US20230303649A1

US20230303649A1 - Modified il-2 polypeptides for treatment of inflammatory and autoimmune diseases

Info

Publication number: US20230303649A1
Application number: US17/861,180
Authority: US
Inventors: Bertolt Kreft; Vijaya Raghavan PATTABIRAMAN; Rubén ALVAREZ SANCHEZ; Magali MULLER; Jean-Philippe CARRALOT
Original assignee: Bright Peak Therapeutics AG
Current assignee: Bright Peak Therapeutics AG
Priority date: 2021-07-09
Filing date: 2022-07-09
Publication date: 2023-09-28
Also published as: US20230183331A1; KR20240034221A; WO2023281483A1; CA3222357A1; AU2022306974A1; WO2023281485A1

Abstract

The present disclosure relates to modified IL-2 polypeptides, compositions comprising modified IL-2 polypeptides, methods of making the same, and methods of using the modified IL-2 polypeptides for treatment of diseases including autoimmune diseases. In one aspect, the disclosure relates to the treatment of autoimmune diseases using the modified IL-2 polypeptides. In some embodiments, the disclosed IL-2 polypeptides exhibit enhanced binding to IL-2 receptor α and/or reduced binding to IL-2 receptor β. In another aspect, the modified IL-2 polypeptides exhibit enhanced ability to activate T regulatory cells compared to T effector cells.

Description

CROSS REFERENCE

This application claims the benefit of U.S. Provisional Application No. 63/219,995 filed Jul. 9, 2021, and of U.S. Provisional Application No. 63/219,989 filed Jul. 9, 2021, which applications are incorporated herein by reference in their entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML copy, created on Aug. 26, 2022, is named 94917-0051_729201US_SL.xml and is 67,717 bytes in size.

BACKGROUND

Interleukin-2 (IL-2) is a cytokine signaling molecule important in regulating the immune system. IL-2 is implicated in helping the immune system differentiate between foreign and endogenous cell types, thereby preventing the immune system from attacking a subject’s own cells. IL-2 accomplishes its activity through interactions with IL-2 receptors (IL-2R) expressed by lymphocytes. Through these binding interactions, IL-2 can modulate a subject’s populations of T-effector (T_eff) cells, natural killer (NK) cells, and regulatory T-cells (T_reg).
IL-2′s ability to regulate the immune system is driven at least partially by its different affinities for the IL-2R α subunit (CD25) and the IL-2R β subunit (CD122). Native IL-2 acts on resting lymphocytes via intermediate-affinity receptors consisting of IL-2R β and IL-2R γ subunits. Activated lymphocytes and T_reg cells additionally express the IL-2R α subunit, which combines with the β and γ subunits to form a receptor with high affinity for IL-2. When acting on the high affinity αβγ receptor, IL-2 can enhance the activation and proliferation of T_reg cells, thus regulating the subject’s immune response.
For these reasons, IL-2 has been used in the treatment of various diseases involving the immune system, both alone and in combination with other therapies. However, use of IL-2 as a treatment has been limited by toxicities, which include life threatening and sometimes fatal vascular leak syndrome, as well as by its short half-life, requiring dosing three times per day over eight days. There exists a need for improved IL-2 polypeptides with different selectivity for various IL-2 receptor subunits, for example, enhanced binding of the IL-2Rα to enhance therapeutic potential and minimize the risk of side effects of IL-2 therapies.

BRIEF SUMMARY

In one aspect, provided herein, is a modified interleukin-2 (IL-2) polypeptide, comprising:a modified IL-2 polypeptide, wherein the modified IL-2 polypeptide comprises up to seven natural amino acid substitutions, wherein the seven natural amino acid substitutions comprise amino acid substitutions at residues Y31, K35, and Q74; and wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO:1 as a reference sequence.
In another aspect, provided herein, is a modified IL-2 polypeptide, comprising: a modified IL-2 polypeptide, wherein the modified IL-2 polypeptide exhibits a binding affinity for the IL-2 receptor alpha subunit (IL-2Rα) which is between about 0.1 nM and about 100 nM, and wherein the modified IL-2 polypeptide exhibits a binding affinity for the IL-2 receptor beta subunit (IL-2Rβ) which is at least about 1000 nM.
Additional aspects and advantages of the present disclosure will become readily apparent to those skilled in this art from the following detailed description, wherein only illustrative embodiments of the present disclosure are shown and described. As will be realized, the present disclosure is capable of other and different embodiments, and its several details are capable of modifications in various obvious respects, all without departing from the disclosure. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. To the extent publications and patents or patent applications incorporated by reference contradict the disclosure contained in the specification, the specification is intended to supersede and/or take precedence over any such contradictory material.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawing (also “figure” and “FIG.” herein), of which:

FIG. 1 shows a synthetic scheme used to synthesize a modified IL-2 polypeptide as provided herein as a linear depsipeptide.

FIG. 2 shows a scheme for rearranging and folding a linear depsipeptide to provide a folded modified IL-2 polypeptide as provided herein.

FIG. 3 shows a scheme for producing a PEGylated modified IL-2 polypeptide as provided herein.

FIG. 4A shows mean fluorescence intensity (MFI) of STAT5 phosphorylation in T_eff cells by aldesleukin, composition A, and composition A1 at various concentrations.

FIG. 4B shows MFI of STAT5 phosphorylation in T_reg cells by aldesleukin, composition A, and composition A1 at various concentrations.

FIG. 4C shows EC50 values of STAT5 phosphorylation of a variety of T cell subtypes by modified IL-2 polypeptides provided herein.

FIG. 4D shows the EC50 values of STAT5 phosphorylation of a variety of T cell subtypes by modified IL-2 polypeptides compositions provided herein.

FIG. 5 shows binding affinities of composition A1 and aldesleukin to the IL-2Rα and IL-2Rβ subunits as determined by biolayer interferometry (BLI).

FIG. 6 shows pharmacokinetics of composition A1 administered subcutaneously to mice at 0.1 mg/kg or 0.3 mg/kg.

FIG. 7 shows the immuno-pharmacodynamic effect of composition A1 or aldesleukin on various lymphocyte populations at various time points after administration of the indicated doses. Top left graph shows T_reg %pSTAT5 positive cells; Top center graph shows T_eff %pSTAT5 positive cells; Top right graph shows NK %pSTAT5 positive cells; Middle left graph shows T_reg %Ki67 positive cells; Middle center graph shows T_eff %Ki67 positive cells; Middle right graph shows NK %Ki67 positive cells; Bottom left graph shows T_reg counts fold change versus baseline; Bottom center graph shows T_eff counts fold change versus baseline; Bottom right graph shows NK counts fold change versus baseline.

FIG. 8A shows an experimental design to assess composition A1′s ability to delay hypersensitivity to keyhole limpet hemocyanin in mice.

FIG. 8B shows ear thickness difference between the right ear (challenged with KLH) and the contralateral ear (injected with saline) reported in mm as a measure of swelling at 24, 48, 72 and 96 hrs. Performing a two-way ANOVA revealed a significant effect of time (F(4, 216)= 48.16; p<0.0001) and treatment (F(5, 54) = 13.74; p<0.0001), suggesting changes over time that were modulated by treatment by composition A1. Data is reported as mean ± SEM (n=10 per experimental group).

FIG. 8C shows ear thickness difference between the right ear (challenged with KLH) and the contralateral ear (injected with saline) reported as area under the curve (AUC) as a measure of overall swelling after challenge. Performing a one-way ANOVA revealed a significant effect of treatment (F(5, 54) = 12.59; p<0.0001), suggesting that this parameter was modulated by treatments. Multiple comparison with the Dunnett’s test vs vehicle showed that composition A1 significantly reduced ear swelling at all regimens (** p<0.01, **** p<0.0001). Data is reported as mean ± SEM (n=10 per experimental group).

DETAILED DESCRIPTION

The present disclosure relates to modified interleukin-2 (IL-2) polypeptides useful as therapeutic agents. Modified IL-2 polypeptides provided herein can be used as treatments for various diseases and disorders, including inflammatory or other autoimmune diseases. Such modified IL-2 polypeptides may display binding characteristics for the IL-2 receptor (IL-2R) that differ from wild-type IL-2 (SEQ ID NO:1) or aldesleukin (SEQ ID NO: 2). In one aspect, modified IL-2 polypeptides described herein have increased affinity for the IL-2R α complex. In some embodiments, the modified IL-2 polypeptides have an unmodulated affinity for the IL-2R βγ complex. In some embodiments, the modified IL-2 polypeptides have a reduced affinity for the IL-2R βγ complex. In some embodiments, the modified IL-2 polypeptides provided herein may comprise amino acid substitutions that enhance the binding affinity for the IL-2Rα receptor subunit. In some embodiments, the modified IL-2 polypeptides provided herein comprise amino acid substitutions that lower the modified IL-2 polypeptides affinity for the IL-2Rβ receptor subunit. In some embodiments, the modified IL-2 polypeptides have a biological activity of inducing fewer T-effector (T_eff) cells when administered in vivo compared to a wild type IL-2 or aldesleukin. In some embodiments, the modified IL-2 polypeptides provided herein have comparable ability (e.g., have an EC₅₀ no more than 10x greater, no more than 100x greater) to induce regulatory T-cells (T_reg) when administered in vivo compared to a wild type IL-2 or aldesleukin.
In some embodiments, the modified IL-2 polypeptides described herein contain modified amino acid residues. Such modifications can take the form of amino acid substitutions of a wild type IL-2 polypeptide such as the amino acid sequence of SEQ ID NO: 1, addition or deletion of amino acids from the sequence of SEQ ID NO: 1, or the addition of moieties to amino acid residues. In some embodiments, the modified IL-2 polypeptide described herein contains a deletion of the first amino acid from the sequence of SEQ ID NO: 1. In some embodiments, the modified IL-2 polypeptide described herein comprises a C125S substitution, using the sequence of SEQ ID NO: 1 as a reference sequence. In some embodiments, the modified IL-2 polypeptide described herein comprises substitutions at one or more residues selected from Y31, K35, Q74, and/or N88, wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO:1 as a reference sequence. These substitutions may be in combination with the C125S substitution and/or an N-terminal deletion, such as a deletion of the first amino acids from the sequence of SEQ ID NO:1. In some embodiments, the Y31 substitution is a Y31H substitution. In some embodiments, the K35 substitutions is a K35R substitution. In some embodiments, the Q74 substitution is a Q74P substitutions. In some embodiments, the N88 substitution is an N88D substitution. In some embodiments, the modified IL-2 polypeptide comprises a Y31H substitution, a K35R substitution, and a Q74P substitution. In some embodiments, the modified IL-2 polypeptide comprises a Y31H substitution, a K35R substitution, a Q74P substitution, and an N88D substitution. In some embodiments, the modified IL-2 polypeptide comprises a Y31H substitution, a K35S substitution, a Q74P substitution, and a C125S substitution. In some embodiments, the modified IL-2 polypeptide comprises a Y31H substitution, a K35S substitution, a Q74P substitution, a N88D substitution, and a C125S substitution.
In some embodiments, the modified IL-2 polypeptide is a synthetic polypeptide. In some embodiments, the modified IL-2 polypeptide is synthesized by α-ketoacid-hydroxylamine (KAHA) amide-forming ligation. In some embodiments, the modified IL-2 polypeptide comprises unnatural amino acids, such as homoserine, which are used during the KAHA ligation reaction to join multiple polypeptide fragments to synthesize the full-length modified IL-2 polypeptide. In some embodiments, these are the only unnatural amino acids in the modified IL-2 polypeptide. In some embodiments, the modified IL-2 polypeptide comprises norleucine (Nle) residue substitutions at one or more methionine residues present in wild type IL-2 or aldesleukin. In some embodiments, the modified IL-2 polypeptide comprises norleucine residues at positions 23, 39, and 46.
A modified IL-2 polypeptide as described herein can comprise one or more non-canonical amino acids (also referred to herein as “unnatural amino acids”). “Non-canonical” amino acids can refer to amino acid residues in D- or L-form that are not among the 20 canonical amino acids generally incorporated into naturally occurring proteins. In some embodiments, one or more amino acids of the modified IL-2 polypeptides are substituted with one or more non-canonical amino acids. Non-canonical amino acids include, but are not limited to N-alpha-(9-Fluorenylmethyloxycarbonyl)-L-azidolysine (Fmoc-L-Lys(N₃)-OH), N-alpha-(9-Fluorenylmethyloxycarbonyl)-L-biphenylalanine (Fmoc-L-Bip-OH), and N-alpha-(9-Fluorenylmethyloxycarbonyl)-O-benzyl-L-tyrosine (Fmoc-L-Tyr(Bzl)-OH, or their unprotected analogs.
Additionally, polymers may be added to modified IL-2 polypeptides. In some embodiments, the polymers are added in order to increase the half-life of the polypeptides. Such half-life extending polymers can be added to the N-terminus of the modified IL-2 polypeptides. The half-life extending polymers may be of any size, including up to about 6 kDa, up to about 30 kDa, or up to about 50 kDa. In some embodiments, the half-life extending polymers are PEG polymers.
In some embodiments, the modified IL-2 polypeptide comprises one or more amino acid substitutions or deletions selected from Table 1.

