3.
Embodiment 101 is the linker polypeptide of any one of embodiments 80-100, wherein the receptor-binding domain is an IL-2 polypeptide sequence.
Embodiment 102 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-2 polypeptide sequence has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 1-4.
Embodiment 103 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-2 polypeptide sequence comprises the sequence of any one of SEQ ID NOs: 1-4.
Embodiment 104 is the linker polypeptide of any one of embodiments 101-103, wherein the IL-2 polypeptide sequence is a human IL-2 polypeptide sequence.
Embodiment 105 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-2 polypeptide sequence comprises the sequence of SEQ ID NO: 1.
Embodiment 106 is the linker polypeptide of any one of embodiments 101-104, wherein the IL-2 polypeptide sequence comprises the sequence of SEQ ID NO: 2.
Embodiment 107 is the linker polypeptide of any one of the preceding embodiments, wherein the inhibitory polypeptide sequence comprises an IL-2 binding domain of an IL-2 receptor (IL-2R).
Embodiment 108 is the linker polypeptide of the immediately preceding embodiment, wherein the inhibitory polypeptide sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 10-29 and 40-51.
Embodiment 109 is the linker polypeptide of embodiment 107 or 108, wherein the IL-2R is a human IL-2R.
Embodiment 110 is the linker polypeptide of any one of the preceding embodiments, wherein the inhibitory polypeptide sequence comprises an IL-2-binding immunoglobulin domain.
Embodiment 111 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-2-binding immunoglobulin domain is a human IL-2-binding immunoglobulin domain.
Embodiment 112 is the linker polypeptide of embodiment 110 or 111, wherein the IL-2-binding immunoglobulin domain comprises a VH region comprising hypervariable regions (HVRs) HVR-1, HVR-2, and HVR-3 having the sequences of SEQ ID NOs: 37, 38, and 39, respectively, and a VL region comprising HVR-1, HVR-2, and HVR-3 having the sequences of SEQ ID NOs: 34, 35, and 36, respectively.
Embodiment 113 is the linker polypeptide of any one of embodiments 110-112, wherein the IL-2-binding immunoglobulin domain comprises a VH region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 33 and a VL region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 32, or a VH region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 749 and a VL region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 748.
Embodiment 114 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-2-binding immunoglobulin domain comprises a VH region comprising the sequence of SEQ ID NO: 33 and a VL region comprising the sequence of SEQ ID NO: 32, or a VH region comprising the sequence of SEQ ID NO: 749 and a VL region comprising the sequence of SEQ ID NO: 748.
Embodiment 115 is the linker polypeptide of any one of embodiments 110-114, wherein the IL-2-binding immunoglobulin domain is an scFv.
Embodiment 116 is the linker polypeptide of embodiment 110, 111, or 114, wherein the IL-2-binding immunoglobulin domain comprises the CDRs of an amino acid sequence of SEQ ID NO: 30, 31, 747, 850-856, or 863-870.
Embodiment 117 is the linker polypeptide of embodiment 110, 111, 114, or 116, wherein the IL-2-binding immunoglobulin domain comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 30, 31, 747, 850-856, or 863-870.
Embodiment 118 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-2-binding immunoglobulin domain comprises the sequence of SEQ ID NO: 30, 31, 747, 850-856, or 863-870.
Embodiment 119 is the linker polypeptide of any one of the preceding embodiments, wherein the receptor-binding domain is an IL-10 polypeptide sequence.
Embodiment 120 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-10 polypeptide sequence has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 900.
Embodiment 121 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-10 polypeptide sequence comprises the sequence of SEQ ID NO: 900.
Embodiment 122 is the linker polypeptide of any one of embodiments 119-121, wherein the IL-10 polypeptide sequence is a human IL-10 polypeptide sequence.
Embodiment 123 is the linker polypeptide of any one of embodiments 118-122, wherein the inhibitory polypeptide sequence comprises an IL-10 binding domain of an IL-10 receptor (IL-10R).
Embodiment 124 is the linker polypeptide of the immediately preceding embodiment, wherein the inhibitory polypeptide sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 1011 or 1012.
Embodiment 125 is the linker polypeptide of embodiment 123 or 124, wherein the IL-10R is a human IL-10R.
Embodiment 126 is the linker polypeptide of any one of the preceding embodiments, wherein the inhibitory polypeptide sequence comprises an IL-10-binding immunoglobulin domain.
Embodiment 127 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-O-binding immunoglobulin domain is a human IL-O-binding immunoglobulin domain.
Embodiment 128 is the linker polypeptide of embodiment 126 or 127, wherein the IL-10-binding immunoglobulin domain comprises a VH region comprising hypervariable regions (HVRs) HVR-1, HVR-2, and HVR-3 having the sequences of SEQ ID NOs: 946, 947, and 948, respectively, and a VL region comprising HVR-1, HVR-2, and HVR-3 having the sequences of SEQ ID NOs: 942, 943, and 944, respectively.
Embodiment 129 is the linker polypeptide of any one of embodiments 126-128, wherein the IL-10-binding immunoglobulin domain comprises a VH region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 945 and a VL region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 941.
Embodiment 130 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-10-binding immunoglobulin domain comprises a VH region comprising the sequence of SEQ ID NO: 945 and a VL region comprising the sequence of SEQ ID NO: 941.
Embodiment 131 is the linker polypeptide of any one of embodiments 126-130, wherein the IL-10-binding immunoglobulin domain is an scFv.
Embodiment 132 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-10-binding immunoglobulin domain comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 939 or 940.
Embodiment 133 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-10-binding immunoglobulin domain comprises the sequence of SEQ ID NO: 939 or 940.
Embodiment 134 is the linker polypeptide of any one of the preceding embodiments, wherein the receptor-binding domain is an IL-15 polypeptide sequence.
Embodiment 135 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-15 polypeptide sequence has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 901.
Embodiment 136 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-15 polypeptide sequence comprises the sequence of SEQ ID NO: 901.
Embodiment 137 is the linker polypeptide of any one of embodiments 134-136, wherein the IL-15 polypeptide sequence is a human IL-15 polypeptide sequence.
Embodiment 138 is the linker polypeptide of any one of embodiments 133-137, wherein the inhibitory polypeptide sequence comprises an IL-15 binding domain of an IL-15 receptor (IL-15R).
Embodiment 139 is the linker polypeptide of the immediately preceding embodiment, wherein the inhibitory polypeptide sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 1016-1019.
Embodiment 140 is the linker polypeptide of embodiment 97 or 98, wherein the IL-15R is a human IL-15R.
Embodiment 141 is the linker polypeptide of any one of the preceding embodiments, wherein the inhibitory polypeptide sequence comprises an IL-15-binding immunoglobulin domain.
Embodiment 142 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-15-binding immunoglobulin domain is a human IL-15-binding immunoglobulin domain.
Embodiment 143 is the linker polypeptide of embodiment 141 or 142, wherein the IL-15-binding immunoglobulin domain comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of any one of SEQ ID NOs: 950, 955, 957, 960, 963, 966, 969, 972, 975, 978, 981, 985, and 988, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of any one of SEQ ID NOs: 952, 954, 958, 961, 964, 967, 970, 973, 976, 979, 982, 984, and 987.
Embodiment 144 is the linker polypeptide of any one of embodiments 141-143, wherein the IL-15-binding immunoglobulin domain comprises a VH region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 950, 955, 957, 960, 963, 966, 969, 972, 975, 978, 981, 985, and 988 and a VL region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 952, 954, 958, 961, 964, 967, 970, 973, 976, 979, 982, 984, and 987.
Embodiment 145 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-15-binding immunoglobulin domain comprises a VH region comprising the sequence of any one of SEQ ID NOs: 950, 955, 957, 960, 963, 966, 969, 972, 975, 978, 981, 985, and 988 and a VL region comprising the sequence of any one of SEQ ID NOs: 952, 954, 958, 961, 964, 967, 970, 973, 976, 979, 982, 984, and 987.
Embodiment 146 is the linker polypeptide of any one of embodiments 141-145, wherein the IL-15-binding immunoglobulin domain is an scFv.
Embodiment 147 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-15-binding immunoglobulin domain comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 953, 956, 959, 962, 965, 968, 971, 974, 977, 980, 983, and 986.
Embodiment 148 is the linker polypeptide of the immediately preceding embodiment, wherein the IL-15-binding immunoglobulin domain comprises the sequence of any one of SEQ ID NOs: 953, 956, 959, 962, 965, 968, 971, 974, 977, 980, 983, and 986.
Embodiment 149 is the linker polypeptide of any one of the preceding embodiments, wherein the receptor-binding domain is an CXCL9 polypeptide sequence.
Embodiment 150 is the linker polypeptide of the immediately preceding embodiment, wherein the CXCL9 polypeptide sequence has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 902.
Embodiment 151 is the linker polypeptide of the immediately preceding embodiment, wherein the CXCL9 polypeptide sequence comprises the sequence of SEQ ID NO: 902.
Embodiment 152 is the linker polypeptide of any one of embodiments 149-150, wherein the CXCL9 polypeptide sequence is a human CXCL9 polypeptide sequence.
Embodiment 153 is the linker polypeptide of any one of embodiments 148-152, wherein the inhibitory polypeptide sequence comprises a CXCL9 binding domain of CXCR3.
Embodiment 154 is the linker polypeptide of the immediately preceding embodiment, wherein the inhibitory polypeptide sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 1020 or 1021.
Embodiment 155 is the linker polypeptide of embodiment 153 or 154, wherein the CXCR3 is a human CXCR3.
Embodiment 156 is the linker polypeptide of any one of the preceding embodiments, wherein the inhibitory polypeptide sequence comprises an CXCL9-binding immunoglobulin domain.
Embodiment 157 is the linker polypeptide of the immediately preceding embodiment, wherein the CXCL9-binding immunoglobulin domain is a human CXCL9-binding immunoglobulin domain.
Embodiment 158 is the linker polypeptide of any one of the preceding embodiments, wherein the receptor-binding domain is an CXCL10 polypeptide sequence.
Embodiment 159 is the linker polypeptide of the immediately preceding embodiment, wherein the CXCL10 polypeptide sequence has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 903.
Embodiment 160 is the linker polypeptide of the immediately preceding embodiment, wherein the CXCL10 polypeptide sequence comprises the sequence of SEQ ID NO: 903.
Embodiment 161 is the linker polypeptide of any one of embodiments 158-160, wherein the CXCL10 polypeptide sequence is a human CXCL10 polypeptide sequence.
Embodiment 162 is the linker polypeptide of any one of embodiments 156-161, wherein the inhibitory polypeptide sequence comprises an CXCL10 binding domain of CXCR3.
Embodiment 163 is the linker polypeptide of the immediately preceding embodiment, wherein the inhibitory polypeptide sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 1020 or 1021.
Embodiment 164 is the linker polypeptide of embodiment 162 or 163, wherein the CXCR3 is a human CXCR3.
Embodiment 165 is the linker polypeptide of any one of the preceding embodiments, wherein the inhibitory polypeptide sequence comprises an CXCL10-binding immunoglobulin domain.
Embodiment 166 is the linker polypeptide of the immediately preceding embodiment, wherein the CXCL10-binding immunoglobulin domain is a human CXCL10-binding immunoglobulin domain.
Embodiment 167 is the linker polypeptide of embodiment 165 or 166, wherein the CXCL10-binding immunoglobulin domain comprises a VH region comprising hypervariable regions (HVRs) HVR-1, HVR-2, and HVR-3 having the sequences of SEQ ID NOs: 993, 994, and 995, respectively, and a VL region comprising HVR-1, HVR-2, and HVR-3 having the sequences of SEQ ID NOs: 996, 997, and 998, respectively.
Embodiment 168 is the linker polypeptide of any one of embodiments 165-167, wherein the CXCL10-binding immunoglobulin domain comprises a VH region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 991 and a VL region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 992.
Embodiment 169 is the linker polypeptide of the immediately preceding embodiment, wherein the CXCL10-binding immunoglobulin domain comprises a VH region comprising the sequence of SEQ ID NO: 991 and a VL region comprising the sequence of SEQ ID NO: 992.
Embodiment 170 is the linker polypeptide of any one of embodiments 165-169, wherein the CXCL10-binding immunoglobulin domain is an scFv.
Embodiment 171 is the linker polypeptide of the immediately preceding embodiment, wherein the CXCL10-binding immunoglobulin domain comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 989 or 990.
Embodiment 172 is the linker polypeptide of the immediately preceding embodiment, wherein the CXCL10-binding immunoglobulin domain comprises the sequence of SEQ ID NO: 989 or 990.
Embodiment 173 is the linker polypeptide of any one of the preceding embodiments, wherein the inhibitory polypeptide sequence interferes with binding between the first active domain and a receptor of the first active domain and/or with binding between the second active domain and a receptor of the second active domain.
Embodiment 174 is the linker polypeptide of any one of the preceding embodiments, wherein the inhibitory polypeptide sequence and the pharmacokinetic modulator are different elements of the linker polypeptide.
Embodiment 175 is the linker polypeptide of any one of the preceding embodiments, wherein the inhibitory polypeptide sequence comprises a steric blocker.
Embodiment 176 is the linker polypeptide of any one of the preceding embodiments, wherein the inhibitory polypeptide sequence comprises at least a portion of the pharmacokinetic modulator.
Embodiment 177 is the linker polypeptide of any one of the preceding embodiments, wherein the pharmacokinetic modulator comprises at least a portion of an immunoglobulin constant domain.
Embodiment 178 is the linker polypeptide of the immediately preceding embodiment, wherein the pharmacokinetic modulator comprises at least a portion of an immunoglobulin Fc region.
Embodiment 179 is the linker polypeptide of the immediately preceding embodiment, wherein the pharmacokinetic modulator comprises an immunoglobulin Fc region.
Embodiment 180 is the linker polypeptide of any one of embodiments 177-179, wherein the immunoglobulin is a human immunoglobulin.
Embodiment 181 is the linker polypeptide of any one of embodiments 177-180, wherein the immunoglobulin is IgG.
Embodiment 182 is the linker polypeptide of the immediately preceding embodiment, wherein the IgG is IgG1, IgG2, IgG3, or IgG4.
Embodiment 183 is the linker polypeptide of any of the preceding embodiments, further comprising a growth factor-binding polypeptide sequence or a growth factor receptor-binding polypeptide sequence.
Embodiment 184 is the linker polypeptide of the immediately preceding embodiment, wherein the growth factor-binding polypeptide sequence comprises a TGF-βR extracellular domain sequence.
Embodiment 185 is the linker polypeptide of the immediately preceding embodiment, wherein the TGF-βR extracellular domain sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 1022 or 1023.
Embodiment 186 is the linker polypeptide of the embodiment 142-144, wherein the growth factor-binding polypeptide sequence comprises a growth factor-binding immunoglobulin domain.
Embodiment 187 is the linker polypeptide of the immediately preceding embodiment, wherein the growth factor-binding immunoglobulin domain is configured to bind to a TGF-β.
Embodiment 188 is the linker polypeptide of embodiment 145 or 146, wherein the growth factor-binding immunoglobulin domain comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of SEQ ID NO: 1008, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of SEQ ID NO: 1010.
Embodiment 189 is the linker polypeptide of the immediately preceding embodiment, wherein the growth factor-binding immunoglobulin domain comprises a VH region comprising the amino acid sequence of SEQ ID NO: 1008; and a VL region comprising the amino acid sequence of SEQ ID NO: 1010.
Embodiment 190 is the linker polypeptide of embodiment 185-189, wherein the growth factor-binding immunoglobulin domain comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 1007 or 1009.
Embodiment 191 is the linker polypeptide of embodiment 183-190, wherein the growth factor receptor-binding polypeptide sequence comprises a TGF-β sequence.
Embodiment 192 is the linker polypeptide of the immediately preceding embodiment, wherein the TGF-β sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs. 904-906.
Embodiment 193 is the linker polypeptide of the embodiment 183-192, wherein the growth factor receptor-binding polypeptide sequence comprises a growth factor receptor-binding immunoglobulin domain.
Embodiment 194 is the linker polypeptide of the immediately preceding embodiment, wherein the growth factor receptor-binding immunoglobulin domain is configured to bind to a TGF-βR extracellular domain sequence.
Embodiment 195 is the linker polypeptide of embodiment 193 or 194, wherein the growth factor receptor-binding immunoglobulin domain comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of SEQ ID NO: 999 or 1003, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of SEQ ID NO: 1000 or 1004.
Embodiment 196 is the linker polypeptide of the immediately preceding embodiment, wherein the growth factor receptor-binding immunoglobulin domain comprises a VH region comprising the amino acid sequence of SEQ ID NO: 999 or 1003; and a VL region comprising the amino acid sequence of SEQ ID NO: 1000 or 1004.
Embodiment 197 is the linker polypeptide of embodiment 152-155, wherein the growth factor receptor-binding immunoglobulin domain comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 1001, 1002, 1005, and 1006.
Embodiment 198 is the linker polypeptide of any one of the preceding embodiments, comprising a plurality of protease-cleavable polypeptide sequences.
Embodiment 199 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is C-terminal to a VH region, C-terminal to at least a portion of a CH1 domain, between a CH1 domain and a CH2 domain, N-terminal to at least a portion of a CH2 domain, N-terminal to a disulfide bond between heavy chains, N-terminal to a disulfide bond within a CH2 domain, or N-terminal to a hinge region, or is within a hinge region.
Embodiment 200 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is C-terminal to the first targeting sequence and to the second targeting sequence.
Embodiment 201 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is N-terminal to the first targeting sequence and to the second targeting sequence.
Embodiment 202 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is C-terminal to a first plurality of targeting sequences and is N-terminal to a second plurality of targeting sequences.
Embodiment 203 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is C-terminal to a plurality of targeting sequences and is N-terminal to at least one targeting sequence.
Embodiment 204 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is N-terminal to a plurality of targeting sequences and is C-terminal to at least one targeting sequence.
Embodiment 205 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is C-terminal to the first targeting sequence and to the second targeting sequence and is not N-terminal to a targeting sequence.
Embodiment 206 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is N-terminal to the first targeting sequence and to the second targeting sequence and is not C-terminal to a targeting sequence.
Embodiment 207 is the linker polypeptide of any one of the preceding embodiments, wherein the linker polypeptide is configured to release the first active domain from a remaining portion of the linker polypeptide upon cleavage of the protease-cleavable polypeptide sequence.