TABLE 1

WT IL-2 Residue Number^∗	WT IL-2 Residue	Substitutions or modification
1	A	Deletion
18	L	R, K
22	Q	N, H, K, Y, I, E
23	M	L, R, S, T, V, A
29	N	S
31	Y	H
35	K	R, E, D, Q
37	T	A, R
46	M	A
48	K	E, C
69	V	A
71	N	R
74	Q	P
81	R	A, G, S, T
85	L	V
86	I	V
88	N	A, D, E, F, G, H, I, M, Q, R, S, T, V, W
89	I	V
92	I	K, R
125	C	S, E, K, H, W, I, V, A
126	Q	A, C, D, E, F, G, H, I, K, L, M, N, R, S, T, Y
^∗Residue position numbering based on SEQ ID NO:1 as a reference sequence

In some embodiments, a modified IL-2 polypeptide provided herein comprises one or more amino acid substitutions selected from Table 2.

TABLE 2

WT IL-2 Residue Number^∗	WT IL-2 Residue	Mutations
18	L	R
22	Q	E
23	M	A
29	N	S
31	Y	H
35	K	R
37	T	A
39	M	A
42	F	(4-NH₂)-Phe
46	M	A
48	K	E
69	V	A
71	N	R
74	Q	P
80	L	F
81	R	D
85	L	V
86	I	V
88	N	D, Dgp (gp = O-(2-aminoethyl)-O′-(2-aminoethyl)octaethylene glycol)
89	I	V
92	I	F
126	Q	T
^∗Residue position numbering based on SEQ ID NO:1 as a reference sequence

In some embodiments, a modified IL-2 polypeptide provided herein comprises one or more polymers selected from Table 3. In some embodiments, the one or more polymer is covalently attached the N-terminus of the modified IL-2 polypeptide.

TABLE 3

Polymer Identifier	Polymer Structure	Molecular Weight
Formula A		~30 kDa
Formula B		~6 kDa
Formula C		~30 kDa
Formula D		~500 Da
Formula E		~11 kDa

The modified IL-2 polypeptides described herein may also be synthesized chemically rather than expressed as recombinant polypeptides. The modified IL-2 polypeptides can be made by synthesizing one or more fragments of the full-length modified IL-2 polypeptides, ligating the fragments together, and folding the ligated full-length polypeptide. In some embodiments, the modified IL-2 polypeptide comprises Y31H, K35R, Q74P, and C125S substitutions and optionally a PEG polymer covalently attached to the N-terminus of the modified IL-2 polypeptide. In some embodiments, the modified IL-2 polypeptide comprises Y31H, K35R, Q74P, N88D, and C125S substitutions and optionally a PEG polymer covalently attached to the N-terminus of the modified IL-2 polypeptide.
In some embodiments, the modified IL-2 polypeptides enhance regulatory T-cell (T_reg) cell proliferation or activation when administered to a subject. In some embodiments, the modified IL-2 polypeptides enhance T_reg proliferation or activation while sparing T-effector cells (T_eff) and/or natural killer (NK) cells when administered to a subject. In some embodiments, the modified IL-2 polypeptides increase Treg cells without substantially increasing CD8+ T cells and NK cells when administered to a subject.
The following description and examples illustrate embodiments of the present disclosure in detail. It is to be understood that this present disclosure is not limited to the particular embodiments described herein and as such can vary. Those of skill in the art will recognize that there are numerous variations and modifications of this present disclosure, which are encompassed within its scope.
Although various features of the present disclosure may be described in the context of a single embodiment, the features may also be provided separately or in any suitable combination. Conversely, although the present disclosure may be described herein in the context of separate embodiments for clarity, the present disclosure may also be implemented in a single embodiment.
The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.
All terms are intended to be understood as they would be understood by a person skilled in the art. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the disclosure pertains.
The following definitions supplement those in the art and are directed to the current application and are not to be imputed to any related or unrelated case, e.g., to any commonly owned patent or application. Although any methods and materials similar or equivalent to those described herein can be used in the practice for testing of the present disclosure, the preferred materials and methods are described herein. Accordingly, the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting.

I. Definitions

The terminology used herein is for the purpose of describing particular cases only and is not intended to be limiting. In this application, the use of the singular includes the plural unless specifically stated otherwise. As used herein, the singular forms “a”, “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise.
In this application, the use of “or” means “and/or” unless stated otherwise. The terms “and/or” and “any combination thereof” and their grammatical equivalents as used herein, can be used interchangeably. These terms can convey that any combination is specifically contemplated. Solely for illustrative purposes, the following phrases “A, B, and/or C” or “A, B, C, or any combination thereof” can mean “A individually; B individually; C individually; A and B; B and C; A and C; and A, B, and C.” The term “or” can be used conjunctively or disjunctively, unless the context specifically refers to a disjunctive use.
The term “about” or “approximately” can mean within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, “about” can mean within 1 or more than 1 standard deviation, per the practice in the art. Alternatively, “about” can mean a range of up to 20%, up to 15%, up to 10%, up to 5%, or up to 1% of a given value. Alternatively, particularly with respect to biological systems or processes, the term can mean within an order of magnitude, within 5-fold, or within 2-fold, of a value. Where particular values are described in the application and claims, unless otherwise stated the term “about” meaning within an acceptable error range for the particular value should be assumed.
As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps. It is contemplated that any embodiment discussed in this specification can be implemented with respect to any method or composition of the present disclosure, and vice versa. Furthermore, compositions of the present disclosure can be used to achieve methods of the present disclosure.
Reference in the specification to “some embodiments,” “an embodiment,” “one embodiment” or “other embodiments” means that a particular feature, structure, or characteristic described in connection with the embodiments is included in at least some embodiments, but not necessarily all embodiments, of the present disclosures. To facilitate an understanding of the present disclosure, a number of terms and phrases are defined below.
Referred to herein are polymers which are “attached” or “covalently attached” to residues of IL-2 polypeptides. As used herein, “attached” or “covalently attached” means that the polymer is tethered to the indicated residue, and such tethering can include a linking group (i.e., a linker). Thus, for a polymer “attached” or “covalently attached” to a residue, it is expressly contemplated that such linking groups are also encompassed.
Binding affinity refers to the strength of a binding interaction between a single molecule and its ligand/binding partner. A higher binding affinity refers to a higher strength bond than a lower binding affinity. In some instances, binding affinity is measured by the dissociation constant (K_D) between the two relevant molecules. When comparing K_D values, a binding interaction with a lower value will have a higher binding affinity than a binding interaction with a higher value. For a protein-ligand interaction, K_D is calculated according to the following formula:
$K_{D} = \frac{[L] [P]}{[L P]}$
where [L] is the concentration of the ligand, [P] is the concentration of the protein, and [LP] is the concentration of the ligand/protein complex.
Referred to herein are certain amino acid sequences (e.g., polypeptide sequences) which have a certain percent sequence identity to a reference sequence or refer to a residue at a position corresponding to a position of a reference sequence. Sequence identity is measured by protein-protein BLAST algorithm using parameters of Matrix BLOSUM62, Gap Costs Existence:11, Extension:1, and Compositional Adjustments Conditional Compositional Score Matrix Adjustment. This alignment algorithm is also used to assess if a residue is at a “corresponding” position through an analysis of the alignment of the two sequences being compared.
The term “pharmaceutically acceptable” refers to approved or approvable by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, including humans.
A “pharmaceutically acceptable excipient, carrier or diluent” refers to an excipient, carrier or diluent that can be administered to a subject, together with an agent, and which does not destroy the pharmacological activity thereof and is nontoxic when administered in doses sufficient to deliver a therapeutic amount of the agent.
A “pharmaceutically acceptable salt” suitable for the disclosure may be an acid or base salt that is generally considered in the art to be suitable for use in contact with the tissues of human beings or animals without excessive toxicity, irritation, allergic response, or other problem or complication. Such salts include mineral and organic acid salts of basic residues such as amines, as well as alkali or organic salts of acidic residues such as carboxylic acids. Specific pharmaceutical salts include, but are not limited to, salts of acids such as hydrochloric, phosphoric, hydrobromic, malic, glycolic, fumaric, sulfuric, sulfamic, sulfanilic, formic, toluenesulfonic, methanesulfonic, benzene sulfonic, ethane disulfonic, 2-hydroxyethyl sulfonic, nitric, benzoic, 2-acetoxybenzoic, citric, tartaric, lactic, stearic, salicylic, glutamic, ascorbic, pamoic, succinic, fumaric, maleic, propionic, hydroxymaleic, hydroiodic, phenylacetic, alkanoic such as acetic, HOOC-(CH₂)n-COOH where n is 0-4, and the like. Similarly, pharmaceutically acceptable cations include, but are not limited to sodium, potassium, calcium, aluminum, lithium and ammonium. Those of ordinary skill in the art will recognize from this disclosure and the knowledge in the art that further pharmaceutically acceptable salts include those listed by Remington’s Pharmaceutical Sciences, 17th ed., Mack Publishing Company, Easton, PA, p. 1418 ( 1985). In general, a pharmaceutically acceptable acid or base salt can be synthesized from a parent compound that contains a basic or acidic moiety by any conventional chemical method. Briefly, such salts can be prepared by reacting the free acid or base forms of these compounds with a stoichiometric amount of the appropriate base or acid in an appropriate solvent.
Ranges provided herein are understood to be shorthand for all of the values within the range. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50, as well as all intervening decimal values between the aforementioned integers such as, for example, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, and 1.9. With respect to sub-ranges, “nested sub-ranges” that extend from either end point of the range are specifically contemplated. For example, a nested sub-range of an exemplary range of 1 to 50 may comprise 1 to 10, 1 to 20, 1 to 30, and 1 to 40 in one direction, or 50 to 40, 50 to 30, 50 to 20, and 50 to 10 in the other direction.
The term “subject” refers to an animal which is the object of treatment, observation, or experiment. By way of example only, a subject includes, but is not limited to, a mammal, including, but not limited to, a human or a non-human mammal, such as a non-human primate, bovine, equine, canine, ovine, or feline.
Certain formulas and other illustrations provided herein depict triazole reaction products resulting from azide-alkyne cycloaddition reactions. While such formulas generally depict only a single regioisomer of the resulting triazole formed in the reaction, it is intended that the formulas encompass both resulting regioisomers. Thus, while the formulas depict only a single regioisomer (e.g.
it is intended that the other regioisomer (e.g.
is is also encompassed.
The term “optional” or “optionally” denotes that a subsequently described event or circumstance can but need not occur, and that the description includes instances where the event or circumstance occurs and instances in which it does not.
The term “moiety” refers to a specific segment or functional group of a molecule. Chemical moieties are often recognized chemical entities embedded in or appended to a molecule.
As used herein “an N-terminus with glutaric acid and 0.5 kDa azido PEG” refers to a modification to an N-terminal amine of an IL-2 polypeptide provided herein with a structure of
While described as having an azide functionality, it is contemplated that the azide can be replaced with an alternative conjugation handle in each case wherein a modified IL-2 polypeptide comprises the N-terminus with glutaric acid and 0.5 kDa azido PEG.
“Composition A” refers to a modified IL-2 polypeptide of SEQ ID NO: 3 which comprises an N-terminus with glutaric acid and 0.5 kDa azido PEG.
“Composition A1” refers to the reaction product formed between composition A and a DBCO containing PEG having a molecular weight of about 30 kDa.
“Composition B” refers to a modified IL-2 polypeptide of SEQ ID NO: 4 which comprises an N-terminus with glutaric acid and 0.5 kDa azido PEG.
“Composition B1” refers to the reaction product formed between composition B and a DBCO containing PEG having a molecular weight of about 30 kDa..
“Composition C” refers to a modified IL-2 polypeptide of SEQ ID NO: 5 which comprises an N-terminus with glutaric acid and 0.5 kDa azido PEG.
“Composition C1” refers to the reaction product formed between composition B and a DBCO containing PEG having a molecular weight of about 30 kDa.
“Composition D” refers to a modified IL-2 polypeptide of SEQ ID NO: 6 which comprises an N-terminus with glutaric acid and 0.5 kDa azido PEG.
“Composition D1” refers to the reaction product formed between composition D and a DBCO containing PEG having a molecular weight of about 30 kDa.
“Composition E” refers to a modified IL-2 polypeptide of SEQ ID NO: 7 which comprises an N-terminus with glutaric acid and 0.5 kDa azido PEG.
“Composition E1” refers to the reaction product formed between composition E and a DBCO containing PEG having a molecular weight of about 30 kDa.
“Composition F” refers to a modified IL-2 polypeptide of SEQ ID NO: 8 which comprises an N-terminus with glutaric acid and 0.5 kDa azido PEG.
As used herein, “conjugation handle” refers to a reactive group capable of forming a bond upon contacting a complementary reactive group. In some instances, a conjugation handle preferably does not have a substantial reactivity with other molecules which do not comprise the intended complementary reactive group. Non-limiting examples of conjugation handles, their respective complementary conjugation handles, and corresponding reaction products can be found in the table below. While table headings place certain reactive groups under the title “conjugation handle” or “complementary conjugation handle,” it is intended that any reference to a conjugation handle can instead encompass the complementary conjugation handles listed in the table (e.g., a trans-cyclooctene can be a conjugation handle, in which case tetrazine would be the complementary conjugation handle). In some instances, amine conjugation handles and conjugation handles complementary to amines are less preferable for use in biological systems owing to the ubiquitous presence of amines in biological systems and the increased likelihood for off-target conjugation.