Embodiment 208 is the linker polypeptide of the immediately preceding embodiment, wherein the first active domain is configured to remain connected to one or more of: one of the first targeting sequence and the second targeting sequence, one of the at least one targeting sequence, one of the first plurality of targeting sequences, one of the second plurality of targeting sequences, one of the plurality of targeting sequences, and the pharmacokinetic modulator upon cleavage of the protease-cleavable polypeptide sequence.
Embodiment 209 is the linker polypeptide of any one of the preceding embodiments, wherein the linker polypeptide is configured to release the second active domain from a remaining portion of the linker polypeptide upon cleavage of the protease-cleavable polypeptide sequence.
Embodiment 210 is the linker polypeptide of the immediately preceding embodiment, wherein the second active domain is configured to remain connected to one or more of: one of the first targeting sequence and the second targeting sequence, one of the at least one targeting sequence, one of the first plurality of targeting sequences, one of the second plurality of targeting sequences, one of the plurality of targeting sequences, and the pharmacokinetic modulator upon cleavage of the protease-cleavable polypeptide sequence.
Embodiment 211 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is recognized by a metalloprotease, a serine protease, a cysteine protease, an aspartate protease, a threonine protease, a glutamate protease, a gelatinase, an asparagine peptide lyase, a cathepsin, a kallikrein, a plasmin, a collagenase, a hK1, a hK10, a hK15, a stromelysin, a Factor Xa, a chymotrypsin-like protease, a trypsin-like protease, a elastase-like protease, a subtilisin-like protease, an actinidain, a bromelain, a calpain, a caspase, a Mir 1-CP, a papain, a HIV-1 protease, a HSV protease, a CMV protease, a chymosin, a renin, a pepsin, a matriptase, a legumain, a plasmepsin, a nepenthesin, a metalloexopeptidase, a metalloendopeptidase, an ADAM 10, an ADAM 17, an ADAM 12, an urokinase plasminogen activator (uPA), an enterokinase, a prostate-specific target (PSA, hK3), an interleukin-1b converting enzyme, a thrombin, a FAP (FAP-a), a dipeptidyl peptidase, or dipeptidyl peptidase IV (DPPIV/CD26), a type II transmembrane serine protease (TTSP), a neutrophil elastase, a proteinase 3, a mast cell chymase, a mast cell tryptase, or a dipeptidyl peptidase.
Embodiment 212 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence comprises the sequence of any one of SEQ ID NOs: 701-742, or a variant having one or two mismatches relative to the sequence of any one of SEQ ID NOs: 701-742.
Embodiment 213 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is recognized by a matrix metalloprotease.
Embodiment 214 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is recognized by MMP-1.
Embodiment 215 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is recognized by MMP-2.
Embodiment 216 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is recognized by MMP-3.
Embodiment 217 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is recognized by MMP-7.
Embodiment 218 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is recognized by MMP-8.
Embodiment 219 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is recognized by MMP-9.
Embodiment 220 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is recognized by MMP-12.
Embodiment 221 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is recognized by MMP-13.
Embodiment 222 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is recognized by MMP-14.
Embodiment 223 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is recognized by more than one MMP.
Embodiment 224 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence is recognized by two, three, four, five, six, or seven of MMP-2, MMP-7, MMP-8, MMP-9, MMP-12, MMP-13, and MMP-14.
Embodiment 225 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence comprises the sequence of any one of SEQ ID NOs: 80-94 or a variant sequence having one or two mismatches relative to the sequence of any one of SEQ ID NOs: 80-90.
Embodiment 226 is the linker polypeptide of any one of the preceding embodiments, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 80 or a variant sequence having one or two mismatches relative thereto.
Embodiment 227 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 81 or a variant sequence having one or two mismatches relative thereto.
Embodiment 228 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 82 or a variant sequence having one or two mismatches relative thereto.
Embodiment 229 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 83 or a variant sequence having one or two mismatches relative thereto.
Embodiment 230 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 84 or a variant sequence having one or two mismatches relative thereto.
Embodiment 231 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 85 or a variant sequence having one or two mismatches relative thereto.
Embodiment 232 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 86 or a variant sequence having one or two mismatches relative thereto.
Embodiment 233 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 87 or a variant sequence having one or two mismatches relative thereto.
Embodiment 234 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 88 or a variant sequence having one or two mismatches relative thereto.
Embodiment 235 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 89 or a variant sequence having one or two mismatches relative thereto.
Embodiment 236 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 90 or a variant sequence having one or two mismatches relative thereto.
Embodiment 237 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of any one of SEQ ID NO: 80-90.
Embodiment 238 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 91.
Embodiment 239 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 92.
Embodiment 240 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 93.
Embodiment 241 is the linker polypeptide of any one of embodiments 1-225, wherein the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 94.
Embodiment 242 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind an extracellular matrix component, heparin, an integrin, or a syndecan; or is configured to bind, in a pH-sensitive manner, an extracellular matrix component, heparin, IgB (CD79b), an integrin, a cadherin, a heparan sulfate proteoglycan, a syndecan, or a fibronectin; or the targeting sequence comprises the sequence of any one of SEQ ID NOs: 179-665 or a variant having one or two mismatches relative to the sequence of any one of SEQ ID NOs: 179-665.
Embodiment 243 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently comprises the sequence of any one of SEQ ID NOs: 179-665, or a variant having one or two mismatches relative to the sequence of any one of SEQ ID NOs: 179-665.
Embodiment 244 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently comprises the sequence of any one of SEQ ID NOs: 179-665.
Embodiment 245 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently comprises the sequence of any one of SEQ ID NOs: 200, 330, 619, 653, and 663-665, or a variant having one or two mismatches relative to the sequence of any one of SEQ ID NOs: 200, 330, 619, 653, and 663-665.
Embodiment 246 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently comprises the sequence of any one of SEQ ID NOs: 200, 330, 619, 653, and 663-665.
Embodiment 247 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind to denatured collagen.
Embodiment 248 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind to collagen.
Embodiment 249 is the linker polypeptide of embodiment 247 or 248, wherein the collagen is collagen I.
Embodiment 250 is the linker polypeptide of embodiment 247 or 248, wherein the collagen is collagen II.
Embodiment 251 is the linker polypeptide of embodiment 247 or 248, wherein the collagen is collagen III.
Embodiment 252 is the linker polypeptide of embodiment 247 or 248, wherein the collagen is collagen IV.
Embodiment 253 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind to integrin.
Embodiment 254 is the linker polypeptide of the immediately preceding embodiment, wherein the integrin is one or more of α1β1 integrin, α2β1 integrin, α3β1 integrin, α4β1 integrin, α5β1 integrin, α6β1 integrin, α7β1 integrin, α9β1 integrin, α4β7 integrin, αvβ integrin, αvβ5 integrin, αIIbβ3 integrin, αIIIbβ3 integrin, αMβ2 integrin, or αIIbβ3 integrin.
Embodiment 255 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind to von Willebrand factor.
Embodiment 256 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind to IgB.
Embodiment 257 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind to heparin.
Embodiment 258 is the linker polypeptide of any one of the preceding embodiments, wherein the first targeting sequence is configured to bind to heparin and the second targeting sequence is configured to bind to heparin, wherein the first targeting sequence is configured to bind to collagen IV and the second targeting sequence is configured to bind to heparin, or wherein the first targeting sequence is configured to bind to heparin and the second targeting sequence is configured to bind to collagen IV.
Embodiment 259 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind to heparin and a syndecan, a heparan sulfate proteoglycan, or an integrin, optionally wherein the integrin is one or more of α1β1 integrin, α2β1 integrin, α3β1 integrin, α4β1 integrin, α5β1 integrin, α6β1 integrin, α7β1 integrin, α9β1 integrin, α4β7 integrin, αvβ integrin, αvβ5 integrin, αIIbβ3 integrin, αIIIbβ3 integrin, αMβ2 integrin, or αIIbβ3 integrin.
Embodiment 260 is the linker polypeptide of the immediately preceding embodiment, wherein the syndecan is one of more of syndecan-1, syndecan-4, and syndecan-2(w).
Embodiment 261 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind to a heparan sulfate proteoglycan.
Embodiment 262 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind to a sulfated glycoprotein.
Embodiment 263 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind to hyaluronic acid.
Embodiment 264 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind to fibronectin.
Embodiment 265 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind to cadherin.
Embodiment 266 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target in a pH-sensitive manner.
Embodiment 267 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently has a higher affinity for its target at a pH below normal physiological pH than at normal physiological pH, optionally wherein the pH below normal physiological pH is below 7, or below 6.
Embodiment 268 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently has a higher affinity for its target at a pH in the range of 5-7, e.g., 5-5.5, 5.5-6, 6-6.5, or 6.5-7, than at normal physiological pH.
Embodiment 269 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently comprises one or more histidines, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 histidines.
Embodiment 270 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently comprises the sequence of any one of SEQ ID NOs: 641-663, or a variant having one or two mismatches relative to the sequence of any one of SEQ ID NOs: 641-663.
Embodiment 271 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently comprises the sequence of any one of SEQ ID NOs: 641-665.
Embodiment 272 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind, in a pH-sensitive manner, an extracellular matrix component, IgB (CD79b), an integrin, a cadherin, a heparan sulfate proteoglycan, a syndecan, or a fibronectin.
Embodiment 273 is the linker polypeptide of the immediately preceding embodiment, wherein the extracellular matrix component is hyaluronic acid, heparin, heparan sulfate, or a sulfated glycoprotein.
Embodiment 274 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind a fibronectin in a pH-sensitive manner.
Embodiment 275 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 0.1 nM to 1 nM, from 1 nM to 10 nM, from 10 nM to 100 nM, from 100 nM to 1 μM, from 1 μM to 10 μM, or from 10 μM to 100 μM.
Embodiment 276 is the linker polypeptide of the immediately preceding embodiment, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 0.1 nM to 1 nM.
Embodiment 277 is the linker polypeptide of embodiment 275, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 1 nM to 10 nM.
Embodiment 278 is the linker polypeptide of embodiment 275, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 10 nM to 100 nM.
Embodiment 279 is the linker polypeptide of embodiment 275, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 100 nM to 1 M.
Embodiment 280 is the linker polypeptide of embodiment 275, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 1 μM to 10 μM.
Embodiment 281 is the linker polypeptide of embodiment 275, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 10 μM to 100 μM.
Embodiment 282 is the linker polypeptide of any one of the preceding embodiments, wherein at least one of the first linker and the second linker comprises one of the first targeting sequence and the second targeting sequence, one of the at least one targeting sequence, one of the first plurality of targeting sequences, one of the second plurality of targeting sequences, or one of the plurality of targeting sequences.
Embodiment 283 is the linker polypeptide of the immediately preceding embodiment, wherein the protease-cleavable polypeptide sequence comprises one of the first targeting sequence and the second targeting sequence, one of the at least one targeting sequence, one of the first plurality of targeting sequences, one of the second plurality of targeting sequences, or one of the plurality of targeting sequences.
Embodiment 284 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences increases a serum half-life of the linker polypeptide.
Embodiment 285 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences synergistically increases a serum half-life of the linker polypeptide together with the pharmacokinetic modulator or with another one of the first targeting sequence and the second targeting sequence, another one of the at least one targeting sequence, another one of the first plurality of targeting sequences, another one of the second plurality of targeting sequences, or another one of the plurality of targeting sequences.
Embodiment 286 is the linker polypeptide of any one of the preceding embodiments, wherein one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently increases a serum half-life of the linker polypeptide.
Embodiment 287 is the linker polypeptide of any one of the preceding embodiments, further comprising a blocker conjugated to one of or each of the first active domain and the second active domain.
Embodiment 288 is the linker polypeptide of the immediately preceding embodiment, wherein the blocker is conjugated to one of or each of the first active domain and the second active domain via a protease-cleavable polypeptide sequence.
Embodiment 289 is the linker polypeptide of embodiment 287 or 288, wherein the blocker is an albumin.
Embodiment 290 is the linker polypeptide of any one of embodiments 287-289, wherein the blocker is a serum albumin.
Embodiment 291 is the linker polypeptide of any one of embodiments 287-290, wherein the blocker is a human albumin.
Embodiment 292 is the linker polypeptide of any one of the preceding embodiments, further comprising a chemotherapy drug.
Embodiment 293 is the linker polypeptide of the immediately preceding embodiment, wherein the chemotherapy drug is conjugated to the pharmacokinetic modulator.
Embodiment 294 is the linker polypeptide of embodiment 292 or 293, where the chemotherapy drug is selected from altretamine, bendamustine, busulfan, carboplatin, carmustine, chlorambucil, cisplatin, cyclophosphamide, dacarbazine, ifosfamide, lomustine, mechlorethamine, melphalan, oxaliplatin, temozolomide, thiotepa, trabectedin, carmustine, lomustine, streptozocin, azacitidine, 5-fluorouracil, 6-mercaptopurine, capecitabine, cladribine, clofarabine, cytarabine, decitabine, floxuridine, fludarabine, gemcitabine, hydroxyurea, methotrexate, nelarabine, pemetrexed, pentostatin, pralatrexate, thioguanine, trifluridine, tipiracil, daunorubicin, doxorubicin, epirubicin, idarubicin, valrubicin, bleomycin, dactinomycin, mitomycin-c, mitoxantrone, irinotecan, topotecan, etoposide, mitoxantrone, teniposide, cabazitaxel, docetaxel, paclitaxel, vinblastine, vincristine, vinorelbine, prednisone, methylprednisolone, dexamethasone, retinoic acid, arsenic trioxide, asparaginase, eribulin, hydroxyurea, ixabepilone, mitotane, omacetaxine, pegaspargase, procarbazine, romidepsin, and vorinostat.
Embodiment 295 is the linker polypeptide of any of the preceding embodiments, wherein a molecular weight of one or each of the first active domain and the second active domain independently is about or less than 14 kDa.
Embodiment 296 is the linker polypeptide of the immediately preceding embodiment, wherein the molecular weight is about 12 kDa to about 14 kDa.
Embodiment 297 is the linker polypeptide of embodiment 295, wherein the molecular weight is about 10 kDa to about 12 kDa.
Embodiment 298 is the linker polypeptide of embodiment 295, wherein the molecular weight is about 8 kDa to about 10 kDa.
Embodiment 299 is the linker polypeptide of embodiment 295, wherein the molecular weight is about 6 kDa to about 8 kDa.
Embodiment 300 is the linker polypeptide of embodiment 295, wherein the molecular weight is about 4 kDa to about 6 kDa.
Embodiment 301 is the linker polypeptide of embodiment 295, wherein the molecular weight is about 2 kDa to about 4 kDa.
Embodiment 302 is the linker polypeptide of embodiment 295, wherein the molecular weight is about 800 Da to about 2 kDa.
Embodiment 303 is the linker polypeptide of any of embodiments 1-294, wherein a molecular weight of one or each of the first active domain and the second active domain independently is about or greater than 16 kDa.
Embodiment 304 is the linker polypeptide of the immediately preceding embodiment, wherein the molecular weight is about 16 kDa to about 18 kDa.
Embodiment 305 is the linker polypeptide of embodiment 303, wherein the molecular weight is about 18 kDa to about 20 kDa.
Embodiment 306 is the linker polypeptide of embodiment 303, wherein the molecular weight is about 20 kDa to about 22 kDa.
Embodiment 307 is the linker polypeptide of embodiment 303, wherein the molecular weight is about 22 kDa to about 24 kDa.
Embodiment 308 is the linker polypeptide of embodiment 303, wherein the molecular weight is about 24 kDa to about 26 kDa.
Embodiment 309 is the linker polypeptide of embodiment 303, wherein the molecular weight is about 26 kDa to about 28 kDa.
Embodiment 310 is the linker polypeptide of embodiment 303, wherein the molecular weight is about 28 kDa to about 30 kDa.
Embodiment 311 is the linker polypeptide of embodiment 303, wherein the molecular weight is about 30 kDa to about 50 kDa.
Embodiment 312 is the linker polypeptide of embodiment 303, wherein the molecular weight is about 50 kDa to about 100 kDa.
Embodiment 313 is the linker polypeptide of embodiment 303, wherein the molecular weight is about 100 kDa to about 150 kDa.
Embodiment 314 is the linker polypeptide of embodiment 303, wherein the molecular weight is about 150 kDa to about 200 kDa.
Embodiment 315 is the linker polypeptide of embodiment 303, wherein the molecular weight is about 200 kDa to about 250 kDa.
Embodiment 316 is the linker polypeptide of embodiment 303, wherein the molecular weight is about 250 kDa to about 300 kDa.
Embodiment 317 is the linker polypeptide of any one of the preceding embodiments, comprising a combined targeting sequence and protease cleavable sequence, wherein the combined targeting sequence and protease cleavable sequence is any one of SEQ ID NOs: 667-673.
Embodiment 318 is a linker polypeptide comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 800-848 or 1024-1041.
Embodiment 319 is the linker polypeptide of the immediately preceding embodiment, comprising the sequence of any one of SEQ ID NOs: 800-848 or 1024-1041.
Embodiment 320 is a pharmaceutical composition comprising the linker polypeptide of any one of the preceding embodiments.
Embodiment 321 is the linker polypeptide or pharmaceutical composition of any one of the preceding embodiments, for use in therapy.
Embodiment 322 is the linker polypeptide or pharmaceutical composition of any one of the preceding embodiments, for use in treating a cancer.
Embodiment 323 is a method of treating a cancer, comprising administering the linker polypeptide or pharmaceutical composition of any one of the preceding embodiments to a subject in need thereof.
Embodiment 324 is use of the linker polypeptide or pharmaceutical composition of any one of embodiments 1-321 for the manufacture of a medicament for treating cancer.
Embodiment 325 is the method, use, or linker polypeptide for use of any one of embodiments 322-324, wherein the cancer is a solid tumor.
Embodiment 326 is the method, use, or linker polypeptide for use of the immediately preceding embodiment, wherein the solid tumor is metastatic and/or unresectable.
Embodiment 327 is the method, use, or linker polypeptide for use of any one of embodiments 322-326, wherein the cancer is a PD-L1-expressing cancer.
Embodiment 328 is the method, use, or linker polypeptide for use of any one of embodiments 322-327, wherein the cancer is a melanoma, a colorectal cancer, a breast cancer, a pancreatic cancer, a lung cancer, a prostate cancer, an ovarian cancer, a cervical cancer, a gastric or gastrointestinal cancer, a lymphoma, a colon or colorectal cancer, an endometrial cancer, a thyroid cancer, or a bladder cancer.
Embodiment 329 is the method, use, or linker polypeptide for use of any one of embodiments 322-328, wherein the cancer is a microsatellite instability-high cancer.
Embodiment 330 is the method, use, or linker polypeptide for use of any one of embodiments 322-329, wherein the cancer is mismatch repair deficient.
Embodiment 331 is a nucleic acid encoding the linker polypeptide of any one of embodiments 1-319.
Embodiment 332 is an expression vector comprising the nucleic acid of the immediately preceding embodiment.
Embodiment 333 is a host cell comprising the nucleic acid of embodiment 331 or the vector of embodiment 332.
Embodiment 334 is a method of producing a linker polypeptide, comprising culturing the host cell of the immediately preceding embodiment under conditions wherein the linker polypeptide is produced.
Embodiment 335 is the method of the immediately preceding embodiment, further comprising isolating the linker polypeptide.
This specification describes exemplary embodiments and applications of the disclosure. The disclosure, however, is not limited to these exemplary embodiments and applications or to the manner in which the exemplary embodiments and applications operate or are described herein. The term “or” is used in an inclusive sense, i.e., equivalent to “and/or,” unless the context dictates otherwise. It is noted that, as used in this specification and the appended claims, the singular forms “a,” “an,” and “the,” and any singular use of any word, include plural referents unless expressly and unequivocally limited to one referent. As used herein, the terms “comprise,” “include,” and grammatical variants thereof are intended to be non-limiting, such that recitation of items in a list is not to the exclusion of other like items that can be substituted or added to the listed items. Section divisions in the specification are provided for the convenience of the reader only and do not limit any combination of elements discussed. In case of any contradiction or conflict between material incorporated by reference and the expressly described content provided herein, the expressly described content controls.
Provided herein are linker polypeptides comprising a first targeting sequence; a second targeting sequence; and a first linker between the first targeting sequence and the second targeting sequence, the linker comprising a protease-cleavable polypeptide sequence. In some embodiments, the linker polypeptide comprises a first active domain; a second active domain; a pharmacokinetic modulator; and a first linker between the pharmacokinetic modulator and the first active domain, the first linker comprising a protease-cleavable polypeptide sequence. In some embodiments, the linker polypeptide comprises a first active domain; an inhibitory polypeptide sequence capable of blocking an activity of the first active domain; a first linker between the first active domain and the inhibitory polypeptide sequence, the linker comprising a protease-cleavable polypeptide sequence; and a first targeting sequence.
Proteolysis of the protease-cleavable polypeptide sequence can release the first and/or second binding domain, so that it can, for example, neutralize a tumor antigen and/or activate immune cells. Additionally, in some embodiments, each of the active domains can bind growth factor to reduce the extent to which the growth factor exerts an activity in vivo, such as stimulating cancer cell growth.
In some embodiments, the protease-cleavable polypeptide sequence is cleavable by a protease expressed at higher levels in the tumor microenvironment (TME) than in healthy tissue of the same type. In some embodiments, the protease-cleavable polypeptide sequence is a matrix metalloprotease (MMP)-cleavable linker, such as any of the MMP-cleavable linkers described herein. Without wishing to be bound by any particular theory, increased expression and/or activation of proteases, including but not necessarily limited to MMPs, in the tumor microenvironment (TME) can provide a mechanism for achieving selective or preferential activation of the linker polypeptide at or near a tumor site. Certain protease-cleavable polypeptide sequences described herein are considered particularly suitable for achieving such selective or preferential activation.
In other embodiments, the first and/or second targeting sequence binds an extracellular matrix component, an integrin, or a syndecan, or is configured to bind fibronectin in a pH-sensitive manner. In some embodiments, the targeting sequence is a targeting sequence described herein, e.g., a targeting sequence configured to bind an extracellular matrix component, heparin, an integrin, or a syndecan; or configured to bind an extracellular matrix component, heparin, IgB (CD79b), an integrin, a cadherin, a heparan sulfate proteoglycan, a syndecan, or a fibronectin in a pH-sensitive manner; or a targeting sequence comprising the sequence of any one of SEQ ID NOs: 179-665. The targeting sequence can facilitate accumulation and/or increased residence time of the linker polypeptide and/or the released active domain in the extracellular matrix (ECM). In some embodiments, a targeting sequence is combined with a protease-cleavable polypeptide sequence expressed at higher levels in the TME and/or cleavable by an MMP.
In some embodiments, the pharmacokinetic modulator may, for example, extend the half-life of the linker polypeptide.
Sequences of exemplary components of linker polypeptides are shown in Tables 1 and 2. In Table 1, “XHy” designates a hydrophobic amino acid residue. In some embodiments, the hydrophobic amino acid residue is any one of glycine (Gly), alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile), proline (Pro), phenylalanine (Phe), methionine (Met), and tryptophan (Trp). In some embodiments, the hydrophobic amino acid residue is any one of Ala, Leu, Val, Ile, Pro, Phe, Met, and Trp. In some embodiments, the hydrophobic amino acid residue is any one of Leu, Val, Ile, Pro, Phe, Met, and Trp. In some embodiments, the hydrophobic amino acid residue is any one of Ala, Leu, Val, Ile, Phe, Met, and Trp. In some embodiments, the hydrophobic amino acid residue is any one of Leu, Val, Ile, Phe, Met, and Trp. “(Pip)” represents piperidine. “(Hof)” represents homophenylalanine. “(Cit)” represents citrulline. “(Et)” represents ethionine. “C(me)” represents methylcysteine. In certain sequences, underlining is used to indicate mutated positions.
This disclosure further provides uses of these linker polypeptides, e.g., for treating cancer. In some embodiments, the linker polypeptide is selectively or preferentially cleaved in the tumor microenvironment, which may result in beneficial effects, e.g., improved recruitment and/or activation of immune cells in the vicinity of the tumor, and/or reduced systemic exposure to certain components of the linker polypeptides.
As used herein, an “active domain” refers to a polypeptide or a collection of polypeptides that have affinity towards a target, which may be one or more polypeptides, nucleic acids, sugars, and/or combinations thereof. In some embodiments, an active domain is an agonist or antagonist of its target, or will bring about and/or inhibit signal transduction relating to the target. The active domain need not have exclusive affinity towards the target but instead only needs to have affinity towards the target that is significantly higher (e.g., 10 times or more) than the domain's affinity towards a non-target. A dissociation constant (KD) between a active domain and a target may be in the range of pM, nM, μM, or mM. An active domain may comprise one or more subdomains or subunits that each has distinctive functions and together have the function of the active domain. For example, an active domain that comprises an IL-12 polypeptide sequence may comprise two subunits.
As used herein, an “immunoglobulin antigen-binding domain” refers to a domain that is an immunoglobulin or a fragment thereof, such as an Fv, scFv, Fab, or VHH. Exemplary immunoglobulin antigen-binding domains are provided in Table 1.
As used herein, a “receptor-binding domain” refers to an active domain, such as a cytokine polypeptide sequence, that is not an immunoglobulin antigen-binding domain.
As used herein, a “cytokine polypeptide sequence” refers to a polypeptide sequence (which may be part of a larger sequence, e.g., a fusion polypeptide) with significant sequence identity to a wild-type cytokine and which can bind and activate a cytokine receptor (e.g., when separated from an inhibitory polypeptide sequence). In some embodiments, a cytokine polypeptide sequence has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a wild-type cytokine, e.g., a wild-type human cytokine. In some embodiments, a cytokine polypeptide sequence has no more than one, two, three, four, five, six, seven, eight, nine, or ten amino acid differences from a wild-type cytokine, e.g., a wild-type human cytokine. Cytokines include but are not limited to chemokines. Exemplary cytokine polypeptide sequences are provided in Table 1. This definition applies to IL-2 polypeptide sequences with substitution of “IL-2” for “cytokine.”
As used herein, an “inhibitory polypeptide sequence” refers to a polypeptide or a collection of polypeptides that inhibits an activity of an active domain in the linker polypeptide. The inhibitory polypeptide sequence may bind or sterically obstruct the active domain. In some embodiments, such binding is reduced or eliminated by action of an appropriate protease on a protease-cleavable polypeptide sequence of the linker polypeptide. Exemplary inhibitory polypeptide sequences are provided in Table 1. The inhibitory polypeptide sequence may, for example, comprise a polypeptide with significant sequence identity to a part of a wild-type target of an active domain, or an immunoglobulin or a fraction thereof, such as an Fv, scFv, Fab, or VHH.
As used herein, a “protease-cleavable polypeptide sequence” is a sequence that is a substrate for cleavage by a protease. The protease-cleavable polypeptide sequence is located in a linker polypeptide such that its cleavage releases one or more elements of the linker polypeptide from the remainder of the linker polypeptide, or reduces or eliminates binding of an inhibitory polypeptide sequence to an active domain.
As used herein, a protease-cleavable polypeptide sequence “is recognized by” a given protease or class thereof if exposing a polypeptide comprising the protease-cleavable polypeptide sequence to the protease under conditions permissive for cleavage by the protease results in a significantly greater amount of cleavage than is seen for a control polypeptide having an unrelated sequence, and/or if the protease-cleavable polypeptide sequence corresponds to a known recognition sequence for the protease (e.g., as described elsewhere herein for various exemplary proteases).
As used herein, a “pharmacokinetic modulator” is a moiety that extends the in vivo half-life of a linker polypeptide or an element of the linker polypeptide. The pharmacokinetic modulator may be a fused domain in a linker polypeptide or may be a chemical entity attached post-translationally. The attachment may be, but is not necessarily, covalent. Exemplary pharmacokinetic modulator polypeptide sequences are provided in Table 1. Exemplary non-polypeptide pharmacokinetic modulators are described elsewhere herein.
As used herein, a “targeting sequence” is a sequence that results in a greater fraction of a linker polypeptide localizing to an area of interest, e.g., a tumor microenvironment. The targeting sequence may bind an extracellular matrix component or other entity found in the area of interest, e.g., an integrin or syndecan. Exemplary targeting sequences are provided in Table 2.
As used herein, an “extracellular matrix component” refers to an extracellular protein or polysaccharide found in vivo. Integral and peripheral membrane proteins on a cell, including fibronectins, cadherins, integrins, and syndecans, are not considered extracellular matrix components.
As used herein, an “immunoglobulin constant domain” refers to a domain that occurs in or has significant sequence identity to a domain of a constant region of an immunoglobulin, such as an IgG. Exemplary constant domains are CH2 and CH3 domains. Unless indicated otherwise, a linker polypeptide comprising an immunoglobulin constant domain may comprise more than one immunoglobulin constant domain. In some embodiments, an immunoglobulin constant domain has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a wild-type immunoglobulin constant domain, e.g., a wild-type human immunoglobulin constant domain. In some embodiments, an immunoglobulin constant domain has no more than one, two, three, four, five, six, seven, eight, nine, or ten amino acid differences from a wild-type immunoglobulin constant domain, e.g., a wild-type human immunoglobulin constant domain. In some embodiments, immunoglobulin constant domain has an identical sequence to a wild-type immunoglobulin constant domain, e.g., a wild-type human immunoglobulin constant domain. Exemplary immunoglobulin constant domains are contained within sequences provided in Table 1. This definition applies to CH2 and CH3 domains, respectively, with substitution of “CH2” or “CH3” for “immunoglobulin constant,” with the qualification that a CH2 domain sequence does not have greater percent identity to a non-CH2 immunoglobulin constant domain wild-type sequence than to a CH2 domain wild-type sequence, and a CH3 domain sequence does not have greater percent identity to a non-CH3 immunoglobulin constant domain wild-type sequence than to a CH3 domain wild-type sequence. These definitions also include domains having minor truncations relative to wild-type sequences, to the extent that the truncation does not abrogate substantially normal folding of the domain.
As used herein, a “immunoglobulin Fc region” refers to a region of an immunoglobulin heavy chain comprising a CH2 and a CH3 domain, as defined above. The Fc region does not include a variable domain or a CH1 domain.
As used herein, a given component is “between” a first component and a second component if the first component is on one side of the given component and the second component is on the other side of the given component, e.g., in the primary sequence of a polypeptide. This term does not require immediate adjacency. Thus, in the structure 1-2-3-4, 2 is between 1 and 4, and is also between 1 and 3.
As used herein, a “domain” may refer, depending on the context, to a structural domain of a polypeptide or to a functional assembly of at least one domain (but possibly a plurality of structural domains). For example, a CH2 domain refers to a part of a sequence that qualifies as such. An immunoglobulin cytokine-binding domain may comprise VH and VL structural domains.
As used herein, “denatured collagen” encompasses gelatin and cleavage products resulting from action of an MMP on collagen, and more generally refers to a form of collagen or fragments thereof that does not exist in the native structure of full-length collagen.
As used herein, “configured to bind . . . in a pH-sensitive manner” means that a polypeptide sequence (e.g., a targeting sequence) shows differential binding affinity for its binding partner depending on pH. For example, the polypeptide sequence may have a higher affinity at a relatively acidic pH than at normal physiological pH (about 7.4). The higher affinity may occur at a pH below 7, e.g., in the range of pH 5.5-7, 6-7, or 5.5-6.5, or below pH 6.
As used herein, a “cytokine-binding domain of a cytokine receptor” refers to an extracellular portion of a cytokine receptor, or a fragment or truncation thereof that can bind a cytokine polypeptide sequence. In some embodiments, the sequence of a cytokine binding domain of a cytokine receptor has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a cytokine binding domain of a wild-type cytokine receptor, e.g., a cytokine binding domain of a wild-type human cytokine receptor. Exemplary sequences of a cytokine binding domain of a cytokine receptor are provided in Table 1. This definition applies to IL-2, IL-10, IL-15, CXCL9, CXCL10, and TGF-β-binding domains of an IL-2, IL-10, IL-15, CXCL9, CXCL10, and TGF-β receptor with substitution of “IL-2,” “IL-10,” “IL-15,” “CXCL9,” “CXCL10,” and “TGF-β,” respectively, for “cytokine.”
As used herein, an “immunoglobulin cytokine-binding domain” refers to one or more immunoglobulin variable domains (e.g., a VH and a VL region) that can bind a cytokine polypeptide sequence. Exemplary sequences of a cytokine-binding immunoglobulin domain are provided in Table 1. This definition applies to IL-2, IL-10, IL-15, CXCL9, CXCL10, and TGF-β-binding domains of an IL-2, IL-10, IL-15, CXCL9, CXCL10, and TGF-β receptor with substitution of “IL-2,” “IL-10,” “IL-15,” “CXCL9,” “CXCL10,” and “TGF-β,” respectively, for “cytokine.”
As used herein, a first element of the linker polypeptide being “proximal to” a second element relative to a third element means that in the primary polypeptide sequence of the linker polypeptide, the first element is closer to the second element than to the third element, regardless of whether the first element is spacially closer to the second element than to the third element when the linker polypeptide is folded.
As used herein, “substantially” and other grammatical forms thereof mean sufficient to work for the intended purpose. The term “substantially” thus allows for minor, insignificant variations from an absolute or perfect state, dimension, measurement, result, or the like such as would be expected by a person of ordinary skill in the field but that do not appreciably affect overall performance. When used with respect to numerical values or parameters or characteristics that can be expressed as numerical values, “substantially” means within ten percent.
As used herein, the term “plurality” can be 2, 3, 4, 5, 6, 7, 8, 9, 10, or more.
As used herein, a first sequence is considered to “comprise a sequence with at least X % identity to” a second sequence if an alignment of the first sequence to the second sequence shows that X % or more of the positions of the second sequence in its entirety are matched by the first sequence. For example, the sequence QLYV (SEQ ID NO: 1168) comprises a sequence with 100% identity to the sequence QLY because an alignment would give 100% identity in that there are matches to all three positions of the second sequence. Exemplary alignment algorithms are the Smith-Waterman and Needleman-Wunsch algorithms, which are well-known in the art. One skilled in the art will understand what choice of algorithm and parameter settings are appropriate for a given pair of sequences to be aligned; for sequences of generally similar length and expected identity >50% for amino acids or >75% for nucleotides, the Needleman-Wunsch algorithm with default settings of the Needleman-Wunsch algorithm interface provided by the EBI at the www.ebi.ac.uk web server is generally appropriate.
As used herein, a “subject” refers to any member of the animal kingdom. In some embodiments, “subject” refers to humans. In some embodiments, “subject” refers to non-human animals. In some embodiments, “subject” refers to primates. In some embodiments, subjects include, but are not limited to, mammals, birds, reptiles, amphibians, fish, insects, and/or worms. In certain embodiments, the non-human subject is a mammal (e.g., a rodent, a mouse, a rat, a rabbit, a monkey, a dog, a cat, a sheep, cattle, a primate, and/or a pig). In some embodiments, a subject may be a transgenic animal, genetically-engineered animal, and/or a clone. In certain embodiments of the present invention the subject is an adult, an adolescent or an infant. In some embodiments, the terms “individual” or “patient” are used and are intended to be interchangeable with “subject”.
The linker polypeptide may comprise a first targeting sequence; a second targeting sequence; and a first linker between the first targeting sequence and the second targeting sequence, the linker comprising a protease-cleavable polypeptide sequence. In some embodiments, the first targeting sequence and/or the second targeting sequence may each comprise two or more targeting subsequences that each binds to a target. In some embodiments, some or all of the two or more targeting subsequences may bind to the same target (e.g., tandem repeats). In some embodiments, the linker polypeptide comprises a first active domain; a second active domain; a pharmacokinetic modulator; and a first linker between the pharmacokinetic modulator and the first active domain, the first linker comprising a protease-cleavable polypeptide sequence. In some embodiments, the linker polypeptide comprises a first active domain; an inhibitory polypeptide sequence capable of blocking an activity of the first active domain; a first linker between the first active domain and the inhibitory polypeptide sequence, the linker comprising a protease-cleavable polypeptide sequence; and a first targeting sequence.
These elements of the linker polypeptide may be covalently connected to form a single polypeptide chain or may be present in a plurality of associated polypeptide chains, which may be linked noncovalently or covalently (e.g., via one or more disulfide bonds).
In some embodiments, the linker polypeptide comprises a first polypeptide chain comprising a first active domain, a first domain of a pharmacokinetic modulator, and a first linker between the first active domain and the first domain of the pharmacokinetic modulator, wherein the first active domain is C-terminal to the first domain of the pharmacokinetic modulator; a second polypeptide chain, comprising a second domain of the pharmacokinetic modulator, an inhibitory polypeptide sequence capable of blocking an activity of the first active domain, and a second linker between the second domain of the pharmacokinetic modulator and the inhibitory polypeptide sequence; wherein the first linker comprises a protease-cleavable polypeptide sequence; and the first polypeptide chain or the second polypeptide chain further comprises at least one targeting sequence.