Table of Conjugation Handles
Conjugation Handle	Complementary Conjugation Handle	Reaction Product
Sulfhydryl	alpha-halo-carbonyl (e.g., bromoacetamide), alpha-beta unsaturated carbonyl (e.g., maleimide, acrylamide)	thioether
Azide	alkyne (e.g., terminal alkyne, substituted cyclooctyne (e.g., dibenzocycloocytne (DBCO), difluorocyclooctyne, bicyclo[6.1.0]nonyne, etc.) )	triazole
Phosphine	Azide/ester pair	amide
Tetrazine	trans-cyoclooctene	dihydropyridaz ine
Amine	Activated ester (e.g., N-hydroxysuccinimide ester, pentaflurophenyl ester)	amide
isocyanate	amine	urea
epoxide	amine	alkyl-amine
hydroxyl amine	aldehyde, ketone	oxime
hydrazide	aldehyde, ketone	hydrazone
potassium acyl trifluoroborate	O-substituted hydroxylamine (e.g., O-carbamoylhydroxylamine)	amide

As used herein, the term “number average molecular weight” (Mn) means the statistical average molecular weight of all the individual units in a sample, and is defined by Formula (1):
$Formula (1)$
where M_i is the molecular weight of a unit and N_i is the number of units of that molecular weight.
As used herein, the term “weight average molecular weight” (Mw) means the number defined by Formula (2):
$Formula (2)$
where M_i is the molecular weight of a unit and N_i is the number of units of that molecular weight.
As used herein, “peak molecular weight” (Mp) means the molecular weight of the highest peak in a given analytical method (e.g. mass spectrometry, size exclusion chromatography, dynamic light scattering, analytical centrifugation, etc.).

II. Description

In one aspect, described herein, is a modified IL-2 polypeptide which is biased in favor of activation of T_reg cells compared to T_eff cells. In one aspect, described herein is a modified polypeptide that comprises a modified interleukin-2 (IL-2) polypeptide, wherein the modified IL-2 polypeptide comprises one or more amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises at least one amino acid substitutions at residues selected from Y31, K35, Q74, and N88, wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO:1 as a reference sequence. In some embodiments, the modified IL-2 polypeptide comprises amino acid substitutions at each of residues Y31, K35, and Q74, wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO:1 as a reference sequence. In some embodiments, the modified IL-2 polypeptide comprises the amino acid substitutions of Y31H, K35R, and Q74P. In some embodiments, the modified IL-2 polypeptide comprises amino acid substitutions at each of residues Y31, K35, Q74, and N88, wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO:1 as a reference sequence. In some embodiments, the modified IL-2 polypeptide comprises the amino acid substitutions of Y31H, K35R, Q74P, and N88D. In some embodiments, the modified IL-2 polypeptide does not comprise any additional substitutions that have a substantial impact on the binding of the modified IL-2 polypeptide to the IL-2Rα receptor.
In another aspect, described herein is a modified polypeptide, comprising: a modified interleukin-2 (IL-2) polypeptide, wherein the modified IL-2 polypeptide exhibits substantially lower ability to activate T_eff cells than an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2. In some embodiments, the modified IL-2 polypeptide retains the ability to activate T_reg cells. In some embodiments, the modified IL-2 polypeptide exhibits an enhanced ability to activate T_reg cells compared to an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2 In some embodiments, the modified IL-2 polypeptide exhibits at least about 4x lower dissociation constant (K_d) of IL-2Rα than an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2. In some embodiments, the modified IL-2 polypeptide exhibits a 2-fold to 10-fold lower dissociation constant (K_d) of IL-2Rα than an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2.

Binding Affinity

In one aspect, described herein is a modified IL-2 polypeptide that exhibits a greater affinity for IL-2 receptor α subunit than an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2. In some embodiments, the affinity to IL-2 receptor a subunit is measured by dissociation constant (K_d). As used herein, the phrase “the K_d of the modified IL-2 polypeptide/IL-2 receptor α subunit” means the dissociation constant of the binding interaction of the modified IL-2 polypeptide and CD25.
In some embodiments, the K_d of the modified IL-2 polypeptide/IL-2 receptor α subunit is less than 10 nM. In some embodiments the K_d of the modified IL-2 polypeptide/IL-2 receptor α subunit is less than 10 nM, less than 7.5 nM, less than 5 nM, less than 4 nM, or less than 3 nM. In some embodiments, the K_d of the modified IL-2 polypeptide/IL-2 receptor α subunit between about 1 nM and 0.1 nM. In some embodiments, the K_d of the modified IL-2 polypeptide/IL-2 receptor α subunit between about 10 nM and about 0.1 nM. In some embodiments, the K_d of the modified IL-2 polypeptide/IL-2 receptor α subunit between about 10 nM and about 1 nM. In some embodiments, the K_d of the modified IL-2 polypeptide/IL-2 receptor α subunit between about 7.5 nM and about 0.1 nM. In some embodiments, the K_d of the modified IL-2 polypeptide/IL-2 receptor α subunit between about 7.5 nM and about 1 nM. In some embodiments, the K_d of the modified IL-2 polypeptide/IL-2 receptor α subunit between about 5 nM and about 0.1 nM. In some embodiments, the K_d of the modified IL-2 polypeptide/IL-2 receptor α subunit between about 5 nM and about 1 nM. In some embodiments, the K_d is measured by surface plasmon resonance.
In some embodiments, the modified IL-2 polypeptide that exhibits at least about a 10%, 50%, 100%, 250%, or 500% greater affinity for IL-2 receptor α subunit than an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2. In some embodiments, the modified IL-2 polypeptide exhibits at most about a 500%, 750%, or 1000% greater affinity for IL-2 receptor α subunit than an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2.
In some embodiments, the modified IL-2 polypeptide exhibits about 1.5-fold to about 10-fold greater affinity for IL-2 receptor α subunit than an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2.
In some embodiments, the modified IL-2 polypeptide exhibits substantially the same binding affinity for the IL-2Rα as compared to an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2. In some embodiments, the modified IL-2 polypeptide exhibits a K_d with IL-2Rα that is within about 2-fold, about 4-fold, about 6-fold, about 8-fold, or about 10-fold of the K_d between an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2 and IL-2Rα .
In some embodiments, the modified IL-2 polypeptide exhibits reduced affinity for the IL-2 receptor β subunit (IL-2Rβ) as compared to an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2. In some embodiments, the modified IL-2 polypeptide exhibits at least about 10-fold, at least about 25-fold, at least about 50-fold, at least about 100-fold, or at least about 500-fold fold lower affinity for the IL-2Rβ. In some embodiments, the modified IL-2 polypeptide exhibits at least about 100-fold lower affinity for IL-2Rβ. In some embodiments, the modified IL-2 polypeptide exhibits substantially no affinity for IL-2Rβ. In some embodiments, the affinity is measured as the dissociation constant K_d (e.g., a lower affinity correlating with a higher dissociation constant).
In some embodiments, the modified IL-2 polypeptide exhibits a binding affinity for IL-2Rβ which is at least 500 nM, at least 1000 nM, at least 5000 nM, at least 10000 nM, at least 50000 nM, or at least 100000 nM. In some embodiments, the modified IL-2 polypeptide exhibits substantially no binding affinity for IL-2Rβ.
In some embodiments, the modified IL-2 polypeptide exhibits an affinity for IL-2Rα which is at least about 30-fold greater, at least about 50-fold grater, at least about 75-fold greater, at least about 100-fold greater, at least about 500-fold greater, or at least about 1000-fold greater than for IL-2Rβ. In some embodiments, the modified IL-2 polypeptide exhibits an affinity for IL-2Rα which is at least about 100-fold greater than for IL-2Rβ. In some embodiments, the modified IL-2 polypeptide exhibits an affinity for IL-2Rα which is at least about 1000-fold greater than for IL-2Rβ.