In some embodiments, the linker polypeptide comprises a first polypeptide chain comprising a first active domain, a first domain of a pharmacokinetic modulator, and a first linker between the first active domain and the first domain of the pharmacokinetic modulator, wherein the first active domain is N-terminal to the first domain of the pharmacokinetic modulator; a second polypeptide chain, comprising a second domain of the pharmacokinetic modulator, an inhibitory polypeptide sequence capable of blocking an activity of the first active domain, and a second linker between the second domain of the pharmacokinetic modulator and the inhibitory polypeptide sequence; wherein the first linker comprises a protease-cleavable polypeptide sequence; and the first polypeptide chain or the second polypeptide chain further comprises at least one targeting sequence.
In some embodiments, the first active domain comprises an immunoglobulin antigen-binding domain. In some embodiments, the second active domain comprises an immunoglobulin antigen-binding domain.
In some embodiments, the immunoglobulin antigen-binding domain comprises a VH region and a VL region. In some embodiments, the immunoglobulin antigen-binding domain comprises an Fv, scFv, Fab, or VHH. The immunoglobulin antigen-binding domain may be humanized or fully human.
In some embodiments, the immunoglobulin antigen-binding domain binds to one or more sequences selected from a cancer cell surface antigen sequence, a growth factor sequence, and a growth factor receptor sequence.
Under physiological conditions, cells receive signals from surrounding tissue in the form of growth factors. Growth factors can influence normal cell differentiation as well as constitutively activate growth-promoting pathways in cancer cells. The linker polypeptides disclosed herein may bind to growth factors to facilitate neutralization of the activity of the growth factor to at least some extent, e.g., in the vicinity of a tumor. Thus, the linker polypeptides disclosed here, through an immunoglobulin antigen-binding domain, can in some embodiments reduce the pro-growth signaling received by cancer cells and stromal cells, including fibroblast and endothelial cells, while also activating or recruiting immune cells to the tumor. In some embodiments, the immunoglobulin antigen-binding domain may also promote localization of linker polypeptides to tissues that specifically express particular growth factors or tissues that express particular growth factors in high amounts, e.g., in and around tumors.
Growth factor receptors are generally transmembrane proteins that bind to specific growth factors and transmit the instructions conveyed by the factors on the outside of a cell to intracellular space. In general, growth factor receptors comprise extracellular, transmembrane, and cytoplasmic domains. In some embodiments, the linker polypeptides disclosed here, through an immunoglobulin antigen-binding domain, can inhibit binding of a growth factor to the growth factor receptor. This may facilitate reduction of signaling by the growth factor to at least some extent, e.g., in the vicinity of a tumor.
In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain of the linker polypeptide independently is configured to bind to a HER2 sequence. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain of the linker polypeptide independently comprises hypervariable regions (HVRs) HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of SEQ ID NO: 910, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of SEQ ID NO: 909. In general, a person skilled in the art can identify the HVRs in VH and VL sequences, e.g., by assigning amino acids to framework and HVR domains within the VH and VL sequences in accordance with the definitions of Kabat et al. in Sequences of Proteins of Immunological Interest, 5th Ed., US Dept. of Health and Human Services, PHS, NIH, NIH Publication no. 91-3242, 1991. Other numbering systems for the amino acids in immunoglobulin chains include IMGT™ (international ImMunoGeneTics information system; Lefranc et al, Dev. Comp. Immunol. 29:185-203; 2005) and AHo (Honegger and Pluckthun, J. Mol. Biol. 309(3):657-670; 2001). In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a VH region comprising the amino acid sequence of SEQ ID NO: 910; and a VL region comprising the amino acid sequence of SEQ ID NO: 909. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 909 or 910. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently is an antigen-binding domain of trastuzumab.
In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain of the linker polypeptide independently is configured to bind to an EGFR extracellular domain sequence. In some embodiments, each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of SEQ ID NO: 914, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of SEQ ID NO: 913. In general, a person skilled in the art can identify the HVRs in VH and VL sequences, e.g., by assigning amino acids to framework and HVR domains within the VH and VL sequences in accordance with the definitions of Kabat et al. in Sequences of Proteins of Immunological Interest, 5th Ed., US Dept. of Health and Human Services, PHS, NIH, NIH Publication no. 91-3242, 1991. Other numbering systems for the amino acids in immunoglobulin chains include IMGT™ (international ImMunoGeneTics information system; Lefranc et al, Dev. Comp. Immunol. 29:185-203; 2005) and AHo (Honegger and Pluckthun, J. Mol. Biol. 309(3):657-670; 2001). In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a VH region comprising the amino acid sequence of SEQ ID NO: 914; and a VL region comprising the amino acid sequence of SEQ ID NO: 913. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 913 or 914. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain is an antigen-binding domain of cetuximab.
In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain of the linker polypeptide independently is configured to bind to a PD-1 extracellular domain sequence. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of SEQ ID NO: 917, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of SEQ ID NO: 918. In general, a person skilled in the art can identify the HVRs in VH and VL sequences, e.g., by assigning amino acids to framework and HVR domains within the VH and VL sequences in accordance with the definitions of Kabat et al. in Sequences of Proteins of Immunological Interest, 5th Ed., US Dept. of Health and Human Services, PHS, NIH, NIH Publication no. 91-3242, 1991. Other numbering systems for the amino acids in immunoglobulin chains include IMGT™ (international ImMunoGeneTics information system; Lefranc et al, Dev. Comp. Immunol. 29:185-203; 2005) and AHo (Honegger and Pluckthun, J. Mol. Biol. 309(3):657-670; 2001). In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a VH region comprising the amino acid sequence of SEQ ID NO: 917; and a VL region comprising the amino acid sequence of SEQ ID NO: 918. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 917 or 918. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently is an antigen-binding domain of nivolumab.
In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain of the linker polypeptide independently is configured to bind to a PD-L1 extracellular domain sequence. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of SEQ ID NO: 921, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of SEQ ID NO: 922. In general, a person skilled in the art can identify the HVRs in VH and VL sequences, e.g., by assigning amino acids to framework and HVR domains within the VH and VL sequences in accordance with the definitions of Kabat et al. in Sequences of Proteins of Immunological Interest, 5th Ed., US Dept. of Health and Human Services, PHS, NIH, NIH Publication no. 91-3242, 1991. Other numbering systems for the amino acids in immunoglobulin chains include IMGT™ (international ImMunoGeneTics information system; Lefranc et al, Dev. Comp. Immunol. 29:185-203; 2005) and AHo (Honegger and Pluckthun, J. Mol. Biol. 309(3):657-670; 2001). In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a VH region comprising the amino acid sequence of SEQ ID NO: 921; and a VL region comprising the amino acid sequence of SEQ ID NO: 922. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 921 or 922. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently is an antigen-binding domain of atezolizumab.
In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain of the linker poly peptide independently is configured to bind to a CD3 extracellular domain sequence. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of any one of SEQ ID NOs: 925, 929, 933, and 937, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of any one of SEQ ID NOs: 926, 930, 934, and 938. In general, a person skilled in the art can identify the HVRs in VH and VL sequences, e.g., by assigning amino acids to framework and HVR domains within the VH and VL sequences in accordance with the definitions of Kabat et al. in Sequences of Proteins of Immunological Interest, 5th Ed., US Dept. of Health and Human Services, PHS, NIH, NIH Publication no. 91-3242, 1991. Other numbering systems for the amino acids in immunoglobulin chains include IMGT™ (international ImMunoGeneTics information system; Lefranc et al, Dev. Comp. Immunol. 29:185-203; 2005) and AHo (Honegger and Pluckthun, J. Mol. Biol. 309(3):657-670; 2001). In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a VH region comprising the amino acid sequence of any one of SEQ ID NOs: 925, 929, 933, and 937; and a VL region comprising the amino acid sequence of any one of SEQ ID NOs: 926, 930, 934, and 938. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 925, 926, 929, 930, 933, 934, 937, and 938. In some embodiments, one or each of the first immunoglobulin antigen-binding domain and the second immunoglobulin antigen-binding domain independently is an antigen-binding domain of teplizumab, muromonab, otelixizumab, or visilizumab.
In some embodiments, the first active domain comprises a receptor-binding domain. The receptor-binding domain may comprise, for example, a cytokine polypeptide sequence.
The receptor-binding domain may be a wild-type receptor-binding domain or a sequence with one or more differences from the wild-type receptor-binding domain. In some embodiments, the receptor-binding domain is a human receptor-binding domain (which may be wild-type or may have one or more differences). In some embodiments, the receptor-binding domain comprises a modification to prevent disulfide bond formation, and optionally otherwise comprises wild-type sequence. In some embodiments, the receptor-binding domain has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a wild-type receptor-binding domain or to a receptor-binding domain in Table 1. In some embodiments, the receptor-binding domain is a dimeric receptor-binding domain, e.g., a heterodimeric cytokine. In some embodiments, the receptor-binding domain is a homodimeric receptor-binding domain, e.g., a homodimeric cytokine. The monomers may be linked as a fusion protein, e.g., with a linker, or by a covalent bond (e.g., disulfide bond), or by a noncovalent interaction. In some embodiments, the receptor-binding domain is an interleukin polypeptide sequence. In some embodiments, the receptor-binding domain is capable of binding a receptor comprising CD132. In some embodiments, the receptor-binding domain is capable of binding a receptor comprising CD122. In some embodiments, the receptor-binding domain is capable of binding a receptor comprising CD25.
In some embodiments, the receptor-binding domain is an IL-2 polypeptide sequence. The IL-2 polypeptide sequence may be a wild-type IL-2 polypeptide sequence or a sequence with one or more differences from the wild-type IL-2 polypeptide sequence. In some embodiments, the IL-2 polypeptide sequence is a human IL-2 polypeptide sequence (which may be wild-type or may have one or more differences). In some embodiments, the IL-2 comprises a modification to prevent disulfide bond formation (e.g., the sequence of aldesleukin (marketed as Proleukin®), and optionally otherwise comprises wild-type sequence. In some embodiments, the IL-2 polypeptide sequence has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a wild-type IL-2 polypeptide sequence or to an IL-2 polypeptide sequence in Table 1.
In some embodiments, the IL-2 polypeptide sequence comprises the sequence of any one of SEQ ID NOs: 1-4. In some embodiments, the IL-2 polypeptide sequence comprises the sequence of SEQ ID NO: 1. In some embodiments, the IL-2 polypeptide sequence comprises the sequence of SEQ ID NO: 2.
In some embodiments, the receptor-binding domain is an IL-10 polypeptide sequence. The IL-10 polypeptide sequence may be a wild-type IL-10 polypeptide sequence or a sequence with one or more differences from the wild-type IL-10 polypeptide sequence. In some embodiments, the IL-10 polypeptide sequence is a human IL-10 polypeptide sequence (which may be wild-type or may have one or more differences). In some embodiments, the IL-10 comprises a modification to prevent disulfide bond formation, and optionally otherwise comprises wild-type sequence. In some embodiments, the IL-10 polypeptide sequence has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a wild-type IL-10 polypeptide sequence or to an IL-10 polypeptide sequence in Table 1. In some embodiments, the IL-10 polypeptide sequence comprises the sequence of SEQ ID NO: 900.
In some embodiments, the receptor-binding domain is an IL-15 polypeptide sequence. The IL-15 polypeptide sequence may be a wild-type IL-15 polypeptide sequence or a sequence with one or more differences from the wild-type IL-15 polypeptide sequence. In some embodiments, the IL-15 polypeptide sequence is a human IL-15 polypeptide sequence (which may be wild-type or may have one or more differences). In some embodiments, the IL-15 comprises a modification to prevent disulfide bond formation, and optionally otherwise comprises wild-type sequence. In some embodiments, the IL-15 polypeptide sequence has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a wild-type IL-15 polypeptide sequence or to an IL-15 polypeptide sequence in Table 1. In some embodiments, the IL-15 polypeptide sequence comprises the sequence of SEQ ID NO: 901.
In some embodiments, the receptor-binding domain is an CXCL9 polypeptide sequence. The CXCL9 polypeptide sequence may be a wild-type CXCL9 polypeptide sequence or a sequence with one or more differences from the wild-type CXCL9 polypeptide sequence. In some embodiments, the CXCL9 polypeptide sequence is a human CXCL9 polypeptide sequence (which may be wild-type or may have one or more differences). In some embodiments, the CXCL9 comprises a modification to prevent disulfide bond formation, and optionally otherwise comprises wild-type sequence. In some embodiments, the CXCL9 polypeptide sequence has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a wild-type CXCL9 polypeptide sequence or to an CXCL9 polypeptide sequence in Table 1. In some embodiments, the CXCL9 polypeptide sequence comprises the sequence of SEQ ID NO: 902.
In some embodiments, the receptor-binding domain is an CXCL10 polypeptide sequence. The CXCL10 polypeptide sequence may be a wild-type CXCL10 polypeptide sequence or a sequence with one or more differences from the wild-type CXCL10 polypeptide sequence. In some embodiments, the CXCL10 polypeptide sequence is a human CXCL10 polypeptide sequence (which may be wild-type or may have one or more differences). In some embodiments, the CXCL10 comprises a modification to prevent disulfide bond formation, and optionally otherwise comprises wild-type sequence. In some embodiments, the CXCL10 polypeptide sequence has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a wild-type CXCL10 polypeptide sequence or to an CXCL10 polypeptide sequence in Table 1. In some embodiments, the CXCL10 polypeptide sequence comprises the sequence of SEQ ID NO: 903.
In some embodiments, a molecular weight of one or each of the first active domain and the second active domain independently is about or less than 14 kDa. In some embodiments, the molecular weight is about 12 kDa to about 14 kDa. In some embodiments, the molecular weight is about 10 kDa to about 12 kDa. In some embodiments, the molecular weight is about 8 kDa to about 10 kDa. In some embodiments, the molecular weight is about 6 kDa to about 8 kDa. In some embodiments, the molecular weight is about 4 kDa to about 6 kDa. In some embodiments, the molecular weight is about 2 kDa to about 4 kDa. In some embodiments, the molecular weight is about 800 Da to about 2 kDa.
In some embodiments, the molecular weight of one or each of the first active domain and the second active domain independently is about or greater than 16 kDa. In some embodiments, the molecular weight is about 16 kDa to about 18 kDa. In some embodiments, the molecular weight is about 18 kDa to about 20 kDa. In some embodiments, the molecular weight is about 20 kDa to about 22 kDa. In some embodiments, the molecular weight is about 22 kDa to about 24 kDa. In some embodiments, the molecular weight is about 24 kDa to about 26 kDa. In some embodiments, the molecular weight is about 26 kDa to about 28 kDa. In some embodiments, the molecular weight is about 28 kDa to about 30 kDa. In some embodiments, the molecular weight is about 30 kDa to about 50 kDa. In some embodiments, the molecular weight is about 50 kDa to about 100 kDa. In some embodiments, the molecular weight is about 100 kDa to about 150 kDa. In some embodiments, the molecular weight is about 150 kDa to about 200 kDa. In some embodiments, the molecular weight is about 200 kDa to about 250 kDa. In some embodiments, the molecular weight is about 250 kDa to about 300 kDa.
In some embodiments, the linker polypeptide comprises an inhibitory polypeptide sequence capable of blocking an activity of an active domain, such as a receptor-binding domain. In some embodiments, the linker polypeptide further comprises a second linker between the receptor-binding domain and the inhibitory polypeptide sequence, the second linker comprising a protease-cleavable polypeptide sequence.
Various types of inhibitory polypeptide sequences may be used in a linker polypeptide according to the disclosure. In some embodiments, the inhibitory polypeptide sequence is a sequence that binds the active domain, such as a ligand-binding domain from a receptor, or an immunoglobulin domain. In some embodiments, the inhibitory polypeptide sequence is a steric blocker, i.e., a sequence that sterically obstructs the active domain. For example, a steric blocker can be an immunoglobulin Fc region, an albumin domain, or other relatively inert domain, which can be placed in proximity to the active domain to render it less accessible until the active domain is liberated from the inhibitory polypeptide sequence by cleavage. In some embodiments, the inhibitory polypeptide sequence interferes with binding between the first active domain and a receptor of the first active domain and/or with binding between the second active domain and a receptor of the second active domain. In some embodiments, the inhibitory polypeptide sequence and the pharmacokinetic modulator are different elements of the linker polypeptide. In some embodiments, the inhibitory polypeptide sequence comprises at least a portion of the pharmacokinetic modulator.
In some embodiments, the inhibitory polypeptide sequence comprises a cytokine-binding domain. The cytokine-binding domain may be the cytokine-binding domain of a cytokine receptor. The cytokine-binding domain of a cytokine receptor may be provided as an extracellular portion of the cytokine receptor or a portion thereof sufficient to bind the cytokine polypeptide sequence of the linker polypeptide. In some embodiments, the inhibitory polypeptide sequence has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a wild-type cytokine-binding domain of a cytokine receptor, e.g., a wild-type cytokine-binding domain of a human cytokine receptor.
The cytokine-binding domain may be a fibronectin cytokine-binding domain. In some embodiments, the inhibitory polypeptide sequence has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a wild-type fibronectin cytokine-binding domain of a cytokine receptor, e.g., a wild-type human fibronectin cytokine-binding domain.
In some embodiments, the inhibitory polypeptide sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 10-29, 40-51, 747, 748 and 749, 850-856, 939, 940, 941 and 945, 950 and 952, 953, 954 and 955, 956, 957 and 958, 959, 960 and 961, 962, 963 and 964, 965, 966 and 967, 968, 969 and 970, 971, 972 and 973, 974, 975 and 976, 977, 978 and 979, 980, 981 and 982, 983, 984 and 985, 986, 987 and 988, 989, 990, 991 and 992, 999 and 1000, 1001, 1002, 1003 and 1004, 1005, 1006, 1008 and 1010 (where pairs of SEQ ID NOs linked by “and” indicate a VH and VL pair that together can form an inhibitory polypeptide sequence, e.g., as separate chains or as a single chain joined by a linker). In some embodiments, the inhibitory polypeptide sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 1011 or 1012. In some embodiments, the inhibitory polypeptide sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 1016-1019. In some embodiments, the inhibitory polypeptide sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 1020, 1021, or 1023. In any of the foregoing embodiments, the VH and VL domains may comprise CDRs identical to the CDRs of the referenced SEQ ID NO(s). CDRs may be identified by any appropriate method, such as that of Kabat (as described in Kabat et al., (5th Ed. 1991) Sequences of Proteins of Immunological Interest, available at books.google.co.uk/books?id=3jMvZYW2ZtwC&lpg=PA1137-IA1&pg=PP1#v=onepage&q&f=false) or Chothia (as described in Al-Lazikani et al., (1997) JMB 273, 927-948). In some embodiments, the inhibitory polypeptide sequence comprises VH and VL domains comprising the CDRs of any of SEQ ID NO: 747, 748 and 749, 939, 940, 941 and 945, 950 and 952, 953, 954 and 955, 956, 957 and 958, 959, 960 and 961, 962, 963 and 964, 965, 966 and 967, 968, 969 and 970, 971, 972 and 973, 974, 975 and 976, 977, 978 and 979, 980, 981 and 982, 983, 984 and 985, 986, 987 and 988, 989, 990, 991 and 992, 999 and 1000, 1001, 1002, 1003 and 1004, 1005, 1006, 1008 and 1010. In some embodiments, the inhibitory polypeptide sequence comprises the sequence of any of SEQ ID NO: 747, 748 and 749, 939, 940, 941 and 945, 950 and 952, 953, 954 and 955, 956, 957 and 958, 959, 960 and 961, 962, 963 and 964, 965, 966 and 967, 968, 969 and 970, 971, 972 and 973, 974, 975 and 976, 977, 978 and 979, 980, 981 and 982, 983, 984 and 985, 986, 987 and 988, 989, 990, 991 and 992, 999 and 1000, 1001, 1002, 1003 and 1004, 1005, 1006, 1008 and 1010.
In some embodiments, the inhibitory polypeptide sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 850-856 and 863-870. In any of the foregoing embodiments, the VHH domain may comprise CDRs identical to the CDRs of any one of SEQ ID NOs: 850-856 and 863-870. In some embodiments, the inhibitory polypeptide sequence comprises a VHH comprising the CDRs of any one of SEQ ID NOs: 850-856 and 863-870. In some embodiments, the inhibitory polypeptide sequence comprises the sequence of any one of SEQ ID NOs: 850-856 and 863-870.
In some embodiments, the cytokine-binding domain may be an immunoglobulin cytokine-binding domain. In some embodiments, the immunoglobulin cytokine-binding domain comprises a VH region and a VL region that bind the cytokine. In some embodiments, the immunoglobulin cytokine-binding domain may be an Fv, scFv, Fab, VHH, or other immunoglobulin sequence having antigen-binding activity for the cytokine polypeptide sequence. A VHH antibody (or nanobody) is an antigen binding fragment of a heavy chain only antibody.
Additional examples of inhibitory polypeptide sequences that may be provided to inhibit the cytokine polypeptide sequence of the linker polypeptide are anticalins, affilins, affibody molecules, affimers, affitins, alphabodies, avimers, DARPins, fynomers, kunitz domain peptides, monobodies, and binding domains based on other engineered scaffolds such as SpA, GroEL, lipocallin and CTLA4 scaffolds.
In linker polypeptides comprising an IL-2 polypeptide sequence, the inhibitory polypeptide sequence may be an IL-2 inhibitory polypeptide sequence of any of the types described above. In some embodiments, the IL-2 inhibitory polypeptide sequence is an immunoglobulin IL-2 inhibitory polypeptide sequence.
In some embodiments, the IL-2 inhibitory polypeptide sequence comprises an anti-IL-2 antibody or a functional fragment thereof. In some embodiments, the inhibitory polypeptide sequence comprises an IL-2-binding immunoglobulin domain. In some embodiments, the IL-2-binding immunoglobulin domain is a human IL-2-binding immunoglobulin domain.
In some embodiments, the IL-2-binding immunoglobulin domain is an scFv. In some embodiments, the IL-2-binding immunoglobulin domain comprises a set of six anti-IL-2 hypervariable regions (HVRs) set forth in Table 1 (e.g., SEQ ID NOs: 34-39 or 750-755). In some embodiments, the IL-2-binding immunoglobulin domain comprises a set of anti-IL-2 VH and VL regions comprising sequences having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a set of anti-IL-2 VH and VL regions comprising sequences set forth in Table 1, either as individual sequences or as part of an scFv. In some embodiments, an IL-2-binding immunoglobulin domain comprises a set of anti-IL-2 VH and VL regions having the sequence of a set of anti-IL-2 VH and VL sequences set forth in Table 1, either as individual sequences or as part of an scFv.
Exemplary IL-2 inhibitory polypeptide sequences include SEQ ID NOs: 10-31, 40-51, 747, and 850-856, and a combination of SEQ ID NOs: 32 and 33 or a combination of SEQ ID NOs: 748 and 749. In some embodiments, the IL-2 inhibitory polypeptide sequence comprises an IL-2-binding immunoglobulin domain, which comprises a VH region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 33 and a VL region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 32. In some embodiments, the IL-2-binding immunoglobulin domain comprises a VH region comprising the sequence of SEQ ID NO: 33 and a VL region comprising the sequence of SEQ ID NO: 32.
In some embodiments, the IL-2-binding immunoglobulin domain comprises a VH region comprising hypervariable regions HVR-1, HVR-2, and HVR-3 having the sequences of SEQ ID NOs: 37, 38, and 39, respectively, and a VL region comprising HVR-1, HVR-2, and HVR-3 having the sequences of SEQ ID NOs: 34, 35, and 36, respectively. In some embodiments, the IL-2-binding immunoglobulin domain comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 30 or 31. In some embodiments, the IL-2-binding immunoglobulin domain comprises the sequence of SEQ ID NO: 30 or 31.
In some embodiments, the inhibitory polypeptide sequence comprises an IL-2 binding domain of an IL-2 receptor (IL-2R). In some embodiments, the IL-2R is a human IL-2R.
In linker polypeptides comprising an IL-10 polypeptide sequence, the inhibitory polypeptide sequence may be an IL-10 inhibitory polypeptide sequence of any of the types described above. In some embodiments, the IL-10 inhibitory polypeptide sequence is an immunoglobulin IL-10 inhibitory polypeptide sequence.
In some embodiments, the IL-10 inhibitory polypeptide sequence comprises an anti-IL-10 antibody or a functional fragment thereof. In some embodiments, the inhibitory polypeptide sequence comprises an IL-10-binding immunoglobulin domain. In some embodiments, the IL-10-binding immunoglobulin domain is a human IL-10-binding immunoglobulin domain.
In some embodiments, the IL-10-binding immunoglobulin domain is an scFv. In some embodiments, the IL-10-binding immunoglobulin domain comprises a set of six anti-IL-10 hypervariable regions (HVRs) set forth in Table 1 (e.g., SEQ ID NOs: 942-944 and 946-948). In some embodiments, the IL-10-binding immunoglobulin domain comprises a set of anti-IL-10 VH and VL regions comprising sequences having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a set of anti-IL-10 VH and VL regions comprising sequences set forth in Table 1, either as individual sequences or as part of an scFv. In some embodiments, an IL-10-binding immunoglobulin domain comprises a set of anti-IL-10 VH and VL regions having the sequence of a set of anti-IL-10 VH and VL sequences set forth in Table 1, either as individual sequences or as part of an scFv.
Exemplary IL-10 inhibitory polypeptide sequences include SEQ ID NOs: 939-948, 1011, and 1012. In some embodiments, the IL-10 inhibitory polypeptide sequence comprises an IL-10-binding immunoglobulin domain, which comprises a VH region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 945 and a VL region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 941. In some embodiments, the IL-10-binding immunoglobulin domain comprises a VH region comprising the sequence of SEQ ID NO: 945 and a VL region comprising the sequence of SEQ ID NO: 941.
In some embodiments, the IL-10-binding immunoglobulin domain comprises a VH region comprising hypervariable regions HVR-1, HVR-2, and HVR-3 having the sequences of SEQ ID NOs: 946, 947, and 948, respectively, and a VL region comprising HVR-1, HVR-2, and HVR-3 having the sequences of SEQ ID NOs: 942, 943, and 944, respectively. In some embodiments, the IL-10-binding immunoglobulin domain comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 939 or 940. In some embodiments, the IL-10-binding immunoglobulin domain comprises the sequence of SEQ ID NO: 939 or 940.
In some embodiments, the inhibitory polypeptide sequence comprises an IL-10 binding domain of an IL-10 receptor (IL-10R). In some embodiments, the IL-10R is a human IL-10R.
In linker polypeptides comprising an IL-15 polypeptide sequence, the inhibitory polypeptide sequence may be an IL-15 inhibitory polypeptide sequence of any of the types described above. In some embodiments, the IL-15 inhibitory polypeptide sequence is an immunoglobulin IL-15 inhibitory polypeptide sequence.
In some embodiments, the IL-15 inhibitory polypeptide sequence comprises an anti-IL-15 antibody or a functional fragment thereof. In some embodiments, the inhibitory polypeptide sequence comprises an IL-15-binding immunoglobulin domain. In some embodiments, the IL-15-binding immunoglobulin domain is a human IL-15-binding immunoglobulin domain.
In some embodiments, the IL-15-binding immunoglobulin domain is an scFv. In some embodiments, the IL-15-binding immunoglobulin domain comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of any one of SEQ ID NOs: 950, 955, 957, 960, 963, 966, 969, 972, 975, 978, 981, 985, and 988, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of any one of SEQ ID NOs: 952, 954, 958, 961, 964, 967, 970, 973, 976, 979, 982, 984, and 987. In general, a person skilled in the art can identify the HVRs in VH and VL sequences, e.g., by assigning amino acids to framework and HVR domains within the VH and VL sequences in accordance with the definitions of Kabat et al. in Sequences of Proteins of Immunological Interest, 5th Ed., US Dept. of Health and Human Services, PHS, NIH, NIH Publication no. 91-3242, 1991. Other numbering systems for the amino acids in immunoglobulin chains include IMGT™ (international ImMunoGeneTics information system; Lefranc et al, Dev. Comp. Immunol. 29:185-203; 2005) and AHo (Honegger and Pluckthun, J. Mol. Biol. 309(3):657-670; 2001). In some embodiments, the IL-15-binding immunoglobulin domain comprises a set of anti-IL-15 VH and VL regions comprising sequences having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a set of anti-IL-15 VH and VL regions comprising sequences set forth in Table 1, either as individual sequences or as part of an scFv. In some embodiments, an IL-15-binding immunoglobulin domain comprises a set of anti-IL-15 VH and VL regions having the sequence of a set of anti-IL-15 VH and VL sequences set forth in Table 1, either as individual sequences or as part of an scFv.
Exemplary IL-15 inhibitory polypeptide sequences include SEQ ID NOs: 953, 956, 959, 962, 965, 968, 971, 974, 977, 980, 983, and 986. In some embodiments, the IL-15 inhibitory polypeptide sequence comprises an IL-15-binding immunoglobulin domain, which comprises a VH region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to any one of SEQ ID NOs: 950, 955, 957, 960, 963, 966, 969, 972, 975, 978, 981, 985, and 988 and a VL region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the any one of SEQ ID NOs: 952, 954, 958, 961, 964, 967, 970, 973, 976, 979, 982, 984, and 987. In some embodiments, the IL-15-binding immunoglobulin domain comprises a VH region comprising the sequence of any one of SEQ ID NOs: 950, 955, 957, 960, 963, 966, 969, 972, 975, 978, 981, 985, and 988 and a VL region comprising the sequence of any one of SEQ ID NOs: 952, 954, 958, 961, 964, 967, 970, 973, 976, 979, 982, 984, and 987.
In some embodiments, the inhibitory polypeptide sequence comprises an IL-15 binding domain of an IL-15 receptor (IL-15R). In some embodiments, the IL-15R is a human IL-15R.
In linker polypeptides comprising an CXCL9 polypeptide sequence, the inhibitory polypeptide sequence may be an CXCL9 inhibitory polypeptide sequence of any of the types described above. In some embodiments, the CXCL9 inhibitory polypeptide sequence is an immunoglobulin CXCL9 inhibitory polypeptide sequence.
In some embodiments, the CXCL9 inhibitory polypeptide sequence comprises an anti-CXCL9 antibody or a functional fragment thereof. In some embodiments, the inhibitory polypeptide sequence comprises an CXCL9-binding immunoglobulin domain. In some embodiments, the CXCL9-binding immunoglobulin domain is a human CXCL9-binding immunoglobulin domain.
Exemplary CXCL9 inhibitory polypeptide sequences include SEQ ID NOs: 1020-1021. In some embodiments, the inhibitory polypeptide sequence comprises an CXCL9 binding domain of an CXCL9 receptor (CXCR3). In some embodiments, the CXCR3 is a human CXCR3.
In linker polypeptides comprising an CXCL10 polypeptide sequence, the inhibitory polypeptide sequence may be an CXCL10 inhibitory polypeptide sequence of any of the types described above. In some embodiments, the CXCL10 inhibitory polypeptide sequence is an immunoglobulin CXCL10 inhibitory polypeptide sequence.
In some embodiments, the CXCL10 inhibitory polypeptide sequence comprises an anti-CXCL10 antibody or a functional fragment thereof. In some embodiments, the inhibitory polypeptide sequence comprises an CXCL10-binding immunoglobulin domain. In some embodiments, the CXCL10-binding immunoglobulin domain is a human CXCL10-binding immunoglobulin domain.
In some embodiments, the CXCL10-binding immunoglobulin domain is an scFv. In some embodiments, the CXCL10-binding immunoglobulin domain comprises a set of six anti-CXCL10 hypervariable regions (HVRs) set forth in Table 1 (e.g., SEQ ID NOs: 993-998). In some embodiments, the CXCL10-binding immunoglobulin domain comprises a set of anti-CXCL10 VH and VL regions comprising sequences having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a set of anti-CXCL10 VH and VL regions comprising sequences set forth in Table 1, either as individual sequences or as part of an scFv. In some embodiments, a CXCL10-binding immunoglobulin domain comprises a set of anti-CXCL10 VH and VL regions having the sequence of a set of anti-CXCL10 VH and VL sequences set forth in Table 1, either as individual sequences or as part of an scFv.
Exemplary CXCL10 inhibitory polypeptide sequences include SEQ ID NOs: 989 and 990. In some embodiments, the CXCL10 inhibitory polypeptide sequence comprises an CXCL10-binding immunoglobulin domain, which comprises a VH region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 991 and a VL region comprising an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 992. In some embodiments, the CXCL10-binding immunoglobulin domain comprises a VH region comprising the sequence of SEQ ID NO: 991 and a VL region comprising the sequence of SEQ ID NO: 992.
In some embodiments, the CXCL10-binding immunoglobulin domain comprises a VH region comprising hypervariable regions HVR-1, HVR-2, and HVR-3 having the sequences of SEQ ID NOs: 993, 994, and 995, respectively, and a VL region comprising HVR-1, HVR-2, and HVR-3 having the sequences of SEQ ID NOs: 996, 997, and 998, respectively. In some embodiments, the CXCL10-binding immunoglobulin domain comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 989 or 990. In some embodiments, the CXCL10-binding immunoglobulin domain comprises the sequence of SEQ ID NO: 989 or 990.
In some embodiments, the inhibitory polypeptide sequence comprises an CXCL10 binding domain of an CXCL10 receptor (CXCR3). In some embodiments, the CXCR3 is a human CXCR3.
A variety of linkers may be used in accordance with the present disclosure. In many embodiments, a linker may be used to connect any two domains in a linker polypeptide. In some embodiments, a linker polypeptide comprises one linker. In other embodiments, a linker polypeptide may comprise two or more linkers. In some embodiments, a first linker exists between a pharmacokinetic modulator and a first active domain. In some embodiments, a second linker exists between a receptor-binding domain and an inhibitory polypeptide sequence. In some embodiments, the first linker and/or the second linker comprises a protease-cleavable polypeptide sequence. In some embodiments, after the protease-cleavable polypeptide sequence is cleaved, the first active domain and/or the second active domain is released from the remainder of the linker polypeptide. In some embodiments, the linker polypeptide comprises a plurality of protease-cleavable polypeptide sequences.
In these embodiments, different linkers may be used to provide different release properties for different linked domains. For example, a linker for releasing a target binding domain, such as an immunoglobulin antigen-binding domain, may differ from a linker for releasing a receptor-binding domain, such as a cytokine polypeptide sequence. A linker may comprise any of the exemplary linker sequences disclosed herein, e.g., in Table 1.
The protease-cleavable sequence may comprise a sequence cleavable and/or recognized by various types of proteases, e.g., a metalloprotease, a serine protease, a cysteine protease, an aspartate protease, a threonine protease, a glutamate protease, a gelatinase, an asparagine peptide lyase, a cathepsin, a kallikrein, a plasmin, a collagenase, a hK1, a hK10, a hK15, a stromelysin, a Factor Xa, a chymotrypsin-like protease, a trypsin-like protease, a elastase-like protease, a subtilisin-like protease, an actinidain, a bromelain, a calpain, a caspase, a Mir 1-CP, a papain, a HIV-1 protease, a HSV protease, a CMV protease, a chymosin, a renin, a pepsin, a matriptase, a legumain, a plasmepsin, a nepenthesin, a metalloexopeptidase, a metalloendopeptidase, an ADAM 10, an ADAM 17, an ADAM 12, an urokinase plasminogen activator (uPA), an enterokinase, a prostate-specific target (PSA, hK3), an interleukin-1b converting enzyme, a thrombin, a FAP (FAP-a), a dipeptidyl peptidase, or dipeptidyl peptidase IV (DPPIV/CD26), a type II transmembrane serine protease (TTSP), a neutrophil elastase, a proteinase 3, a mast cell chymase, a mast cell tryptase, or a dipeptidyl peptidase. In some embodiments, the protease-cleavable sequence comprises a sequence of any one of those in Table 1 (e.g., SEQ ID NOs: 80-94 and 701-742), or a variant having one or two mismatches relative to a sequence of any one of those in Table 1 (e.g., SEQ ID NOs: 80-90 and 701-742). Proteases generally do not require an exact copy of the recognition sequence, and as such, the exemplary sequences may be varied at one or more portions of their amino acid positions. In some embodiments, the protease-cleavable sequence comprises a sequence that matches an MMP consensus sequence, such as any one of SEQ ID NOs: 91-94.