Biological Activity

In some embodiments, a modified IL-2 polypeptide described herein is capable of expanding a regulatory T-cell (T_reg) cell population. In some embodiments, a modified IL-2 polypeptide described herein spares expansion of effector T-cells (T_eff).
In some embodiments, a modified IL-2 polypeptide has a half maximal effective concentration (EC₅₀) for activation of T_reg cells that at most moderately reduced compared to an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2. In some embodiments, activation of T_reg cells is measured by assessing change in STAT5 phosphorylation in a population of T cells when in contact with the modified IL-2 polypeptide. In some embodiments, a T_reg cell is identified by being CD4⁺, CD25+ and FoxP3⁺. In some embodiments, a T_reg cell is identified by also showing elevated expression of CD25 (CD25^Hi). In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells of at most about 100 nM, at most about 75 nM, at most about 50 nM, at most about 40 nM, at most about 35 nM, at most about 30 nM, or at most about 25 nM. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells of at most about 50 nM, at most about 40 nM, at most about 35 nM, at most about 30 nM, or at most about 25 nM, at most about 20 nM, at most about 15 nM, at most about 10 nM, or at most about 5 nM. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells of at most about 100 nM. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells of at most about 50 nM. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells of at most about 25 nM. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells of from about 0.1 nM to about 100 nM, from about 1 nM to about 100 nM, from about 0.1 nM to about 50 nM, from about 1 nM to about 50 nM, from about 0.1 nM to about 25 nM, from about 1 nM to about 25 nM, from about 0.1 nM to about 10 nM, or from about 1 nM to about 10 nM.
In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells that is at most 2-fold, at most 5-fold, at most 10-fold, at most 20-fold, at most 50-fold, at most 100-fold, at most 200-fold, at most 500-fold, or at most 1000-fold greater compared to an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells that is at most 2-fold greater. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells that is at most 5-fold greater. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells that is at most 10-fold greater. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells that is at most 50-fold greater. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells that is at most 100-fold greater. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells that is at most 200-fold greater. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells that is at most 500-fold greater. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_reg cells that is at most 1000-fold greater.
In some embodiments, a modified IL-2 polypeptide has a half maximal effective concentration (EC₅₀) for activation of T_eff cells that is substantially greater compared to an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2. In some embodiments, the T_eff cell is 1, 2, or 3 of a CD8 T_eff cell (e.g., CD8⁺), a Naive CD8 cell (e.g., CD8⁺, CD45RA+), or a CD4 Con cell (e.g., CD4⁺, FoxP3^-), or any combination thereof. In some embodiments, activation of cells is measured by assessing change in STAT5 phosphorylation in a population of T cells when in contact with the modified IL-2 polypeptide. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_eff cells of at least about 10 nM, at least about 50 nM, at least about 100 nM, at least about 500 nM, at least about 1000 nM, at least about 2000 nM, at least about 3000 nM, at least about 4000 nM, or at least about 5000 nM. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_eff cells of at least about 100 nM. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_eff cells of at least about 500 nM. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_eff cells of at least about 1000 nM. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_eff cells of at least about 5000 nM. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_eff cells of at least 10-fold, at least 20-fold, at least 50-fold, at least 100-fold, at least 500-fold, or at least 1000-fold greater compared to an IL-2 polypeptide of SEQ ID NO: 1 and/or SEQ ID NO: 2. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_eff cells of at least 10-fold greater. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_eff cells of at least 50-fold greater. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_eff cells of at least 100-fold greater. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_eff cells of at least 500-fold greater. In some embodiments, the modified IL-2 polypeptide has an EC₅₀ for activation of T_eff cells of at least 1000-fold greater.
In some embodiments, the modified IL-2 polypeptide exhibits a substantially greater ability to activate T_reg cells compared to T_eff cells. In some embodiments, a ratio of EC50 for activation of a T_eff cell type over EC50 for activation of a T_reg cell type is at least 10, at least 20, at least 50, at least 100, at least 150, or at least 200. In some embodiments, a ratio of EC50 for activation of a T_eff cell type over EC50 for activation of a T_reg cell type is at least 100. In some embodiments, a ratio of EC50 for activation of a T_eff cell type over EC50 for activation of a T_reg cell type is at least 200. In some embodiments, a ratio of EC50 for activation of a T_eff cell type over EC50 for activation of a T_reg cell type is at least 300. In some embodiments, a ratio of EC50 for activation of a T_eff cell type over EC50 for activation of a T_reg cell type is at least 500. In some embodiments, a ratio of EC50 for activation of a T_eff cell type over EC50 for activation of a T_reg cell type is at least 1000.
In some embodiments, the level of activation is measured after about 0.5 h to about 1 h after incubation with the modified IL-2 polypeptide (e.g., 0.5 h to 1h before fixing the cells for in in vitro experiment).
In some embodiments, a modified IL-2 polypeptide described herein comprises a covalently attached polymer for half-life extension. In some embodiments, the modified IL-2 polypeptide comprises a covalently attached polymer for plasma or serum half-life extension. In some embodiments, a plasma or serum half-life of the modified IL-2 polypeptide with polymer attached is at least 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, or 10-fold longer compared to a plasma or serum half-life of a wild-type IL-2 polypeptide (SEQ ID NO 1) or aldesleukin (SEQ ID NO: 2) without a polymer attached.
In some embodiments, a plasma or serum half-life of a modified IL-2 polypeptide described herein is at least 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, or 10-fold longer compared to a plasma or serum half-life of the modified IL-2 polypeptide without the half-life extending polymer.