One skilled in the art will be familiar with additional sequences recognized by these types of proteases.
i. Matrix Metalloprotease-Cleavable Sequence
In some embodiments, the protease-cleavable sequence is a matrix metalloprotease (MMP)-cleavable sequence and is recognized by a matrix metalloprotease. Exemplary MMP-cleavable sequences are provided in Table 1. In some embodiments, the MMP-cleavable sequence is cleavable and/or recognized by a plurality of MMPs and/or one or more of MMP-1, MMP-2, MMP-3, MMP-7, MMP-8, MMP-9, MMP-12, MMP-13, and/or MMP-14. In some embodiments, the protease-cleavable polypeptide sequence is cleavable and/or recognized by two, three, four, five, six, or seven of MMP-2, MMP-7, MMP-8, MMP-9, MMP-12, MMP-13, and MMP-14. Table 1, e.g., SEQ ID NOs: 80-90, provides exemplary MMP-cleavable sequences.
In some embodiments, the protease-cleavable polypeptide sequence comprises a sequence of any one of SEQ ID NO: 80-90. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 80 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 81 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 82 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 83 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 84 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 85 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 86 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 87 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 88 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 89 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 90 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 91 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 92 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 93 or a variant sequence having one or two mismatches relative thereto. In some embodiments, the protease-cleavable polypeptide sequence comprises the sequence of SEQ ID NO: 94 or a variant sequence having one or two mismatches relative thereto.
In some embodiments, the linker polypeptide comprises a first targeting sequence and/or a second targeting sequence. In some embodiments, the first targeting sequence and/or the second targeting sequence is between a receptor-binding domain and a protease-cleavable polypeptide sequence or one of a plurality of protease-cleavable polypeptide sequences. In some embodiments, at least one of the first linker and the second linker comprises a targeting sequence, e.g., one of the first targeting sequence and the second targeting sequence, at least one targeting sequence, one of a first plurality of targeting sequences, one of a second plurality of targeting sequences, or one of a plurality of targeting sequences. In some embodiments, the protease-cleavable polypeptide sequence comprises a targeting sequence, e.g., one of the first targeting sequence and the second targeting sequence, the at least one targeting sequence, one of the first plurality of targeting sequences, one of the second plurality of targeting sequences, or one of the plurality of targeting sequences.
In some embodiments, one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences increases a serum half-life of the linker polypeptide. In general, an increase in serum half-life may be relative, e.g., to the serum half-life of a linker polypeptide that lacks one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences. In some embodiments, one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences synergistically increases a serum half-life of the linker polypeptide together with another one of the first targeting sequence and the second targeting sequence, another one of the at least one targeting sequence, another one of the first plurality of targeting sequences, another one of the second plurality of targeting sequences, or another one of the plurality of targeting sequences. In some embodiments, one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences synergistically increases a serum half-life of the linker polypeptide together with the pharmacokinetic modulator. In some embodiments, one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently increases a serum half-life of the linker polypeptide.
Serum half-life may be measured, for example, by measuring serum levels of the linker polypeptide over time after administration of the linker polypeptide. In some embodiments, any one of the above targeting sequences may independently increase the serum half-life of the linker polypeptide when the serum half-life is greater than a serum half-life of a linker polypeptide that lacks the one targeting sequence but that is otherwise identical to the linker polypeptide, and when the increase is independent of any other increase derived from another targeting sequence. In some embodiments, any one of the above targeting sequences may synergistically increase the serum half-life of the linker polypeptide together with the other one of the targeting sequences or with the pharmacokinetic modulator when the increase in serum half-life is greater than the sum of the increase derived from the one targeting sequence and the increase derived from the other one of the targeting sequences, or than the sum of the increase derived from the one targeting sequence and the increase derived from the pharmacokinetic modulator.
The targeting sequence may facilitate localization, accumulation, and/or retention of the linker polypeptide and/or the first active domain and/or the second active domain (e.g., after proteolysis of the protease-cleavable sequence) in an area of interest, e.g., a tumor microenvironment (TME). The targeting sequence may be a sequence that binds an extracellular matrix component. Exemplary extracellular matrix components may include, for example, a collagen or denatured collagen (in either case, the collagen may be collagen I, II, III, or IV), poly(I), von Willebrand factor, IgB (CD79b), a heparin, a heparan sulfate, a sulfated glycoprotein, or hyaluronic acid. In some embodiments, the extracellular matrix component is hyaluronic acid, a heparin, a heparan sulfate, or a sulfated glycoprotein.
In some embodiments, the targeting sequence binds a target other than an extracellular matrix component. In some embodiments, the targeting sequence binds one or more of IgB (CD79b), a fibronectin, an integrin, a cadherin, a heparan sulfate proteoglycan, and a syndecan. In some embodiments, the targeting sequence binds at least one integrin, such as one or more of α1β1 integrin, α2β1 integrin, α3β1 integrin, α4β1 integrin, α5β1 integrin, α6β1 integrin, α7β1 integrin, α9β1 integrin, α4β7 integrin, αvβ integrin, αvβ5 integrin, αIIbβ3 integrin, αIIIbβ3 integrin, αMβ2 integrin, or αIIbβ3 integrin. In some embodiments, the targeting sequence binds at least one syndecan, such as one of more of syndecan-1, syndecan-4, and syndecan-2(w). Linker polypeptides comprising such targeting sequences may also comprise an MMP-cleavable linker as set forth elsewhere herein, such as an MMP-cleavable linker comprising any one of SEQ ID NOs: 80-90, or a variant having one or two mismatches relative to the sequence of any one of SEQ ID NOs: 80-90.
In some embodiments, the targeting sequence comprises a sequence set forth in Table 2 (e.g., any one of SEQ ID NOs: 179-665, such as SEQ ID NOs: 179-640), or a variant having one or two mismatches relative to such a sequence.
In some embodiments that include a first targeting sequence and a second targeting sequence, the first targeting sequence is configured to bind to heparin and the second targeting sequence is configured to bind to heparin, wherein the first targeting sequence is configured to bind to collagen IV and the second targeting sequence is configured to bind to heparin, or wherein the first targeting sequence is configured to bind to heparin and the second targeting sequence is configured to bind to collagen IV.
In some embodiments, one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 0.1 nM to 1 nM, from 1 nM to 10 nM, from 10 nM to 100 nM, from 100 nM to 1 μM, from 1 μM to 10 μM, or from 10 μM to 100 μM. In some embodiments, one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 0.1 nM to 1 nM. In some embodiments, one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 1 nM to 10 nM. In some embodiments, one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 10 nM to 100 nM. In some embodiments, one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 100 nM to 1 M. In some embodiments, one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 1 μM to 10 μM. In some embodiments, one or each of the first targeting sequence and the second targeting sequence, one or each of the at least one targeting sequence, one or each of the first plurality of targeting sequences, one or each of the second plurality of targeting sequences, or one or each of the plurality of targeting sequences independently is configured to bind its target with an affinity from 10 μM to 100 μM. In some embodiments, the affinity may be a dissociation constant (KD), which may be measured, for example, through surface plasmon resonance (SPR), an enzyme linked immunosorbent assay (ELISA), or polarization-modulated oblique-incidence reflectivity difference (OI-RD).
1. pH-Sensitive Targeting Sequences
In some embodiments, the targeting sequence is configured to bind its target in a pH-sensitive manner. In some embodiments, the targeting sequence has a higher affinity for its target at a relatively acidic pH than at normal physiological pH (about 7.4). The higher affinity may occur at a pH below 7, e.g., in the range of pH 5.5-7, 6-7, or 5.5-6.5, or below pH 6. The presence of histidines in the targeting sequence can confer pH-sensitive binding. Without wishing to be bound by any particular theory, histidines are considered more likely to be protonated at lower pH and can render binding a negatively-charged target more energetically favorable. Accordingly, in some embodiments, a targeting sequence comprises one or more histidines, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 histidines. Including a pH-sensitive targeting sequence can enhance discrimination between tumor versus normal tissue by the linker polypeptide, such that the linker polypeptide is more preferentially retained in the tumor microenvironment compared to normal extracellular matrix. Thus, a pH-sensitive targeting element can further facilitate tumor specific delivery of the linker polypeptide and thereby further reduce or eliminate toxicity that may result from activity of the linker polypeptide in normal extracellular matrix.
Binding a target in a pH-sensitive manner can be useful where it is desired to localize or retain a linker polypeptide and/or the cytokine polypeptide sequence thereof in an area with a pH different from normal physiological pH. For example, the tumor microenvironment may be more acidic than the blood and/or healthy tissue. As such, binding to a target in a pH-sensitive manner may improve the retention of the linker polypeptide and/or the cytokine polypeptide sequence thereof in the area of interest, which can facilitate lower doses than would otherwise be needed and/or reduce systemic exposure and/or adverse effects.
In some embodiments, the targeting sequence is configured to bind any target described herein in a pH-sensitive manner. In particular embodiments, the target is an extracellular matrix component, IgB (CD79b), an integrin, a cadherin, a heparan sulfate proteoglycan, a syndecan, or a fibronectin. In some embodiments, the extracellular matrix component is hyaluronic acid, heparin, heparan sulfate, or a sulfated glycoprotein. In another particular embodiment, the target is a fibronectin.
Exemplary targeting sequences for conferring target binding in a pH-sensitive manner are provided in Table 2 (e.g., SEQ ID NOs: 641-663). In some embodiments, the targeting sequence comprises the sequence of any one of SEQ ID NOs: 641-663, or a variant having one or two mismatches relative to the sequence of any one of SEQ ID NOs: 641-663.
In some embodiments, the linker polypeptide comprises a targeting sequence is adjacent to a protease cleavable sequence. The targeting sequence and protease cleavable sequence may be any of those described herein. Exemplary combinations of a targeting sequence and a protease cleavable sequence are SEQ ID NOs: 667-673.
In some embodiments, the linker polypeptide comprises a pharmacokinetic modulator. The pharmacokinetic modulator may be covalently or noncovalently associated with the linker polypeptide. The pharmacokinetic modulator can extend the half-life of the linker polypeptide, e.g., so that fewer doses are necessary and less of the linker polypeptide needs to be administered over time to achieve a desired result. Various forms of pharmacokinetic modulator are known in the art and may be used in linker polypeptides of this disclosure. In some embodiments, the pharmacokinetic modulator comprises a polypeptide (see examples below). In some embodiments, the pharmacokinetic modulator comprises a non-polypeptide moiety (e.g., polyethylene glycol, a polysaccharide, or hyaluronic acid). A non-polypeptide moiety can be associated with the linker polypeptide using known approaches, e.g., conjugation to the linker polypeptide; for example, a reactive amino acid residue can be used or added to the linker polypeptide to facilitate conjugation.
In some embodiments, the pharmacokinetic modulator alters the size, shape, and/or charge of the linker polypeptide, e.g., in a manner that reduces clearance. For example, a pharmacokinetic modulator with a negative charge may inhibit renal clearance. In some embodiments, the pharmacokinetic modulator increases the hydrodynamic volume of the linker polypeptide. In some embodiments, the pharmacokinetic modulator reduces renal clearance, e.g., by increasing the hydrodynamic volume of the linker polypeptide.
In some embodiments, the linker polypeptide comprising the pharmacokinetic modulator (e.g., any of the pharmacokinetic modulators described herein) has a molecular weight of at least 70 kDa, e.g., at least 75 or 80 kDa.
For further discussion of various approaches for providing a pharmacokinetic modulator, see, e.g., Strohl, BioDrugs 29:215-19 (2015) and Podust et al., J. Controlled Release 240:52-66 (2016).
In some embodiments, the pharmacokinetic modulator comprises a polypeptide, e.g., an immunoglobulin sequence (see exemplary embodiments below), an albumin, a CTP (a negatively-charged carboxy-terminal peptide of the chorionic gonadotropin 3-chain that undergoes sialylation in vivo and in appropriate host cells), an inert polypeptide (e.g., an unstructured polypeptide such as an XTEN, a polypeptide comprising the residues Ala, Glu, Gly, Pro, Ser, and Thr), a transferrin, a homo-amino-acid polypeptide, or an elastin-like polypeptide.
Exemplary polypeptide sequences suitable for use as a pharmacokinetic modulator are provided in Table 1 (e.g., any one of SEQ ID NOs: 70-74). In some embodiments, the pharmacokinetic modulator has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a pharmacokinetic modulator in Table 1 (e.g., any one of SEQ ID NOs: 70-74).
In any embodiment where the pharmacokinetic modulator comprises a polypeptide sequence from an organism, the polypeptide sequence may be a human polypeptide sequence.
In some embodiments, the pharmacokinetic modulator comprises an immunoglobulin sequence, e.g., at least a portion of one or more immunoglobulin constant domains. In some embodiments, the pharmacokinetic modulator comprises an immunoglobulin constant domain. In some embodiments, the pharmacokinetic modulator comprises at least a portion of an immunoglobulin Fc region. In some embodiments, the pharmacokinetic modulator comprises an immunoglobulin Fc region.
The immunoglobulin sequence (e.g., at least a portion of one or more immunoglobulin constant domains or Fc region) may be a human immunoglobulin sequence. The immunoglobulin sequence (e.g., at least a portion of one or more immunoglobulin constant domains or Fc region) may have has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of a wild-type immunoglobulin sequence (e.g., at least a portion of one or more immunoglobulin constant domains or Fc region), such as a wild-type human immunoglobulin sequence. In any of such embodiments, the immunoglobulin sequence may be an IgG sequence, such as at least a portion of one or more immunoglobulin constant domains or Fc region thereof (e.g., IgG1, IgG2, IgG3, or IgG4, such as at least a portion of one or more immunoglobulin constant domains or Fc region of any of these isotypes). Exemplary immunoglobulin pharmacokinetic modulator sequences include SEQ ID NOs: 70-74, 857, 858, 861, and 862 and the combination of SEQ ID NOs: 756 and 757; 75 and 77; 75 and 78; 76 and 77; 76 and 78; and 859 and 860.
In some embodiments, immunoglobulin pharmacokinetic modulator sequences (such as an Fc region) may perform certain functions and effects by interacting with certain targets, as described in Table 3 below.
In some embodiments, the linker polypeptide comprises a growth factor-binding polypeptide sequence or a growth factor receptor-binding polypeptide sequence. Such a sequence can serve as an active domain.
In some embodiments, the growth factor-binding polypeptide sequence comprises a TGF-βR extracellular domain sequence. In some embodiments, the TGF-βR extracellular domain sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 1022 or 1023.
In some embodiments, the growth factor-binding polypeptide sequence comprises a growth factor-binding immunoglobulin domain. In some embodiments, the growth factor-binding immunoglobulin domain is configured to bind to a TGF-β. In some embodiments, the growth factor-binding immunoglobulin domain comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of SEQ ID NO: 1008, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of SEQ ID NO: 1010. In general, a person skilled in the art can identify the HVRs in VH and VL sequences, e.g., by assigning amino acids to framework and HVR domains within the VH and VL sequences in accordance with the definitions of Kabat et al. in Sequences of Proteins of Immunological Interest, 5th Ed., US Dept. of Health and Human Services, PHS, NIH, NIH Publication no. 91-3242, 1991. Other numbering systems for the amino acids in immunoglobulin chains include IMGT™ (international ImMunoGeneTics information system; Lefranc et al, Dev. Comp. Immunol. 29:185-203; 2005) and AHo (Honegger and Pluckthun, J. Mol. Biol. 309(3):657-670; 2001). In some embodiments, the growth factor-binding immunoglobulin domain comprises a VH region comprising the amino acid sequence of SEQ ID NO: 1008; and a VL region comprising the amino acid sequence of SEQ ID NO: 1010. In some embodiments, the growth factor-binding immunoglobulin domain comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of SEQ ID NO: 1007 or 1009. In some embodiments, the growth factor receptor-binding polypeptide sequence comprises a TGF-0 sequence. In some embodiments, the TGF-0 sequence comprises an amino acid sequence having at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs. 904-906.
In some embodiments, the growth factor receptor-binding polypeptide sequence comprises a growth factor receptor-binding immunoglobulin domain. In some embodiments, the growth factor receptor-binding immunoglobulin domain is configured to bind to a TGF-βR extracellular domain sequence. In some embodiments, the growth factor receptor-binding immunoglobulin domain comprises a VH region comprising HVR-1, HVR-2, and HVR-3 of a VH region comprising the amino acid sequence of SEQ ID NO: 999 or 1003, and a VL region comprising HVR-1, HVR-2, and HVR-3 of a VL region comprising the amino acid sequence of SEQ ID NO: 1000 or 1004. In some embodiments, the growth factor receptor-binding immunoglobulin domain comprises a VH region comprising the amino acid sequence of SEQ ID NO: 999 or 1003; and a VL region comprising the amino acid sequence of SEQ ID NO: 1000 or 1004. In some embodiments, the growth factor receptor-binding immunoglobulin domain comprises a sequence that has at least 80, 85, 90, 95, 97, 98, or 99 percent identity to the sequence of any one of SEQ ID NOs: 1001, 1002, 1005, and 1006.
In some embodiments, the linker polypeptide may comprise a blocker. In some embodiments, the blocker may be conjugated to one of or each of the first active domain and the second active domain. In some embodiments, the blocker is conjugated to one of or each of the first active domain and the second active domain via a protease-cleavable polypeptide sequence.
The blocker may obstruct an immunoglobulin antigen-binding domain from binding to an antigen (e.g., a growth factor or growth factor receptor). In some embodiments, the blocker is linked to the immunoglobulin antigen-binding domain through the N-terminus of a heavy or light chain of the immunoglobulin antigen-binding domain.
In some embodiments, the blocker comprises albumin. In some embodiments, the blocker comprises serium albumin. In some embodiments, the blocker comprises human serum albumin (HAS) (e.g., SEQ ID NO: 72) or a fragment thereof.
In some embodiments, the linker polypeptide may comprise a chemotherapy drug or a plurality of chemotherapy drugs. The drug may, for example, be conjugated to different elements of the linker polypeptide. In some embodiments, a chemotherapy drug is conjugated to a pharmacokinetic modulator of the linker polypeptide.