Site-Specific Modifications

In some embodiments, a modified IL-2 polypeptide described herein comprises one or more modifications at one or more amino acid residues. In some embodiments, the residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO: 1 as a reference sequence. In some embodiments, the residue position numbering of the modified IL-2 polypeptide is based on a wild-type human IL-2 polypeptide as a reference sequence.
Modifications to the polypeptides described herein encompass amino acid substitutions, addition of various functionalities, deletion of amino acids, addition of amino acids, or any other alteration of the wild-type version of the protein or protein fragment. Functionalities which may be added to polypeptides include polymers, linkers, alkyl groups, detectable molecules such as chromophores or fluorophores, reactive functional groups, or any combination thereof. In some embodiments, functionalities are added to individual amino acids of the polypeptides. In some embodiments, functionalities are added site-specifically to the polypeptides.
In one aspect, provided herein is a modified IL-2 polypeptide comprising one or more amino acid substitutions. In some embodiments, the amino acid substitutions affect the binding properties of the modified IL-2 polypeptide to IL-2 receptor subunits (e.g. alpha, beta, or gamma subunits) or to IL-2 receptor complexes (e.g. IL-2 receptor αβγ complex or βγ complex). In some embodiments, the amino acid substitutions are at positions on the interface of binding interactions between the modified IL-2 polypeptide and an IL-2 receptor subunit or an IL-2 receptor complex. In some embodiments, the amino acid substitutions cause an increase in affinity for the IL-2 receptor αβγ complex or alpha subunit. In some embodiments, the amino acid substitutions cause a decrease in affinity for the IL-2 receptor βγ complex or beta subunit.
In one aspect, provided herein is a modified IL-2 polypeptide comprising: a modified IL-2 polypeptide comprising natural amino acid substitutions relative to WT IL-2 (SEQ ID NO: 1). In some embodiments, the modified IL-2 polypeptide comprises up to seven natural amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises up to six amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises up to five amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises up to four amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises up to three amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises from three to seven, three to six, three to five, three to four, four to seven, four to six, four to five, five to seven, five to six, or six to seven natural amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises at least one, at least two, at least three, at least four, at least five, or at least six amino acid substitutions.
In some embodiments, a modified IL-2 polypeptide provided herein comprises natural amino acid substitutions at at least one of Y31, K35, Q74, and N88D wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO: 1 as a reference sequence. In some embodiments, the modified IL-2 polypeptide comprises natural amino acid substitutions at at least two of Y31, K35, Q74, and N88. In some embodiments, the modified IL-2 polypeptide comprises natural amino acid substitutions at at least three of Y31, K35, Q74, and N88. In some embodiments, the modified IL-2 polypeptide. In some embodiments, the modified IL-2 polypeptide comprises natural amino acid substitutions at each of Y31, K35, Q74, and N88. In some embodiments, the modified IL-2 polypeptide comprises the amino acid substitutions Y31H, K35R, Q74P, and N88D. In some embodiments, the modified IL-2 polypeptide further comprises an optional C125 substitution (e.g., C125S or C125A). In some embodiments, the modified IL-2 polypeptide further comprises an optional A1 deletion or substitution of residue A1. In some embodiments, the modified IL-2 polypeptide further comprises an optional A1 deletion.
In some embodiments, a modified IL-2 polypeptide provided herein comprises a Y31 substitution wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO:1 as a reference sequence. In some embodiments, the Y31 substitution is for an aromatic amino acid. In some embodiments, the Y31 substitution is for a basic amino acid. In some embodiments, the basic amino acid is weakly basic. In some embodiments, the Y31 substitution is selected from Y31F, Y31H, Y31W, Y31R, and Y31K. In some embodiments, the Y31 substitution is Y31H.
In some embodiments, a modified IL-2 polypeptide provided herein comprises a K35 substitution, wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO:1 as a reference sequence. In some embodiments, the K35 substitution is for a basic amino acid. In some embodiments, the K35 substitution is for a positively charged amino acid. In some embodiments, the K35 substitution is K35R, K35E, K35D, or K35Q. In some embodiments, the K35 substitution is K35R.
In some embodiments, a modified IL-2 polypeptide provided herein comprises a Q74 substitution, wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO:1 as a reference sequence. In some embodiments, the Q74 substitution is a cyclic amino acid. In some embodiments, the cyclic amino acid comprises a cyclic group covalently attached to the alpha carbon and the nitrogen attached to the alpha carbon. In some embodiments, the Q74 substitution is Q74P.
In some embodiments, a modified IL-2 polypeptide provided herein comprises a N88 substitution, wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO:1 as a reference sequence. In some embodiments, the N88 substitution is a charged amino acid residue. In some embodiments, the N88 substitution is a negatively charged amino acid residue. In some embodiments, the N88 substitution is N88D or N88E. In some embodiments, the N88 substitution is N88D or N88E. In some embodiments, the N88 substitution is N88D.
In some embodiments, a modified IL-2 polypeptide comprises a C125 substitution, wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO:1 as a reference sequence. In some embodiments, the C125 substitution stabilizes the modified IL-2 polypeptide. In some embodiments, the C125 substitution does not substantially alter the activity of the modified IL-2 polypeptide. In some embodiments, the modified IL-2 polypeptide comprises a C125S substitution. In some embodiments, the modified IL-2 polypeptide comprises a C125A substitution.
In some embodiment, a modified IL-2 polypeptide comprises a modification at residue A1, wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ I DNO: 1 as a reference sequence. In some embodiments, the modification is an A1 deletion.
In some embodiments, the modified IL-2 polypeptide comprises additional amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises an additional amino acid substitution that has an effect on binding to the IL-2 receptor alpha subunit or αβγ complex. In some embodiments, the modified IL-2 polypeptide comprises an additional amino acid substitution that has an effect on binding to the IL-2 receptor beta subunit or βγ complex. In some embodiments, the modified IL-2 polypeptide comprises at least one additional amino acid substitution selected from Table 1. In some embodiments, the modified IL-2 polypeptide comprises at least one amino acid substitution at residue E15, N29, N30, T37, K48, V69, N71, N88, I89, or I92. In some embodiments, the modified IL-2 polypeptide comprises at least one amino acid substitution at residue E15, N29, N30, T37, K48, V69, N71, I89, or I92. In some embodiments, the modified IL-2 polypeptide comprises 1, 2, 3, or 4 natural amino acid substitutions at residues selected from E15, N29, N30, T37, K48, V69, N71, N88, I89, or I92. n some embodiments, the modified IL-2 polypeptide comprises 1, 2, 3, or 4 natural amino acid substitutions at residues selected from E15, N29, N30, T37, K48, V69, N71, I89, or I92. In some embodiments, the modified IL-2 polypeptide comprises 1 natural amino acid substitutions at residues selected from E15, N29, N30, T37, K48, V69, N71, N88, I89, or I92. In some embodiments, the modified IL-2 polypeptide comprises 2 In some embodiments, the modified IL-2 polypeptide comprises up to 2 natural amino acid substitutions at residues selected from E15, N29, N30, T37, K48, V69, N71, N88, I89, or I92. In some embodiments, the modified IL-2 polypeptide comprises up to 3 natural amino acid substitutions at residues selected from E15, N29, N30, T37, K48, V69, N71, N88, I89, or I92. In some embodiments, the additional amino acid substitution comprises E15A, E15G, or E15S. In some embodiments, the additional amino acid substitution comprises N29S. In some embodiments, the additional amino acid substitution comprises N30S. In some embodiments, the additional amino acid substitution comprises T37A or T37R. In some embodiments, the additional amino acid substitution comprises K48E. In some embodiments, the additional amino acid substitution comprises V69A. In some embodiments, the additional amino acid substitution comprises N71R. In some embodiments, the additional amino acid substitution comprises N88A, N88D, N88E, N88F, N88G, N88H, N88I, N88M, N88Q, N88R, N88S, N88T, N88V, or N88W. In some embodiments, the additional amino acid substitution comprises N88D. In some embodiments, the additional amino acid substitution comprises I89V. In some embodiments, the additional amino acid substitution comprises I92K or I92R.
In some embodiments, a modified IL-2 polypeptide provided herein comprises substitutions at Y31, K35, Q74, and optionally C125S. In some embodiments, the modified IL-2 polypeptide does not comprise any additional substitutions which substantially affect binding to the IL-2 receptor alpha subunit or αβγ complex. In some embodiments, the modified IL-2 polypeptide does not comprise an additional amino acid substitution that has an effect on binding to the IL-2 receptor beta subunit or βγ complex In some embodiments, the modified IL-2 polypeptide does not comprise any additional natural amino acid substitutions selected from positions identified in Table 1. In some embodiments, the modified IL-2 polypeptide does not comprise any additional amino acid substitutions selected from Table 1. In some embodiments, the modified IL-2 polypeptide does not comprise any additional natural amino acid substitutions at residues E15, N29, N30, T37, K48, V69, N71, N88, I89, or I92. In some embodiments, the modified IL-2 polypeptide does not comprise any additional amino acid substitutions at residues E15, N29, N30, T37, K48, V69, N71, N88, I89, or I92. In some embodiments, the modified IL-2 polypeptide does not have a V69 substitution. In some embodiments, the modified IL-2 polypeptide does not have a V69A substitution. In some embodiments, the modified IL-2 polypeptide does not have a K48 substitution. In some embodiments, the modified IL-2 polypeptide does not have a K48E substitution. In some embodiments, the modified IL-2 polypeptide does not comprise a substitution at V69 or K48. In some embodiments, the modified IL-2 polypeptide does not comprise a substitution at either of V69 or K48. In some embodiments, the modified IL-2 polypeptide does not comprise a V69A or K48E substitution. In some embodiments, the modified IL-2 polypeptide does not comprise either a V69A or K48E substitution.
In some embodiments, a modified IL-2 polypeptide provided herein comprises substitutions at Y31, K35, Q74, N88, and optionally C125S. In some embodiments, the modified IL-2 polypeptide does not comprise any additional substitutions which substantially affect binding to the IL-2 receptor alpha subunit or αβγ complex. In some embodiments, the modified IL-2 polypeptide does not comprise an additional amino acid substitution that has an effect on binding to the IL-2 receptor beta subunit or βγ complex. In some embodiments, the modified IL-2 polypeptide does not comprise any additional natural amino acid substitutions selected from positions identified in Table 1. In some embodiments, the modified IL-2 polypeptide does not comprise any additional amino acid substitutions selected from Table 1. In some embodiments, the modified IL-2 polypeptide does not comprise any additional natural amino acid substitutions at residues E15, N29, N30, T37, K48, V69, N71, I89, or I92. In some embodiments, the modified IL-2 polypeptide does not comprise any additional amino acid substitutions at residues E15, N29, N30, T37, K48, V69, N71, I89, or I92. In some embodiments, the modified IL-2 polypeptide does not have a V69 substitution. In some embodiments, the modified IL-2 polypeptide does not have a V69A substitution. In some embodiments, the modified IL-2 polypeptide does not have a K48 substitution. In some embodiments, the modified IL-2 polypeptide does not have a K48E substitution. In some embodiments, the modified IL-2 polypeptide does not comprise a substitution at V69 or K48. In some embodiments, the modified IL-2 polypeptide does not comprise a substitution at either of V69 or K48. In some embodiments, the modified IL-2 polypeptide does not comprise a V69A or K48E substitution. In some embodiments, the modified IL-2 polypeptide does not comprise either a V69A or K48E substitution.
In some embodiments, a modified IL-2 polypeptide provided herein comprises an N-terminal deletion. In some embodiments, the N-terminal deletion is of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more amino acids. In some embodiments, the N-terminal deletion is of at least 1 amino acid. In some embodiments, the N-terminal deletion is of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids. In some embodiments, the N-terminal deletion is from 1 to 15 amino acids. In some embodiments, the N-terminal deletion is a deletion of a single amino acid (e.g., an A1 deletion of SEQ ID NO: 1).
A modified IL-2 polypeptide as described herein can comprise one or more unnatural amino acids. “Unnatural” amino acids can refer to amino acid residues in D- or L-form that are not among the 20 canonical amino acids generally incorporated into naturally occurring proteins. In some embodiments, one or more amino acids of the modified IL-2 polypeptides are substituted with one or more unnatural amino acids. Unnatural amino acids include, but are not limited to L-azidolysine and L-biphenylalanine.
Exemplary unnatural amino acids also include homoserine, norleucine, p-acetyl-L-phenylalanine, p-iodo-L-phenylalanine, p-propargyloxyphenylalanine, p-propargyl-phenylalanine, L-3-(2-naphthyl) alanine, 3-methyl-phenylalanine, tri-O-acetyl-GlcNAcp-serine, L-Dopa, fluorinated phenylalanine, isopropyl-L-phenylalanine, p-azido-L-phenylalanine, p-acyl-L-phenylalanine, p-benzoyl-L-phenylalanine, p-Boronophenylalanine, p-bromophenylalanine, p-amino-L-phenylalanine, isopropyl-L-phenylalanine, an analogue of a tyrosine amino acid; an analogue of a glutamine amino acid; an analogue of a phenylalanine amino acid; an analogue of a serine amino acid; an analogue of a threonine amino acid; a β-amino acid; a cyclic amino acid other than proline or histidine; an aromatic amino acid other than phenylalanine, tyrosine or tryptophan; or a combination thereof. In some embodiments, the unnatural amino acids are selected from β-amino acids, homoamino acids, and cyclic amino acids. In some embodiments, the unnatural amino acids comprise β-alanine, β-aminopropionic acid, piperidinic acid, aminocaprioic acid, aminoheptanoic acid, aminopimelic acid, desmosine, diaminopimelic acid, N^α-ethylglycine, N^α-ethylaspargine, isodesmosine, allo-isoleucine, N^α-methylglycine, N^α-methylisoleucine, N^α-methylvaline, γ-carboxyglutamate, N^α-acetylserine, N^α-formylmethionine, 3-methylhistidine, and/or other similar amino acids.
In some embodiments, the unnatural amino acid substitutions provided herein can be incorporated into an IL-2 polypeptide in addition to any combination of natural amino acid substitutions provided herein, unless otherwise specified. For example, where a modified IL-2 polypeptide comprising, for example, Y31H, K35R, and Q74P natural amino acid substitutions is described, it is expressly contemplated that the modified IL-2 polypeptide can also comprise unnatural amino acid substitutions (e.g., Hse41, Hse71, Hse104, Nle23, Nle39, and Nle46). As another example, where a modified IL-2 polypeptide provided herein is described as having Y31H, K35R, Q74P, and N88D natural amino acid substitutions, the modified IL-2 polypeptide can further comprise unnatural amino acid substitutions (e.g., Hse41, Hse71, Hse104, Nle23, Nle39, and Nle46). In particular, any combination of natural amino acid substitutions present in a recombinant modified IL-2 polypeptide provided herein can also be incorporated into a synthetic version of the modified IL-2 polypeptide (e.g., the corresponding modified IL-2 polypeptide containing, for example, Hse41, Hse71, Hse104, Nle23, Nle39, and Nle46).
In one aspect, disclosed herein is a modified IL-2 polypeptide comprising one or more unnatural amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises at least two unnatural amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises at least one amino acid substitution at a residue selected from Y31, K35, Q74, and N88, wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO:1 as a reference sequence. In some embodiments, the modified IL-2 polypeptide comprises a homoserine (Hse) residue located in any one of residues 36-45. In some embodiments, the modified IL-2 polypeptide comprises a Hse residue located in any one of residues 61-81. In some embodiments, the modified IL-2 polypeptide comprises a Hse residue located in any one of residues 94-114. In some embodiments, the modified IL-2 polypeptide comprises 1, 2, 3, or more Hse residues. In some embodiments, the modified IL-2 polypeptide comprises Hse41, Hse71, Hse104, or a combination thereof. In some embodiments, the modified IL-2 polypeptide comprises Hse41, Hse71, and Hse104. In some embodiments, the modified IL-2 polypeptide comprises at least two amino acid substitutions, wherein the at least two amino acid substitutions are selected from (a) a homoserine (Hse) residue located in any one of residues 36-45; (b) a homoserine residue located in any one of residues 61-81; and (c) a homoserine residue located in any one of residues 94-114. In some embodiments, the modified IL-2 polypeptide comprises Hse41 and Hse71. In some embodiments, the modified IL-2 polypeptide comprises Hse41 and Hse104. In some embodiments, the modified IL-2 polypeptide comprises Hse71 and Hse104. In some embodiments, the modified IL-2 polypeptide comprises Hse41. In some embodiments, the modified IL-2 polypeptide comprises Hse71. In some embodiments, the modified IL-2 polypeptide comprises Hse104. In some embodiments, the modified IL-2 polypeptide comprises 1, 2, 3, or more norleucine (Nle) residues. In some embodiments, the modified IL-2 polypeptide comprises a Nle residue located in any one of residues 18-28. In some embodiments, the modified IL-2 polypeptide comprises one or more Nle residues located in any one of residues 34-50. In some embodiments, the modified IL-2 polypeptide comprises a Nle residue located in any one of residues 20-60. In some embodiments, the modified IL-2 polypeptide comprises three Nle substitutions. In some embodiments, the modified IL-2 polypeptide comprises Nle23, Nle39, and Nle46. In some embodiments, the modified IL-2 polypeptide comprises SEQ ID NO: 3. In some embodiments, the modified IL-2 polypeptide comprises SEQ ID NO: 3 with an A1 deletion.
In some embodiments, a modified IL-2 polypeptide provided herein comprises an amino acid sequence of any one of SEQ ID NOs: 3-43 provided in Table 7. In some embodiments, the modified IL-2 polypeptide comprises an amino acid sequence at least 85% identical to the sequence of any one of SEQ ID NOs: 3-43. In some embodiments, the modified IL-2 polypeptide comprises an amino acid sequence at least 85% identical to the sequence of any one of SEQ ID NOs: 3-43, wherein each residue in the reference amino sequence which is substituted relative to SEQ ID NO: 1 is retained. In some embodiments, the modified IL-2 polypeptide comprises an amino acid sequence of SEQ ID NO: 3. In some embodiments, the modified IL-2 polypeptide comprises an amino acid sequence at least 85% identical to the sequence of SEQ ID NO: 3. In some embodiments, the modified IL-2 polypeptide comprises an amino acid sequence at least 85%, at least 90%, at least 95%, or at least 98% identical to the sequence of SEQ ID NO: 3, wherein each residue which is substituted in SEQ ID NO: 3 relative to SEQ ID NO: 1 is retained. In some embodiments, the modified IL-2 polypeptide comprises an amino acid sequence of SEQ ID NO: 4. In some embodiments, the modified IL-2 polypeptide comprises an amino acid sequence at least 85% identical to the sequence of SEQ ID NO: 4, wherein each residue which is substituted in SEQ ID NO: 4 relative to SEQ ID NO: 1 is retained.
In some embodiments, a modified IL-2 polypeptide described herein comprises at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to SEQ ID NO: 3. In some embodiments, a modified IL-2 polypeptide described herein comprises at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to SEQ ID NO: 4. In some embodiments, the sequence identity is measured by protein-protein BLAST algorithm using parameters of Matrix BLOSUM62, Gap Costs Existence:11, Extension:1, and Compositional Adjustments Conditional Compositional Score Matrix Adjustment.
In some embodiments, a modified IL-2 polypeptide described herein comprises at least 3, at least 4, at least 5, at least 6, at least 7, or at least 9 amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises 3 to 9 amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises 3 or 4 amino acid substitutions, 3 to 5 amino acid substitutions, 3 to 6 amino acid substitutions, 3 to 7 amino acid substitutions, 3 to 9 amino acid substitutions, 4 or 5 amino acid substitutions, 4 to 6 amino acid substitutions, 4 to 7 amino acid substitutions, 4 to 9 amino acid substitutions, 5 or 6 amino acid substitutions, 5 to 7 amino acid substitutions, 5 to 9 amino acid substitutions, 6 or 7 amino acid substitutions, 6 to 9 amino acid substitutions, or 7 to 9 amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises 3 amino acid substitutions, 4 amino acid substitutions, 5 amino acid substitutions, 6 amino acid substitutions, 7 amino acid substitutions, or 9 amino acid substitutions. In some embodiments, the modified IL-2 polypeptide comprises at most 4 amino acid substitutions, 5 amino acid substitutions, 6 amino acid substitutions, 7 amino acid substitutions, or 9 amino acid substitutions. In some embodiments, one or more of the amino acid substitutions are selected from Table 1. In some embodiments, one or more of the amino acid substitutions are selected from Table 2.
In some embodiments, the modified IL-2 polypeptide contains a substitution for modified natural amino acid residues which can be used for attachment of additional functional groups which can be used to facilitate conjugation reaction or attachment of various payloads to the modified IL-2 polypeptide (e.g., polymers). The substitution can be for a naturally occurring amino acid which is more amenable to attachment of additional functional groups (e.g., aspartic acid/asparagine cysteine, glutamic acid/glutamine, lysine, serine, threonine, or tyrosine), a derivative of a modified version of any naturally occurring amino acid, or any unnatural amino acid (e.g., an amino acid containing a desired reactive group, such as a CLICK chemistry reagent such as an azide, alkyne, etc.). Non-limiting examples of modified natural amino acid residues include the modified lysine, glutamic acid, aspartic acid, and cysteine provided below:
wherein each n is an integer from 1-30. Other examples of natural amino acids which can be similarly modified include those with heteroatoms capable of easily forming a bond with a suitable group to link the polymeric group to the amino acid (e.g., tyrosine, serine, threonine). These non-limiting examples of modified amino acid residues can be used at any location at which it is desirable to add an additional functionality (e.g., a polymer or additional polypeptide) to the modified IL-2 polypeptide.
In some embodiments, the modified IL-2 polypeptide comprises a modification of a terminal residue (e.g., the N-terminal residue or the C-terminal residue) which comprises a polymer. In some embodiments, the modification to the terminal residue comprises the attachment of a conjugation handle to the terminal residue of the modified IL-2 polypeptide. In some embodiments, the conjugation handle is attached to the modified IL-2 polypeptide through the N-terminal amino group or the C-terminal carboxyl group of the modified IL-2 polypeptide. In some embodiments, the conjugation handle is attached to the modified IL-2 polypeptide through the N-terminal amino group of the modified IL-2 polypeptide. In some embodiments, the conjugation handle is attached to the N-terminal amino group of the modified IL-2 polypeptide through a glutaryl-amino-PEG linker. In some embodiments, the conjugation handle is attached to the N-terminal amino group of the modified IL-2 polypeptide through an adduct having a structure
wherien each n is independently an integer from 1-30 (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30), and wherein X is a conjugation handle (e.g., an azide or other conjugation handle provided herein, such as a DBCO group). In some embodiments, the modified IL-2 polypeptide will comprise the adduct above, but the conjugation handle X is replaced with a reaction product of the conjugation handle and a complementary conjugation handle (e.g., a 1,2,3 triazole) linking the modified IL-2 polypeptide to an additional moiety (e.g., a larger polymer or an additional polypeptide). In some embodiments, the N-terminal amino group of the modified IL-2 polypeptide comprises an adduct having a structure
In some embodiments, a modified IL-2 polypeptide is linked with an additional polypeptide. In some embodiments, the modified IL-2 polypeptide and the additional polypeptide form a fusion polypeptide. In some embodiments, the modified IL-2 polypeptide and the additional polypeptide are conjugated together. In some embodiments, the additional polypeptide comprises an antibody or binding fragment thereof. In some embodiments, the antibody comprises a humanized antibody, a murine antibody, a chimeric antibody, a bispecific antibody, any fragment thereof, or any combination thereof. In some embodiments, the antibody is a monoclonal antibody or any fragment thereof (e.g., an antigen binding fragment).
In some embodiments, the modified IL-2 polypeptide is not conjugated to an additional polypeptide. In some embodiments, the modified IL-2 polypeptide is not conjugated to an antibody. In some embodiments, the modified IL-2 polypeptide is not conjugated to an anti-TNFα antibody.

Polymers

In some embodiments, a herein described modified IL-2 polypeptide comprises one or more polymers covalently attached thereon. In some embodiments, the described modified IL-2 polypeptide comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more polymers covalently attached to the modified IL-2 polypeptide. In some embodiments, the described modified IL-2 polypeptide comprises a polymer covalently attached to the N-terminus of the IL-2 polypeptide. The polymers provided herein may attached directly to a residue of the modified IL-2 polypeptide, may be attached through a small linking group (e.g., attached through a reaction with a conjugation handle incorporated into the modified IL-2 polypeptide).
The polymer as provided herein can be attached at any desired residue of the IL-2 polypeptide. In some embodiments, it is preferable that the polymer be attached at a residue which does not impact binding of the IL-2 polypeptide with the IL-2 receptor or a specific IL-2 receptor subunit (e.g., the IL-2 receptor alpha subunit). In some embodiments, the polymer is attached at or near the N-terminus of the modified IL-2 polypeptide. In some embodiments, the polymer is attached to the N-terminus of the modified IL-2 polypeptide. In some embodiments, the N-terminus is residue A1 of the IL-2 polypeptide, wherein residue position numbering is based on SEQ ID NO: 1 as a reference sequence. In some embodiments, the N-terminus is residue P2 of the IL-2 polypeptide, wherein residue position numbering is based on SEQ ID NO: 1 as a reference sequence (e.g., the modified IL-2 polypeptide comprises a deletion of residue A1 from the sequence). In some embodiments, the polymer is attached at a residue position which blocks or diminished binding of the modified IL-2 polypeptide with the IL-2 receptor beta subunit. Such residues positions are provided in U.S. Pat. Publication No. 20200231644A1, which is hereby incorporated by reference as if set forth herein in its entirety, and include, for example, residue positions K8, K9, L12, E15, H16, L19, D20, Q22, M23, N26, D84, N88, E95, and Q126.
In some embodiments, the polymer comprises a water-soluble polymer. In some embodiments, the water-soluble polymer comprises poly(alkylene oxide), polysaccharide, poly(vinyl pyrrolidone), poly(vinyl alcohol), polyoxazoline, poly(acryloylmorpholine), or a combination thereof. In some embodiments, the water-soluble polymer is poly(alkylene oxide). In some embodiments, the water-soluble polymer is polysaccharide. In some embodiments, the water-soluble polymer is poly(ethylene oxide).
In some embodiments, a modified IL-2 polypeptide described herein comprises a polymer covalently attached to the N-terminus of the IL-2 polypeptide. In some embodiments, the modified IL-2 polypeptide comprises a second polymer covalently attached thereto. In some embodiments, the modified IL-2 polypeptide comprises a second and a third polymer covalently attached thereto.
In some embodiments, the attached polymer such as the polymer has a weight average molecular weight of about 6,000 Daltons to about 50,000 Daltons. In some embodiments, the polymer has a weight average molecular weight of about 6,000 Daltons to about 10,000 Daltons, about 6,000 Daltons to about 30,000 Daltons, about 6,000 Daltons to about 50,000 Daltons, about 10,000 Daltons to about 30,000 Daltons, about 10,000 Daltons to about 50,000 Daltons, or about 30,000 Daltons to about 50,000 Daltons. In some embodiments, the polymer has a weight average molecular weight of about 6,000 Daltons, about 10,000 Daltons, about 30,000 Daltons, or about 50,000 Daltons. In some embodiments, the polymer has a weight average molecular weight of at least about 6,000 Daltons, about 10,000 Daltons, or about 30,000 Daltons. In some embodiments, the polymer has a weight average molecular weight of at most about 10,000 Daltons, about 30,000 Daltons, or about 50,000 Daltons.
In some embodiments, the attached polymer such as the polymer attached to the N-terminus has a weight average molecular weight of about 120 Daltons to about 1,000 Daltons. In some embodiments, the polymer has a weight average molecular weight of about 120 Daltons to about 250 Daltons, about 120 Daltons to about 300 Daltons, about 120 Daltons to about 400 Daltons, about 120 Daltons to about 500 Daltons, about 120 Daltons to about 1,000 Daltons, about 250 Daltons to about 300 Daltons, about 250 Daltons to about 400 Daltons, about 250 Daltons to about 500 Daltons, about 250 Daltons to about 1,000 Daltons, about 300 Daltons to about 400 Daltons, about 300 Daltons to about 500 Daltons, about 300 Daltons to about 1,000 Daltons, about 400 Daltons to about 500 Daltons, about 400 Daltons to about 1,000 Daltons, or about 500 Daltons to about 1,000 Daltons. In some embodiments, the polymer has a weight average molecular weight of about 120 Daltons, about 250 Daltons, about 300 Daltons, about 400 Daltons, about 500 Daltons, or about 1,000 Daltons. In some embodiments, the polymer has a weight average molecular weight of at least about 120 Daltons, about 250 Daltons, about 300 Daltons, about 400 Daltons, or about 500 Daltons. In some embodiments, the polymer has a weight average molecular weight of at most about 250 Daltons, about 300 Daltons, about 400 Daltons, about 500 Daltons, or about 1,000 Daltons.
In some embodiments, the attached polymer comprises a water-soluble polymer. In some embodiments, the water-soluble polymer comprises poly(alkylene oxide), polysaccharide, poly(vinyl pyrrolidone), poly(vinyl alcohol), polyoxazoline, poly(acryloylmorpholine), or a combination thereof. In some embodiments, the water-soluble polymer is poly(alkylene oxide) such as polyethylene glycol (i.e., polyethylene oxide). In some embodiments, the water-soluble polymer is polyethylene glycol. In some embodiments, the water-soluble polymer comprises modified poly(alkylene oxide).
In some embodiments, the modified poly(alkylene oxide) comprises one or more linker groups. In some embodiments, the one or more linker groups comprise bifunctional linkers such as an amide group, an ester group, an ether group, a thioether group, a carbonyl group and alike. In some embodiments, the one or more linker groups comprise an amide linker group. In some embodiments, the modified poly(alkylene oxide) comprises one or more spacer groups. In some embodiments, the spacer groups comprise a substituted or unsubstituted C₁-C₆ alkylene group. In some embodiments, the spacer groups comprise —CH₂—, —CH₂CH₂—, or —CH₂CH₂CH₂—. In some embodiments, the linker group is the product of a biorthogonal reaction (e.g., biocompatible and selective reactions). In some embodiments, the bioorthogonal reaction is a Cu(I)-catalyzed or “copper-free” alkyne-azide triazole-forming reaction, the Staudinger ligation, inverse-electron-demand Diels-Alder (IEDDA) reaction, “photo-click” chemistry, or a metal-mediated process such as olefin metathesis and Suzuki- Miyaura or Sonogashira cross-coupling. In some embodiments, the polymer is attached to the IL-2 polypeptide via click chemistry.
In some embodiments, a modified IL-2 polypeptide provided herein comprises a reaction group that facilitates the conjugation of the modified IL-2 polypeptide with a derivatized molecule or moiety such as an antibody and a polymer (e.g., an additional larger polymer). In some embodiments, the reaction group comprises one or more of: carboxylic acid derived active esters, mixed anhydrides, acyl halides, acyl azides, alkyl halides, N-maleimides, imino esters, isocyanates, and isothiocyanates. In some embodiments, the reaction group comprises azides. In some embodiments, the reaction group comprises alkynes.
In some embodiments, the polymer comprises a conjugation handle which can be used to further attach an additional moiety to the modified IL-2 polypeptide (e.g., the addition of an additional polypeptide, such as an antibody). Any suitable reactive group capable of reacting with a complementary reactive group attached to another moiety can be used as the conjugation handle.
In some embodiments, the polymer comprises a conjugation handle or a reaction product of a conjugation handle with a complementary conjugation handle. In some embodiments, the reaction product of the conjugation handle with the complementary conjugation handle results from a KAT ligation (reaction of potassium acyltrifluoroborate with hydroxylamine), a Staudinger ligation (reaction of an azide with a phosphine), a tetrazine cycloaddition (reaction of a tetrazine with a trans-cyclooctene), or a Huisgen cycloaddition (reaction of an alkyne with an azide). In some embodiments, the polymer comprises a reaction product of a conjugation handle with a complementary conjugation handle which was used to attach the polymer to the modified IL-2 polypeptide. In some embodiments, the polymer comprises an azide moiety. In some embodiments, the polymer comprises an alkyne moiety. In some embodiments, the polymer comprises an azide moiety, an alkyne moiety, or reaction product of an azide-alkyne cycloaddition reaction. In some embodiments, the reaction product of the azide-alkyne cycloaddition reaction is a 1,2,3-triazole.
In some embodiments, the polymer is attached to the modified IL-2 polypeptide through use of a bifunctional linker. In some embodiments, the bifunctional linker reacts with a reactive group of an amino acid residue on the modified IL-2 polypeptide (e.g., a cysteine sulfhydryl) to form a covalent bond. In some embodiments, in a second step, the second reactive group of the bifunctional a linker (e.g., a conjugation handle such as an azide or alkyne) is then used to attach a second moiety, such as the polymer.
In some embodiments, the polymer comprises a linker comprising a structure of Formula (X)