In some embodiments, the chemotherapy drug is selected from altretamine, bendamustine, busulfan, carboplatin, carmustine, chlorambucil, cisplatin, cyclophosphamide, dacarbazine, ifosfamide, lomustine, mechlorethamine, melphalan, oxaliplatin, temozolomide, thiotepa, trabectedin, carmustine, lomustine, streptozocin, azacitidine, 5-fluorouracil, 6-mercaptopurine, capecitabine, cladribine, clofarabine, cytarabine, decitabine, floxuridine, fludarabine, gemcitabine, hydroxyurea, methotrexate, nelarabine, pemetrexed, pentostatin, pralatrexate, thioguanine, trifluridine, tipiracil, daunorubicin, doxorubicin, epirubicin, idarubicin, valrubicin, bleomycin, dactinomycin, mitomycin-c, mitoxantrone, irinotecan, topotecan, etoposide, mitoxantrone, teniposide, cabazitaxel, docetaxel, paclitaxel, vinblastine, vincristine, vinorelbine, prednisone, methylprednisolone, dexamethasone, retinoic acid, arsenic trioxide, asparaginase, eribulin, hydroxyurea, ixabepilone, mitotane, omacetaxine, pegaspargase, procarbazine, romidepsin, and vorinostat.
The recitation of components of a linker polypeptide herein does not imply any particular order beyond what is explicitly stated (for example, it may be explicitly stated that a protease-cleavable sequence is between the cytokine polypeptide sequence and the inhibitory polypeptide sequence). The components of the linker polypeptide may be arranged in various ways to provide properties suitable for a particular use. The components of the linker polypeptide may be all in one polypeptide chain or they may be in a plurality of polypeptide chains bridged by covalent bonds, such as disulfide bonds.
For example, in some embodiments, where a pharmacokinetic modulator comprises an Fc, one or more components (e.g., chemotherapy drugs) may be bound to one chain while one or more other components may be bound to the other chain. The Fc may be a heterodimeric Fc, such as a knob-into-hole Fc (in which one chain of the Fc comprises knob mutations and the other chain of the Fc comprises hole mutations). For an exemplary general discussion of knob and hole mutations, see, e.g., Xu et al., mAbs 7:1, 231-242 (2015). Exemplary knob mutations (e.g., for a human IgG1 Fc) are K360E/K409W. Exemplary hole mutations (e.g., for a human IgG1 Fc) are Q347R/D399V/F405T. See SEQ ID NOs: 756 and 757.
In some embodiments, some or all of the one or more protease-cleavable polypeptide sequences may be C-terminal to a VH region, C-terminal to at least a portion of a CH1 domain, between a CH1 domain and a CH2 domain, N-terminal to at least a portion of a CH2 domain, N-terminal to a disulfide bond between heavy chains, N-terminal to a disulfide bond within a CH2 domain, or N-terminal to a hinge region, or is within a hinge region. In some embodiments, some or all of the one or more protease-cleavable polypeptide sequences may be between the pharmacokinetic modulator and the second active domain, and/or between the blocker and one or each of the first active domain and the second active domain.
In some embodiments, a targeting sequence may be between the receptor-binding domain and the one or more protease-cleavable polypeptide sequences. In some embodiments, at least one of the first linker and the second linker comprises a targeting sequence, and/or a protease-cleavable polypeptide sequence comprises a targeting sequence.
In some embodiments, a targeting sequence may be present on the same side of a protease-cleavable polypeptide sequence as the receptor-binding domain (e.g., cytokine polypeptide sequence), meaning that cleavage of the protease-cleavable polypeptide sequence does not separate the targeting sequence from the receptor-binding domain. Such embodiments can be useful to facilitate localizing or retaining both the linker polypeptide and the released receptor-binding domain in an area of interest, e.g., a tumor microenvironment.
In some embodiments, a targeting sequence may be present on the same side of a protease-cleavable polypeptide sequence as an inhibitory polypeptide sequence, meaning that cleavage of that protease-cleavable polypeptide sequence does not separate the targeting sequence from the cytokine polypeptide sequence. Such embodiments can be useful to provide a gradient of cytokine emanating from an area of interest, or to provide such a gradient more rapidly than would occur if the targeting sequence were on the same side of the protease-cleavable sequence.
In some embodiments, the first active domain is proximal to the first targeting sequence relative to the second targeting sequence. In other embodiments, the second active domain is proximal to the first targeting sequence relative to the second targeting sequence. In some embodiments, the linker polypeptide comprises sequentially, from the N-terminus to the C-terminus or from the C-terminus to the N-terminus, the first active domain, the first targeting sequence, the first linker, the second targeting sequence, and the additional domain.
In some embodiments, the protease-cleavable polypeptide sequence is C-terminal to the first targeting sequence and to the second targeting sequence. In some embodiments, the protease-cleavable polypeptide sequence is N-terminal to the first targeting sequence and to the second targeting sequence. In some embodiments, the protease-cleavable polypeptide sequence is C-terminal to the first plurality of targeting sequences and is N-terminal to the second plurality of targeting sequences. In some embodiments, the protease-cleavable polypeptide sequence is C-terminal to the plurality of targeting sequences and is N-terminal to at least one targeting sequence. In some embodiments, the protease-cleavable polypeptide sequence is N-terminal to the plurality of targeting sequences and is C-terminal to at least one targeting sequence. In some embodiments, the protease-cleavable polypeptide sequence is C-terminal to the first targeting sequence and to the second targeting sequence and is not N-terminal to a targeting sequence. In some embodiments, the protease-cleavable polypeptide sequence is N-terminal to the first targeting sequence and to the second targeting sequence and is not C-terminal to a targeting sequence.
In some embodiments, the linker polypeptide comprises a first active domain, a second active domain, a pharmacokinetic modulator, and a first linker between the pharmacokinetic modulator and the first active domain. In some embodiments, the first linker comprises a protease-cleavable polypeptide sequence and optionally a targeting sequence. In certain embodiments, the active domains comprise immunoglobulin antigen-binding domains. In certain embodiments, the target binding domain may comprise a heavy chain and a light chain or only a heavy chain. In some embodiments, the linker polypeptide comprises a chemotherapy drug.
In some embodiments, the first active domain is released from the remainder of the linker polypeptide after the one or more protease-cleavable polypeptide sequences are cleaved. In some embodiments, the linker polypeptide further comprises a blocker conjugated, via a protease-cleavable polypeptide sequence, to one or each of the first active domain and the second active domain. In some embodiments, the protease-cleavable polypeptide sequence connecting the first active domain to the remainder of the linker polypeptide and the protease-cleavable polypeptide sequences connecting the blockers to the active domains may be cleaved together (e.g., by the same protease). In some embodiments, the protease-cleavable polypeptide sequence connecting the first active domain to the remainder of the linker polypeptide and the protease-cleavable polypeptide sequences connecting the blockers to the active domains may be cleaved separately (e.g., by different proteases).
In some embodiments, the linker polypeptide comprises a first active domain, a second active domain, a pharmacokinetic modulator, and a first linker between the pharmacokinetic modulator and the first active domain, the first linker comprising a protease-cleavable polypeptide sequence and optionally a targeting sequence. In certain embodiments, the first active domain comprises a receptor-binding domain, and the second active domain comprises an immunoglobulin antigen-binding domain, which may comprise a cytokine polypeptide sequence. In some embodiments, the linker polypeptide comprises an inhibitory polypeptide sequence capable of blocking an activity of the receptor-binding domain, and a second linker between the receptor-binding domain and the inhibitory polypeptide sequence, the second linker comprising a protease-cleavable polypeptide sequence.
In some embodiments, the first active domain is released from the remainder of the linker polypeptide after the one or more protease-cleavable polypeptide sequences are cleaved. In some embodiments, the first active domain comprises a receptor-binding domain, which may comprise a cytokine polypeptide sequence, and the second active domain comprises an immunoglobulin antigen-binding domain. In some embodiments, the linker polypeptide further comprises an inhibitory polypeptide sequence capable of blocking an activity of the receptor-binding domain, and a second linker between the receptor-binding domain and the inhibitory polypeptide sequence, the second linker comprising a protease-cleavable polypeptide sequence. In some embodiments, the protease-cleavable polypeptide sequences of the first linker and the second linker may be cleaved together (e.g., by the same protease). In some embodiments, the protease-cleavable polypeptide sequences of the first linker and the second linker may be cleaved separately (e.g., by different proteases).
In some embodiments, e.g., any of those in which first and second polypeptide chains comprising first and second domains of a pharmacokinetic modulator, respectively, are present, the inhibitory polypeptide sequence is C-terminal to the second domain of the pharmacokinetic modulator, or the inhibitory polypeptide sequence is N-terminal to the second domain of the pharmacokinetic modulator. A targeting sequence may be between the protease-cleavable polypeptide sequence and the first domain of the pharmacokinetic modulator, between the protease-cleavable polypeptide sequence and the first active domain, C-terminal to the first active domain, N-terminal to the first active domain, C-terminal to the inhibitory polypeptide sequence, N-terminal to the inhibitory polypeptide sequence, or between the inhibitory polypeptide sequence and the second domain of the pharmacokinetic modulator.
In some embodiments, e.g., any of those in which first and second polypeptide chains comprising first and second domains of a pharmacokinetic modulator, respectively, are present, the linker polypeptide may comprise first and second targeting sequences. In some such embodiments, the first targeting sequence is part of the first polypeptide chain and the second targeting sequence is part of the second polypeptide chain. In some such embodiments, the first targeting sequence is C-terminal to the first active domain and the second targeting sequence is C-terminal to the inhibitory polypeptide sequence.
In some embodiments, e.g., any of those in which first and second polypeptide chains comprising first and second domains of a pharmacokinetic modulator, respectively, are present, the linker polypeptide further comprises a second active domain, optionally wherein the second active domain is part of the second polypeptide chain, and/or the linker polypeptide comprises a first inhibitory polypeptide sequence and the linker polypeptide further comprises a second inhibitory polypeptide sequence. In some embodiments, the second inhibitory polypeptide sequence is part of the second polypeptide chain. In some embodiments, the second inhibitory polypeptide sequence is C-terminal to the first inhibitory polypeptide sequence. The first and/or second inhibitory polypeptide sequences may be immunoglobulin inhibitory polypeptide sequences, such as a VHH.
In some embodiments, e.g., any of those in which first and second polypeptide chains comprising first and second domains of a pharmacokinetic modulator, respectively, are present, the pharmacokinetic modulator comprises a heterodimeric Fc or heterodimeric CH3 domains. The heterodimeric Fc or heterodimeric CH3 domains may be in separate polypeptide chains. In some embodiments, the heterodimeric Fc or heterodimeric CH3 domains comprise a knob CH3 domain and a hole CH3 domain.
In some embodiments, the linker polypeptide comprises the polypeptide sequence of any one of SEQ ID NOs: 800-848 and 1024-1041. In some embodiments, the linker polypeptide comprises the polypeptide sequence of any one of SEQ ID NOs: 1042-1137.
Pharmaceutical formulations or compositions of a linker polypeptide as described herein may be prepared by mixing such linker polypeptide having the desired degree of purity with one or more optional pharmaceutically acceptable carriers (Remington's Pharmaceutical Sciences 16th edition, Osol, A. Ed. (1980)), in the form of lyophilized formulations or compositions, or aqueous solutions. Pharmaceutically acceptable carriers are generally nontoxic to recipients at the dosages and concentrations employed, and include, but are not limited to: buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride; benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g. Zn-protein complexes); and/or non-ionic surfactants such as polyethylene glycol (PEG).
The formulations or compositions to be used for in vivo administration are generally sterile. Sterility may be readily accomplished, e.g., by filtration through sterile filtration membranes.
In some embodiments, any one or more of the linker polypeptides, compositions, or pharmaceutical formulations described herein is for use in therapy, such as in preparing a medicament for treating or preventing a disease or disorder in a subject, such as cancer. In some embodiments, any one or more of the linker polypeptides, compositions, or pharmaceutical formulations described herein is for use in a method of treating a cancer, comprising, for example, administering the linker polypeptide or pharmaceutical composition to a subject in need thereof
In some embodiments, a method of treating or preventing a disease or disorder in subject is provided, comprising administering to a subject any of the linker polypeptides or pharmaceutical compositions described herein. In some embodiments, the disease or disorder is a cancer, e.g., a solid tumor. In some embodiments, the cancer is a melanoma, a colorectal cancer, a breast cancer, a pancreatic cancer, a lung cancer, a prostate cancer, an ovarian cancer, a cervical cancer, a gastric or gastrointestinal cancer, a lymphoma, a colon or colorectal cancer, an endometrial cancer, a thyroid cancer, or a bladder cancer. The cancer (e.g., any of the foregoing cancers) may have one or more of the following features: being PD-L1-positive; being metastatic; being unresectable; being mismatch repair defective (MMRd); and/or being microsatellite-instability high (MSI-H). In some embodiments, the cancer is a TGFβR-expressing cancer. In some embodiments, the cancer is a TGFβ-expressing cancer. In some embodiments, the cancer is a TGFβ-dependent cancer. A cancer is considered dependent on a growth factor such as TGFβ if cells of the cancer grow significantly more slowly in the absence of the growth factor than in its presence.
In some embodiments, a method of boosting T regulatory cells and/or reducing inflammation or autoimmune activity is provided comprising administering a linker polypeptide to an area of interest, e.g., an area of inflammation. The linker polypeptide for use in such methods may comprise an IL-2 polypeptide sequence. In some embodiments, a method of treating an autoimmune and/or inflammatory disease is provided, comprising administering a linker polypeptide to an area of interest, e.g., an area of inflammation or autoimmune activity. The linker polypeptide for use in such methods may comprise an IL-2 polypeptide sequence. These methods take advantage of the ability of certain cytokines at relatively low levels to stimulate T regulatory cells, which can exert anti-inflammatory effects and reduce or suppress autoimmune activity.
The linker polypeptides in any of the foregoing methods and uses may be delivered to a subject using any suitable route of administration. In some embodiments, the linker polypeptide is delivered parenterally. In some embodiments, the linker polypeptide is delivered intravenously.
A linker polypeptide provided herein can be used either alone or in combination with other agents in a therapy. For instance, a linker polypeptide provided herein may be co-administered with at least one additional therapeutic agent.
Such combination therapies noted above encompass combined administration (where two or more therapeutic agents are included in the same or separate formulations), and separate administration, in which case, administration of the linker polypeptide provided herein can occur prior to, simultaneously, and/or following, administration of the additional therapeutic agent and/or adjuvant.
Linker polypeptides would be formulated, dosed, and administered in a fashion consistent with good medical practice. Factors for consideration in this context include the particular disorder being treated, the particular mammal being treated, the clinical condition of the individual patient, the cause of the disorder, the site of delivery of the agent, the method of administration, the scheduling of administration, and other factors known to medical practitioners. In some embodiments, the linker polypeptide is optionally formulated with one or more agents currently used to prevent or treat the disorder in question. The effective amount of such other agents depends on the amount of linker polypeptide present in the formulation, the type of disorder or treatment, and other factors discussed above. These are generally used in the same dosages and with administration routes as described herein, or about from 1 to 99% of the dosages described herein, or in any dosage and by any route that is empirically/clinically determined to be appropriate.
For the prevention or treatment of disease, the appropriate dosage of an linker polypeptide (when used alone or in combination with one or more other additional therapeutic agents) will depend on the type of disease to be treated, the type of linker polypeptide, the severity and course of the disease, whether the linker polypeptide is administered for preventive or therapeutic purposes, previous therapy, the patient's clinical history and response to therapeutic agents (e.g., antibodies, immunoconjugates, cytokines) that share common elements and/or sequences with the linker polypeptide, and the discretion of the attending physician. The linker polypeptide is suitably administered to the patient at one time or over a series of treatments.
Linker polypeptides or precursors thereof may be produced using recombinant methods and compositions. In some embodiments, an isolated nucleic acid encoding a linker polypeptide described herein is provided. Such nucleic acid may encode an amino acid sequence comprising active domains (including, for example, an immunoglobulin antigen-binding domain, a receptor-binding domain, and/or a cytokine polypeptide sequence), a pharmacokinetic modulator, a linker, and an inhibitory polypeptide sequence, and any other polypeptide components of the linker polypeptide that may be present. In a further embodiment, one or more vectors (e.g., expression vectors) comprising such nucleic acid are provided. In a further embodiment, a host cell comprising such nucleic acid is provided. In some such embodiments, a host cell comprises (e.g., has been transformed with) a vector comprising a nucleic acid that encodes a linker polypeptide according to the disclosure. In some embodiments, the host cell is eukaryotic, e.g., a Chinese Hamster Ovary (CHO) cell or lymphoid cell (e.g., Y0, NS0, Sp20 cell). In some embodiments, a method of making a linker polypeptide disclosed herein is provided, wherein the method comprises culturing a host cell comprising a nucleic acid encoding the linker polypeptide, as provided above, under conditions suitable for expression of the linker polypeptide, and optionally recovering the antibody from the host cell (or host cell culture medium).
For recombinant production of a linker polypeptide, nucleic acid encoding the linker polypeptide, e.g., as described above, is prepared and/or isolated (e.g., following construction using synthetic and/or molecular cloning techniques) and inserted into one or more vectors for further cloning and/or expression in a host cell. Such nucleic acid may be readily prepared and/or isolated using known techniques.
Suitable host cells for cloning or expression of linker polypeptide-encoding vectors include prokaryotic or eukaryotic cells described herein. For example, a linker polypeptide may be produced in bacteria, in particular when glycosylation is not needed. For expression of polypeptides in bacteria, see, e.g., U.S. Pat. Nos. 5,648,237, 5,789,199, and 5,840,523. After expression, the linker polypeptide may be isolated from the bacterial cell paste in a soluble fraction and can be further purified.
In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for linker polypeptide-encoding vectors, including fungi and yeast strains whose glycosylation pathways have been “humanized,” resulting in the production of polypeptides with a partially or fully human glycosylation pattern. See Gerngross, Nat. Biotech. 22:1409-1414 (2004), and Li et al., Nat. Biotech. 24:210-215 (2006).
Suitable host cells for the expression of linker polypeptides are also derived from multicellular organisms (plants, invertebrates, and vertebrates). Examples of invertebrate cells include insect cells. Numerous baculoviral strains have been identified which may be used in conjunction with insect cells, particularly for transfection of Spodoptera frugiperda cells.
Plant cell cultures can also be utilized as hosts. See, e.g., U.S. Pat. Nos. 5,959,177, 6,040,498, 6,420,548, 7,125,978, and 6,417,429.