wherein each of L¹, L², L³, L⁴, L⁵, L⁶, L⁷, L⁸, and L⁹ is independently —O—, -NR^L-, -(C₁-C₆ alkylene)NR^L-, -NR^L(C₁-C₆ alkylene)-, —N(R^L)₂ ⁺—, -(C₁-C₆ alkylene)N(R^L)₂ ⁺-, -N(R^L)₂ ⁺-(C₁-C₆ alkylene)-, —OP(═O)(OR^L)O—, —S—, -(C₁-C₆ alkylene)S-, -S(C₁-C₆ alkylene)-, —S(═O)—, —S(═O)₂—, —C(═O)—, -(C₁-C₆ alkylene)C(═O)—, —C(═O) (C₁-C₆ alkylene)-, —C(═O)O—, —OC(═O)—, —OC(═O)O—, —C(═O)NR^L—, -C(=O)NR^L(C₁-C₆ alkylene)-, -(C₁-C₆ alkylene)C(=O)NR^L-, —NR^LC(═O)—, -(C₁-C₆ alkylene)NR^LC(=O)-, -NR^LC(=O)(C₁-C₆ alkylene)-, —OC(═O)NR^L—, —NR^LC(═O)O—, —NR^LC(═O)NR^L—, —NR^LC(═S)NR^L—, —CR^L═N—, —N═CR^L, —NR^LS(═O)₂—, —S(═O)₂NR^L—, —C(═O)NR^LS(═O)₂—, —S(═O)₂NR^LC(═O)—, substituted or unsubstituted C₁-C₆ alkylene, substituted or unsubstituted C₁-C₆ heteroalkylene, substituted or unsubstituted C₂-C₆ alkenylene, substituted or unsubstituted C₂-C₆ alkynylene, substituted or unsubstituted C₆-C₂₀ arylene, substituted or unsubstituted C₂-C₂₀ heteroarylene, —(CH₂—CH₂—O)_qa-, —(O—CH₂—CH₂)_qb-, —(CH₂—CH(CH₃)—O)_qc-, —(O—CH(CH₃)—CH₂)_qd-, a reaction product of a conjugation handle and a complementary conjugation handle, or absent; (C₁-C₆ alkylene)
each R^L is independently hydrogen, substituted or unsubstituted C₁-C₄ alkyl, substituted or unsubstituted C₁-C₄ heteroalkyl, substituted or unsubstituted C₂-C₆ alkenyl, substituted or unsubstituted C₂-C₅ alkynyl, substituted or unsubstituted C₃-C₈ cycloalkyl, substituted or unsubstituted C₂-C₇ heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and
each of qa, qb, qc and qd is independently an integer from 1-100,
wherein each
is a point of attachment to the modified IL-2 polypeptide or the polymeric portion of the polymer.

In some embodiments, the polymer comprises a linker comprising a structure of Formula (X′)

wherein each L′ is independently —O—, -NR^L-, -(C₁-C₆ alkylene)NR^L-, -NR^L(C₁-C₆ alkylene)-, —N(R^L)₂ ⁺-, -(C₁-C₆ alkylene)N(R^L)₂ ⁺-, —N(RL)₂ ⁺-(C₁-C₆ alkylene)-, —OP(═O)(OR^L)O—, —S—, -(C₁-C₆ alkylene)S-, -S(C₁-C₆ alkylene)-, —S(═O)—, —S(═O)₂—, —C(═O)—, -(C₁-C₆ alkylene)C(═O)—, —C(═O) (C₁-C₆ alkylene)-, —C(═O)O—, —OC(═O)—, —OC(═O)O—, —C(═O)NR^L—, -C(=O)NR^L(C₁-C₆ alkylene)-, -(C₁-C₆ alkylene)C(=O)NR^L-, —NR^LC(═O)—, -(C₁-C₆ alkylene)NR^LC(=O)-, -NR^LC(=O)(C₁-C₆ alkylene)-, —OC(═O)NR^L—, —NR^LC(═O)O—, —NR^LC(═O)NR^L—, —NR^LC(═S)NR^L—, —CR^L═N—, —N═CR^L, —NR^LS(═O)₂—, —S(═O)₂NR^L—, —C(═O)NR^LS(═O)₂—, —S(═O)₂NR^LC(═O)—, substituted or unsubstituted C₁-C₆ alkylene, substituted or unsubstituted C₁-C₆ heteroalkylene, substituted or unsubstituted C₂-C₆ alkenylene, substituted or unsubstituted C₂-C₆ alkynylene, substituted or unsubstituted C₆-C₂₀ arylene, substituted or unsubstituted C₂-C₂₀ heteroarylene, —(CH₂—CH₂—O)_qa-, —(O—CH₂—CH₂)_qb-, —(CH₂—CH(CH₃)—O)_qc-, —(O— CH(CH₃)—CH₂)_qd-, a reaction product of a conjugation handle and a complementary conjugation handle, or absent; (C₁-C₆ alkylene)
each R^L is independently hydrogen, substituted or unsubstituted C₁-C₄ alkyl, substituted or unsubstituted C₁-C₄ heteroalkyl, substituted or unsubstituted C₂-C₆ alkenyl, substituted or unsubstituted C₂-C₅ alkynyl, substituted or unsubstituted C₃-C₈ cycloalkyl, substituted or unsubstituted C₂-C₇ heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
each of qa, qb, qc and qd is independently an integer from 1-100; and
g is an integer from 1-100,
wherein each
is a point of attachment to the modified IL-2 polypeptide or the polymeric portion of the polymer.

In some embodiments, a modified IL-2 polypeptide provided herein comprises a polymer which includes a linker selected from Table 4. In Table 4, each
is a point of attachment to either the modified IL-2 polypeptide (e.g., an amino group of the modified IL-2 polypeptide) or to the polymeric portion of the polymer.

TABLE 4

Linker Identifier	Linker Structure
Formula A
Formula B
Formula C
Formula D
Formula E
Formula F
Formula G
Formula H

In some embodiments, the water-soluble polymer comprises from 1 to 10 polyethylene glycol chains. In some embodiments, the water-soluble polymer comprises 1 polyethylene glycol chains to 10 polyethylene glycol chains. In some embodiments, the first water-soluble polymer comprises 1 polyethylene glycol chains to 2 polyethylene glycol chains, 1 polyethylene glycol chains to 4 polyethylene glycol chains, 1 polyethylene glycol chains to 6 polyethylene glycol chains, 1 polyethylene glycol chains to 10 polyethylene glycol chains, 2 polyethylene glycol chains to 4 polyethylene glycol chains, 2 polyethylene glycol chains to 6 polyethylene glycol chains, 2 polyethylene glycol chains to 10 polyethylene glycol chains, 4 polyethylene glycol chains to 6 polyethylene glycol chains, 4 polyethylene glycol chains to 10 polyethylene glycol chains, or 6 polyethylene glycol chains to 10 polyethylene glycol chains. In some embodiments, the water-soluble polymer comprises 1 polyethylene glycol chains, 2 polyethylene glycol chains, 4 polyethylene glycol chains, 6 polyethylene glycol chains, or 10 polyethylene glycol chains. In some embodiments, the water-soluble polymer comprises at least 1 polyethylene glycol chains, 2 polyethylene glycol chains, 4 polyethylene glycol chains, or 6 polyethylene glycol chains. In some embodiments, the first water-soluble polymer comprises at most 2 polyethylene glycol chains, 4 polyethylene glycol chains, 6 polyethylene glycol chains, or 10 polyethylene glycol chains. In some embodiments, the water-soluble polymer comprises 4 polyethylene glycol chains. In some embodiments, the water-soluble polymer comprises a structure of Formula (I)
wherein each m is independently an integer from 4-30. In some embodiments, at least one polyethylene glycol chain of the water-soluble polymer comprises the structure of Formula (II)
wherein each m is independently an integer from 4-30 and each n is independently an integer from 1-10. In some embodiments, each polyethylene glycol chain of the water-soluble polymer comprises the structure of Formula (II). In some embodiments of Formula (II), m is 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40. In some embodiments of Formula (II), n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
In some embodiments, each of the polyethylene glycol chains independently comprises from about 5 to about 300, from about 10 to about 200, from about 20 to about 100, or from about 25 to about 50 ethylene glycol units. In some embodiments, each of the polyethylene glycol chains independently comprises 5 ethylene glycol units to 300 ethylene glycol units. In some embodiments, each of the polyethylene glycol chains independently comprises 5 ethylene glycol units to 10 ethylene glycol units, 5 ethylene glycol units to 20 ethylene glycol units, 5 ethylene glycol units to 25 ethylene glycol units, 5 ethylene glycol units to 50 ethylene glycol units, 5 ethylene glycol units to 100 ethylene glycol units, 5 ethylene glycol units to 200 ethylene glycol units, 5 ethylene glycol units to 300 ethylene glycol units, 10 ethylene glycol units to 20 ethylene glycol units, 10 ethylene glycol units to 25 ethylene glycol units, 10 ethylene glycol units to 50 ethylene glycol units, 10 ethylene glycol units to 100 ethylene glycol units, 10 ethylene glycol units to 200 ethylene glycol units, 10 ethylene glycol units to 300 ethylene glycol units, 20 ethylene glycol units to 25 ethylene glycol units, 20 ethylene glycol units to 50 ethylene glycol units, 20 ethylene glycol units to 100 ethylene glycol units, 20 ethylene glycol units to 200 ethylene glycol units, 20 ethylene glycol units to 300 ethylene glycol units, 25 ethylene glycol units to 50 ethylene glycol units, 25 ethylene glycol units to 100 ethylene glycol units, 25 ethylene glycol units to 200 ethylene glycol units, 25 ethylene glycol units to 300 ethylene glycol units, 50 ethylene glycol units to 100 ethylene glycol units, 50 ethylene glycol units to 200 ethylene glycol units, 50 ethylene glycol units to 300 ethylene glycol units, 100 ethylene glycol units to 200 ethylene glycol units, 100 ethylene glycol units to 300 ethylene glycol units, or 200 ethylene glycol units to 300 ethylene glycol units. In some embodiments, each of the polyethylene glycol chains independently comprises 5 ethylene glycol units, 10 ethylene glycol units, 20 ethylene glycol units, 25 ethylene glycol units, 50 ethylene glycol units, 100 ethylene glycol units, 200 ethylene glycol units, or 300 ethylene glycol units. In some embodiments, each of the polyethylene glycol chains independently comprises at least 5 ethylene glycol units, 10 ethylene glycol units, 20 ethylene glycol units, 25 ethylene glycol units, 50 ethylene glycol units, 100 ethylene glycol units, or 200 ethylene glycol units. In some embodiments, each of the polyethylene glycol chains independently comprises at most 10 ethylene glycol units, 20 ethylene glycol units, 25 ethylene glycol units, 50 ethylene glycol units, 100 ethylene glycol units, 200 ethylene glycol units, or 300 ethylene glycol units.
In some embodiments, each of the polyethylene glycol chains is independently linear or branched. In some embodiments, each of the polyethylene glycol chains is a linear polyethylene glycol. In some embodiments, each of the polyethylene glycol chains is a branched polyethylene glycol. For example, in some embodiments, each of the first and the second polymers comprises a linear polyethylene glycol chain.
In some embodiments, each of the polyethylene glycol chains is independently terminally capped with a hydroxy, an alkyl, an alkoxy, an amido, or an amino group. In some embodiments, each of the polyethylene glycol chains is independently terminally capped with an amino group. In some embodiments, each of the polyethylene glycol chains is independently terminally capped with an amido group. In some embodiments, each of the polyethylene glycol chains is independently terminally capped with an alkoxy group. In some embodiments, each of the polyethylene glycol chains is independently terminally capped with an alkyl group. In some embodiments, each of the polyethylene glycol chains is independently terminally capped with a hydroxy group. In some embodiments, one or more of the polyethylene glycol chains independently has the structure
wherein n is an integer from 4-30. In some embodiments, one or more of the polyethylene glycol chains independently has the structure
wherein m is an integer from 4-30.
In some embodiments, the modified IL-2 polypeptide comprises multiple polymers covalently attached thereto. In some embodiments, each polymer comprises a water-soluble polymer. In some embodiments, the water-soluble polymer comprises poly(alkylene oxide), polysaccharide, poly(vinyl pyrrolidone), poly(vinyl alcohol), polyoxazoline, poly(acryloylmorpholine), or a combination thereof. In some embodiments, each water-soluble polymer is poly(alkylene oxide). In some embodiments, each water-soluble polymer is polyethylene glycol.
In some embodiments, the modified IL-2 polypeptide comprises from 1 to 10 covalently attached water-soluble polymers. In some embodiments, the modified IL-2 polypeptide comprises 1 to 10 covalently attached water-soluble polymers. In some embodiments, the modified IL-2 polypeptide comprises 1 or 2 covalently attached water-soluble polymers, 1 to 3 covalently attached water-soluble polymers, 1 to 4 covalently attached water-soluble polymers, 1 to 6 covalently attached water-soluble polymers, 1 to 8 covalently attached water-soluble polymers, 1 to 10 covalently attached water-soluble polymers, 2 or 3 covalently attached water-soluble polymers, 2 to 4 covalently attached water-soluble polymers, 2 to 6 covalently attached water-soluble polymers, 2 to 8 covalently attached water-soluble polymers, 2 to 10 covalently attached water-soluble polymers, 3 or 4 covalently attached water-soluble polymers, 3 to 6 covalently attached water-soluble polymers, 3 to 8 covalently attached water-soluble polymers, 3 to 10 covalently attached water-soluble polymers, 4 to 6 covalently attached water-soluble polymers, 4 to 8 covalently attached water-soluble polymers, 4 to 10 covalently attached water-soluble polymers, 6 to 8 covalently attached water-soluble polymers, 6 to 10 covalently attached water-soluble polymers, or 8 to 10 covalently attached water-soluble polymers.
In some embodiments, a water-soluble polymer that can be attached to a modified IL-2 polypeptide comprises a structure of Formula (A):
In some embodiments, a water-soluble polymer that can be attached to a modified IL-2 polypeptide comprises a structure of Formula (B):
In some embodiments, a water-soluble polymer that can be attached to a modified IL-2 polypeptide comprises a structure of Formula (C):
In some embodiments, a water-soluble polymer that can be attached to a modified IL-2 polypeptide comprises a structure of Formula (D):
In some embodiments, a water-soluble polymer that can be attached to a modified IL-2 polypeptide comprises a structure of Formula (E):
In some embodiments, the water-soluble polymer attached to the modified IL-2 polypeptide comprises one or more linkers and/or spacers. In some embodiments, the one or more linkers comprise one or more amide groups. In some embodiments, the one or more linkers comprise one or more lysine groups. .In some embodiment, the water-soluble polymer attached to the modified IL-2 polypeptide comprises a structure of Formula (I), Formula (II), Formula (III), or a combination thereof. In some embodiments, the water-soluble polymer attached to the modified IL-2 polypeptide comprises a structure of Formula (A), Formula (B), Formula (C), Formula (D), Formula (E) or a combination thereof. In some embodiments, the water-soluble polymer attached to the modified IL-2 polypeptide comprises a structure of
In some embodiments, the water-soluble polymer attached at the N-terminus comprises one or more linkers and/or spacers. In some embodiments, the one or more linkers comprise one or more amide groups. In some embodiments, the one or more linkers comprise one or more lysine groups. In some embodiment, the water-soluble polymer attached at the N-terminus comprises a structure of Formula (I), Formula (II), Formula (III), or a combination thereof. In some embodiments, the water-soluble polymer attached at the N-terminus comprises a structure of Formula (A), Formula (B), Formula (C), Formula (D), Formula (E), or a combination thereof. In some embodiments, the water-soluble polymer attached comprises a structure of
In some embodiments, the polymers are synthesized from suitable precursor materials. In some embodiments, the polymers are synthesized from the precursor materials of, Structure 5, Structure 6, Structure 7, or Structure 8, wherein Structure 5 is
Structure 6 is
Structure 7 is
and Structure 8 is