Vertebrate cells may also be used as hosts. For example, mammalian cell lines that are adapted to grow in suspension may be useful. Other examples of useful mammalian host cell lines are monkey kidney CV1 line transformed by SV40 (COS-7); human embryonic kidney line (293 or 293 cells as described, e.g., in Graham et al., J. Gen Virol. 36:59 (1977)); baby hamster kidney cells (BHK); mouse sertoli cells (TM4 cells as described, e.g., in Mather, Biol. Reprod. 23:243-251 (1980); monkey kidney cells (CV1); African green monkey kidney cells (VERO-76); human cervical carcinoma cells (HELA); canine kidney cells (MDCK; buffalo rat liver cells (BRL 3A); human lung cells (W138); human liver cells (Hep G2); mouse mammary tumor (MMT 060562); TRI cells, as described, e.g., in Mather et al., Annals N.Y. Acad. Sci. 383:44-68 (1982); MRC 5 cells; and FS4 cells. Other useful mammalian host cell lines include Chinese hamster ovary (CHO) cells, including DHFR− CHO cells (Urlaub et al., Proc. Natl. Acad. Sci. USA 77:4216 (1980)); and myeloma cell lines such as Y0, NS0 and Sp2/0.
This description and exemplary embodiments should not be taken as limiting. For the purposes of this specification and appended claims, unless otherwise indicated, all numbers expressing quantities, percentages, or proportions, and other numerical values used in the specification and claims, are to be understood as being modified in all instances by the term “about,” to the extent they are not already so modified. “About” indicates a degree of variation that does not substantially affect the properties of the described subject matter, e.g., within 10%, 5%, 2%, or 1%. Accordingly, unless indicated to the contrary, the numerical parameters set forth in the following specification and attached claims are approximations that may vary depending upon the desired properties sought to be obtained. At the very least, and not as an attempt to limit the application of the doctrine of equivalents to the scope of the claims, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques.
The following examples are provided to illustrate certain disclosed embodiments and are not to be construed as limiting the scope of this disclosure in any way.
Coding sequences for all protein domains including linker sequences were synthesized as an entire gene (Genscript, NJ). All synthetic genes were designed to contain a coding sequence for an N-terminal signal peptide (to facilitate protein secretion), a 5′ Kozak sequence, and unique restriction sites at the 5′ and 3′ ends. These genes were then directionally cloned into the mammalian expression vector pcDNA3.1 (Invitrogen, Carlsbad, CA). Examples of fusion protein constructs are listed in Table 4.
Different mammalian cell expression systems were used to produce fusion proteins (ExpiCHO-S™, Expi293F™, Freestyle CHO-S™, and Freestyle 293™, Life Technologies). Briefly, expression constructs were transiently transfected into cells following manufacturer's protocol and using reagents provided in respective expression kits. Fusion proteins were then expressed and secreted into the cell culture supernatant. Samples were collected from the production cultures every day, and cell density and viability were assessed. Protein expression titers and product integrity in cell culture supernatants were analyzed by SDS-PAGE to determine the optimal harvesting time. Cell culture supernatants were generally harvested between 4 and 12 days at culture viabilities of typically >75%. On day of harvest, cell culture supernatants were cleared by centrifugation and vacuum filtration before further use.
Fusion proteins were purified from cell culture supernatants in either a one-step or two-step procedure. Briefly, Fc-domain containing proteins were purified by Protein A affinity chromatography (HiTrap MabSelect SuRe, GE Healthcare). In some cases, Fc-domain containing proteins were further purified by size exclusion chromatography (HPLC SEC5 300A 7.8×300 mm, 5 m, part #5190-2526, Agilent Bio or HiLoad 26/60 Superdex 200). His-tagged proteins were first purified on a Nickel-agarose column (Ni-Penta™ Agarose 6 Fast Flow column, PROTEINDEX™), followed by size exclusion chromatography (HPLC SEC5 300A 7.8×300 mm, 5 m part #5190-2526, Agilent Bio). All purified samples were buffer-exchanged and concentrated by ultrafiltration to a typical concentration of >1 mg/mL. Purity and homogeneity (typically >90%) of final samples were assessed by SDS-PAGE under reducing and non-reducing conditions. Purified proteins were aliquoted and stored at −80° C. until further use.
Recombinant MMP9 (R&D Systems) was first activated with p-aminophenylmercuric acetate, and this activated protease or equivalent amount of activating solution without the protease was used to digest or mock-digest the fusion protein overnight (18-22 hr) at 37° C. Cleavage assays were set up in TCNB buffer: 50 mM Tris, 10 mM CaCl2, 150 mM NaCl, 0.05% Brij-35 (w/v), pH 7.5. Digested protein was aliquoted and stored at −80° C. prior to testing. Aliquots of digests were subsequently analyzed by SDS-PAGE followed by Western blotting to evaluate the extent of cleavage. Digests were also assessed in functional assays such as HEK-Blue Interleukin reporter assays. As shown in
Untreated and digested fusion proteins were evaluated for cleavage products by Western blot. The following antibodies were used: goat anti-mouse IL-2 polyclonal antibody (AF-402-NA; R&D systems), anti-human IL-2 antibody (Invitrogen, cat #MA5-17097, mouse IgG1), and rabbit anti-human IL-15 polyclonal antibody (ThermoFisher, cat #PA5-79466). Detection was performed using either a donkey anti-goat HRP-conjugated antibody, goat anti-rabbit HRP-conjugated antibody, or goat anti-mouse HRP-conjugated (Jackson Immuno Research, West Grove, PA), and developed using the SuperSignal West Femto Maximum sensitivity detection reagent (ThermoFisher) following the manufacturer's recommendations.
An ELISA assay was developed to detect and quantify prodrug fusion proteins comprising IL-2 and IL-2Ra moieties. Wells of a 96-well plate were coated overnight with 100 μL of a rat anti-mouse IL-2 monoclonal antibody (JES6-1A12; ThermoFisher) at 1 mg/mL in PBS. After washing, wells are blocked with TBS/0.05% Tween 20/1% BSA, then fusion proteins and/or unknown biological samples were added for 1 hour at room temperature. After washing, an anti-mouse IL-2Ra biotin-labelled detection antibody (BAF2438, R&D systems) was added and binding was detected using Ultra Strepavidin HRP (ThermoFisher). The ELISA plate was developed by adding the chromogenic tetramethylbenzidine substrate (Ultra TMB, ThermoFisher). The reaction was stopped by addition of 0.5 M H2SO4, and the absorbance was read at 450-650 nm.
IL-2 and IL-15 are members of the four a helix bundle family of cytokines and share the same signaling receptors IL2-Rβ and common 7 chain. Hence, activity of these cytokines was measured using the same reporter cell line HEK Blue IL-2 (Invivogen, San Diego). HEK-Blue™ IL-2 cells were specifically designed to monitor the activation of the JAK-STAT pathway induced by ligand binding to the IL2-Rβ and common 7 chain receptors. Stimulation with the appropriate cytokines triggered the JAK/STAT5 pathway and induced secreted embryonic alkaline phosphatase (SEAP) production. SEAP was readily monitored using QUANTI-Blue™, a SEAP detection medium. These cells responded to human/murine IL-2 and IL-15. For the HEK Blue assay, untreated and digested samples were titrated and added to 50,000 HEK Blue cells per well in 200 μL medium in a 96-well plate and incubated at 37° C. in 5% CO2 for 20-24 hours. The following day, levels of SEAP were measured by adding 20 μL of cell supernatant to QuantiBlue reagent, followed by 1-3 hours of incubation at 37° C. and reading absorbance at 630 nm.
A series of peptides comprising an MMP cleavable site with or without the addition of a targeting sequence were synthesized and conjugated to the fluorophore EDANS (5-((2-Aminoethyl)amino)naphthalene-1-sulfonic acid) (custom synthesis, ThermoFisher). Table 5 shows the list of peptides. These peptides were then tested for their ability to bind ECM proteins such as heparin, fibronectin and collagen which are found in abundance in tumor stroma. In Table 5, the bold text shows MMP cleavage site, the underlined text shows retention motif (targeting sequence) when present, and the italicized asterisk (*) shows Edans fluorophore conjugated to peptide.
FHRRIKA
GPLGVRG-*
KLWVLPK
GPLGVRG-*
All binding assays were set up in 10 mM TrisHCl, pH 7.5 and/or 10 mM TrisHCl, pH 6. Peptides (20 μM) were incubated on a shaker for 2 hours at room temperature with agarose cross-linked to heparin or control agarose beads (Sigma and Pierce respectively). The beads were then washed 4 times and resuspended in 100 μL of binding buffer in a black 96-well plate. Peptide binding was quantified by measuring the fluorescence of samples using excitation/emission spectra of EDANS (Ex 340/Em 490).
For fibronectin and collagen binding peptide assays, streptavidin coupled magnetic beads (Mag Sepharose, Cytiva and Dynabeads, ThermoFisher, respectively) were first incubated with biotin-labelled fibronectin (Cytoskeleton) or biotin-labelled collagen IV (Prospec) for 1 hour with gentle shaking. Following multiple washes, the ECM-coated beads were then incubated with Edans Peptides (20 μM) for 2 hours at room temperature with shaking in neutral or acidic binding buffer. Beads were then washed and resuspended in 100 μL of binding buffer in a black 96-well plate. Peptide binding was quantified by measuring the fluorescence of samples using excitation/emission spectra of EDANS (Ex 340/Em 490).
A series of IL-2 and IL-15 fusion proteins comprising single or multiple targeting sequences in the linker regions or other locations were designed and successfully manufactured (Table 4 and
96-well plates were coated with 10 μg/mL of Heparin-BSA conjugate (provided by Dr. Mueller, Boerhinger Ingelheim) or control BSA for 18-22 hours at room temperature on shaker (350 rpm). After washing, wells are blocked with 2% milk powder in PBS-0.05% Tween 20 or PBS-0.05% Tween 20/1% BSA for 90 minutes. The fusion proteins were then titrated in either 2% milk powder in PBS-0.05% Tween 20 or 1% BSA/PBS-0.05% Tween 20, pH 7.5 and/or pH 6, and added for 2 hours at room temperature with shaking. After washing, an anti-mouse IL-2 biotin-labelled detection antibody (JES6-5H4, ThermoFisher), anti-6×-His Tag HRP conjugate antibody (Invitrogen, 1 mg/mL, cat #MA1-21315-HRP), or anti-human IgG HRP conjugate antibody (SouthernBiotech) was added, and binding was detected using Ultra Streptavidin HRP (ThermoFisher). The plate was developed by adding the chromogenic tetramethylbenzidine substrate (Ultra TMB, ThermoFisher). The reaction was stopped by addition of 0.5 M H2SO4, and the absorbance was read at 450-650 nm. IL-2 fusion proteins Construct Y and Construct CC at acidic pH bound heparin in a dose-dependent manner and with higher affinity than Construct B (
A similar plate-based assay was developed to interrogate binding of IL-2 fusion variants to fibronectin. 96-well plates were coated with fibronectin (4-10 μg/mL, Sigma) or control BSA for 18-22 hours at room temperature on shaker (350 rpm). After washing, wells were blocked with 2% milk powder in PBS-0.05% Tween 20 or protein-free blocking buffer (Pierce) for 90 min, then fusion proteins were titrated in blocking buffer-0.1% Tween 20, pH 7.5 and/or pH 6, and added for 1 hour at room temperature with shaking. After washing, an anti-mouse IL-2 biotin-labelled detection antibody (JES6-5H4, ThermoFisher) or anti-human IgG HRP conjugate antibody (SouthernBiotech) was added, and binding was detected using Ultra Streptavidin HRP (ThermoFisher). The plate was developed by adding the chromogenic tetramethylbenzidine substrate (Ultra TMB, ThermoFisher). The reaction was stopped by addition of 0.5 M H2SO4, and the absorbance was read at 450-650 nm. Construct EE preferentially bound fibronectin at acidic pH and showed dose-dependent binding, while no binding was observed at pH 7.5 (
To test binding to collagen, a pulldown assay using agarose cross-linked to collagen (Sigma) was performed. IL-2 fusion proteins were incubated with collagen-agarose or control agarose beads for 18-22 hours at 4° C. with gentle rotation in 1% BSA/PBS-0.05% Tween 20. After washing, proteins bound to the beads were eluted by resuspending beads in SDS sample buffer (Life Technologies). Bound proteins were then separated by SDS-PAGE on 4-12% BisTris gradient gel, followed by immunoblotting with goat anti-mouse IL-2 polyclonal antibody (AF-402-NA; R&D systems). Donkey anti-goat HRP-conjugated antibody was used for detection (Jackson Immuno Research, West Grove, PA), and the blot was developed using the SuperSignal West Femto Maximum sensitivity detection reagent (ThermoFisher) following the manufacturer's recommendations. The blot image is shown in
The levels of IL-2 fusion proteins present in tumors in vivo were assessed by utilizing fluorescently labelled proteins and real-time whole-body imaging. Non-cleavable Construct GGG and Construct DD were conjugated to Dylight 650 probe according to the manufacturer's protocol (Dylight 650 Antibody labeling kit, ThermoFisher). The conjugation did not significantly alter the proteins' binding to heparin. BALB/c mice were subcutaneously inoculated with EMT6 breast cancer syngeneic model, and when the average tumor volume reached 240 mm3, animals were randomized into 3 groups based on tumor volumes (n=2 mice per treatment group). Table 6 below shows the study design.
Following administration of a single dose of the labeled IL-2 fusion proteins to tumor-bearing mice, fluorescent images (excitation 640/emission 680 consistent with Dylight 650 probe ex/em spectra) were captured over 96 hours on an IVIS system (PerkinElmer, IVIS Lumina Series III) and are shown in
C57BL/6 mice were subcutaneously inoculated with B16F10 melanoma cells and when the average tumor volume reached on average 70-90 mm3, animals were randomized into 6 groups based on tumor volumes (n=8 mice per treatment group). Mice were dosed intravenously every 3 days (Q3D) for a total of 5 doses according to Table 7.
Tumor volumes were measured twice a week for the duration of the study. Mean tumor volume is shown in
The levels of full-length IL-2-IL-2Ra fusion proteins, IL-2, and IFN-7 were quantified in tumor samples collected during a pre-clinical efficacy study comparing a panel of retention linker IL-2 fusion drugs (see Example 10).
Tumors (n=3 per group) were collected 24 hours after the last dose injection, flash frozen, and stored at −80° C. until further processing. Tumor lysates were generated using tissue extraction reagent (ThermoFisher) supplemented with protease and phosphatase inhibitors. Standard techniques and protein concentrations were determined using the BCA assay (Pierce).
Lysates were tested with in-house developed ELISA (see Example 5) to measure full-length IL-2 fusion proteins (IL-2 capture/IL-2Ra detection). Results were normalized to 1 mg of tumor lysate and mean values are shown in
The equivalent serum samples (n=3 per group) were tested with in-house ELISA to quantify full-length IL-2 fusion drugs, and results are shown in
Inflammatory cytokine levels were measured in serum using a multiplex Luminex assay (Essential Th1/Th2 Cytokine 6-Plex Mouse ProcartaPlex™ Panel, cat #EPX060-20831-901, ThermoFisher). Low levels of TNF-α and IL-6 were detected (
C57BL/6 mice were subcutaneously inoculated with MC38 colorectal cancer cells. When the average tumor volume reached 70-90 mm3, animals were randomized into 10 groups based on tumor volumes (n 7 or 6 mice per treatment group). Mice were dosed intraperitoneally (IP) twice-weekly (BIW) for a total of 5 doses according to design shown in Table 8 below:
Tumor volumes were measured twice a week for the duration of the study. Mean tumor volume is shown in
On Day 16, animals were sacrificed, and tumors (n=3 per group) were collected 24 hours after the last dose injection, flash frozen, and stored at −80° C. until further processing. Tumor lysates were generated using tissue extraction reagent (ThermoFisher) supplemented with protease and phosphatase inhibitors and standard techniques, and protein concentrations were determined using the BCA assay (Pierce). Intratumoral levels of IFN-7 (IFNg), the main Th1 cytokine, were mostly elevated in groups treated with targeting constructed, compared to groups treated with parental non-targeting constructs, as shown in
C57BL/6 mice were subcutaneously inoculated with B16F10 melanoma cells. When the average tumor volume reached 70-90 mm3, animals were randomized into 5 groups based on tumor volumes (n=3 mice per treatment group). Mice were dosed twice intraperitoneally on Day 1 and Day 4 with select ODC-IL2 fusions. On Day 6, tumors were harvested and processed into single cell suspension using standard technique (Miltenyi method, which is a combination of enzymatic and mechanical dissociation). Single cell samples were cryopreserved at −80° C. prior to further processing. Upon thawing, cells were washed and stained for surface and intracellular targets, using the antibodies listed in Table 9.
Additional asymmetrical IL-2 Fc fusion proteins containing ECM targeting sequences and single or dual masks were manufactured, purified, and functionally characterized as previously described.
In order to assess the ability of fusion proteins to bind collagen, an image-based retention assay was performed. Fusion proteins were labeled with DyLight 650 Maleimide at reduced sulfhydryl groups following manufacturer's recommended procedure (ThermoFisher, Cat #62295). Fluorescently labeled fusion proteins were then mixed with bovine type I collagen (Advanced Biomatrix, TeloCol-10, catalog #5226) and 10×PBS buffer, pH 7.4 (Invitrogen, REFAM9624) to bring the sample mix to a neutral pH. The final concentrations of each component in mix are shown in Table 10 below.
5 μL of fusion protein-collagen mix was loaded to the inner well of ibidi u-Slide Angiogenesis (Uncoated, Part 81501) pretreated with gelatin solution (2% in H2O, Sigma, Cat #G1393-20ML). The slide was incubated at room temperature for 30 minutes to allow the fusion protein-collagen mix to form gel. Then, 50 μL of bovine type I collagen (1 mg/mL in 1×PBS) was loaded to the upper well of the slide. After the collagen gelled in the upper well, the slide was imaged using a BioTek Lionheart FX automated microscope. The fluorescence intensity of the inner well represented the amount of fusion protein present and retained in the collagen and was measured at excitation/emission 628/685 nm. LED intensity, integration time, and camera gain were adjusted to appropriate levels to avoid excessive exposure and saturating pixel intensities. Fluorescence intensity was measured over 66 hours and images were taken every 30 minutes at room temperature. The mean fluorescence intensity was calculated by Gen5 software and then normalized to the mean fluorescence intensity of the first image (T=0), which was set to 100%. The normalized mean fluorescence intensity over time showed that the fusion protein containing a collagen I binding site is retained in collagen gel to a greater extent than a non-targeting fusion protein (
This application claims the benefit of U.S. Provisional Patent Application No. 63/224,350, filed Jul. 21, 2021, which is incorporated herein by reference in its entirety for all purposes.
| Number | Date | Country | |
|---|---|---|---|
| 63224350 | Jul 2021 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/US22/73970 | Jul 2022 | WO |
| Child | 18416736 | US |