III. Compositions Pharmaceutical Formulation

In one aspect, described herein is a pharmaceutical formulation comprising: a modified IL-2 polypeptide described herein; and a pharmaceutically acceptable carrier or excipient. In some embodiments, the pharmaceutical formulation comprises a plurality of the modified IL-2 polypeptides. In some embodiments, the pharmaceutical formulations further comprises one or more excipient selected from a carbohydrate, an inorganic salt, an antioxidant, a surfactant, or a buffer.
In some embodiments, the pharmaceutical formulation further comprises a carbohydrate. In certain embodiments, the carbohydrate is selected from the group consisting of fructose, maltose, galactose, glucose, D-mannose, sorbose, lactose, sucrose, trehalose, cellobiose raffinose, melezitose, maltodextrins, dextrans, starches, mannitol, xylitol, maltitol, lactitol, xylitol, sorbitol (glucitol), pyranosyl sorbitol, myoinositol, cyclodextrins, and combinations thereof.
In some embodiments, the pharmaceutical formulation comprises an inorganic salt. In certain embodiments, the inoragnic salt is selected from the group consisting of sodium chloride, potassium chloride, magnesium chloride, calcium chloride, sodium phosphate, potassium phosphate, sodium sulfate, or combinations thereof.
In certain embodiments, the pharmaceutical formulation comprises an antioxidant. In certain embodiments, the antioxidant is selected from the group consisting of ascorbyl palmitate, butylated hydroxyanisole, butylated hydroxytoluene, potassium metabisulfite, propyl gallate, sodium metabisulfite, sodium thiosulfate, vitamin E, 3,4-dihydroxybenzoic acid, and combinations thereof.
In certain embodiments, the pharmaceutical formulation comprises a surfactant. In certain embodiments, the surfactant is selected from the group consisting of polysorbates, sorbitan esters, lipids, phospholipids, phosphatidylethanolamines, fatty acids, fatty acid esters, steroids, EDTA, zinc, and combinations thereof.
In certain embodiments, the pharmaceutical formulation comprises a buffer. In certain embodiments, the buffer is selected from the group consisting of citric acid, sodium phosphate, potassium phosphate, acetic acid, ethanolamine, histidine, amino acids, tartaric acid, succinic acid, fumaric acid, lactic acid, tris, HEPES, or combinations thereof.
In some embodiments, the pharmaceutical formulation is prepared for parenteral or enteral administration. In some embodiments, the pharmaceutical formulation is formulated for intravenous or subcutaneous administration. In some embodiments, the pharmaceutical formulation is in a lyophilized form.
In one aspect, described herein is a liquid or lyophilized formulation that comprises a described modified IL-2 polypeptide. In some embodiments, the modified IL-2 polypeptide is a lyophilized powder. In some embodiments, the lyophilized powder is resuspended in a buffer solution. In some embodiments, the buffer solution comprises a buffer, a sugar, a salt, a surfactant, or any combination thereof. In some embodiments, the buffer solution comprises a phosphate salt. In some embodiments, the phosphate salt is sodium Na₂HPO₄. In some embodiments, the salt is sodium chloride. In some embodiments, the buffer solution comprises phosphate buffered saline. In some embodiments, the buffer solution comprises mannitol. In some embodiments, the lyophilized powder is suspended in a solution comprising 10 mM Na₂HPO₄ buffer pH 7.5, 0.022% SDS and 50 mg/mL mannitol.

Dosage Forms

The modified IL-2 polypeptides described herein can be in a variety of dosage forms. In some embodiments, the modified IL-2 polypeptide is dosed as a lyophilized powder. In some embodiments, the modified IL-2 polypeptide is dosed as a suspension. In some embodiments, the modified IL-2 polypeptide is dosed as a solution. In some embodiments, the modified IL-2 polypeptide is dosed as an injectable solution. In some embodiments, the modified IL-2 polypeptides is dosed as an IV solution.

IV. Method of Treatment

In one aspect, described herein, is a method of treating an autoimmune disease or disorder in a subject in need thereof, comprising: administering to the subject an effective amount of a modified IL-2 polypeptide or a pharmaceutical composition as described herein. In one aspect, described herein, is a method of treating an inflammatory disease or disorder in a subject in need thereof, comprising: administering to the subject an effective amount of a modified IL-2 polypeptide or a pharmaceutical composition as described herein. In some embodiments, the autoimmune disease is a T cell mediated autoimmune disease. In some embodiments, the inflammatory disease or disorder comprises inflammation (e.g., cartilage inflammation), an autoimmune disease, an atopic disease, a paraneoplastic autoimmune disease, arthritis, rheumatoid arthritis (e.g., active), juvenile arthritis, juvenile idiopathic arthritis, juvenile rheumatoid arthritis, pauciarticular rheumatoid arthritis, pauciarticular juvenile rheumatoid arthritis, polyarticular juvenile rheumatoid arthritis, systemic onset juvenile rheumatoid arthritis, juvenile psoriatic arthritis, psoriatic arthritis, polyarticular rheumatoid arthritis, systemic onset rheumatoid arthritis, ankylosing spondylitis, juvenile ankylosing spondylitis, juvenile enteropathic arthritis, reactive arthritis, juvenile reactive arthritis, Reiter’s syndrome, juvenile Reiter’s syndrome, juvenile dermatomyositis, juvenile scleroderma, juvenile vasculitis, enteropathic arthritis, SEA syndrome (Seronegativity, Enthesopathy, Arthropathy syndrome), dermatomyositis, psoriatic arthritis, scleroderma, vasculitis, myolitis, polymyolitis, dermatomyolitis, polyarteritis nodossa, Wegener’s granulomatosis, arteritis, ploymyalgia rheumatica, sarcoidosis, sclerosis, primary biliary sclerosis, sclerosing cholangitis, Sjogren’s syndrome, psoriasis, plaque psoriasis, guttate psoriasis, inverse psoriasis, pustular psoriasis, erythrodermic psoriasis, dermatitis, atopic dermatitis, dermatitis herpetiformis, Behcet’s disease, alopecia, alopecia areata, alopecia totalis, atherosclerosis, lupus, Still’s disease, myasthenia gravis, inflammatory bowel disease (IBD), Crohn’s disease, ulcerative colitis, celiac disease, asthma, COPD, rhinosinusitis, rhinosinusitis with polyps, eosinophilic esophogitis, eosinophilic bronchitis, Guillain-Barre disease, thyroiditis (e.g., Graves’ disease), Addison’s disease, Raynaud’s phenomenon, autoimmune hepatitis, graft versus host disease, steroid refractory chronic graft versus host disease, transplantation rejection (e.g. kidney, lung, heart, skin, and the like), kidney damage, hepatitis C-induced vasculitis, spontaneous loss of pregnancy, vitiligo, focal segmental glomerulosclerosis (FSGS), minimal change disease, membranous nephropathy, ANCA-associated Glomerulonephropathy, Membranoproliferative Glomerulonephritis, IgA nephropathy, lupus nephritis, or a combination thereof.
In some embodimetns, the inflammatory disease or disorder is a neuroinflammatory disorder. In some embodiments, the neuroinflammatory disorder is neuromyelitis optica spectrum disorder, multiple sclerosis, anti-myelin oligodendrocyte glycoprotein antibody disorder, autoimmune encepahlitis, transverse myelitis, optic neuritis, or neurosarcoidosis. In some embodiments, the diesease or disorder is amyotrophic lateral sclerosis.

V. Methods of Manufacturing

In one aspect, described herein, is a method of making a modified IL-2 polypeptide. In another aspect, described herein, is a method of making a modified IL-2 polypeptide comprising synthesizing two or more fragments of the modified IL-2 polypeptide and ligating the fragments. In another aspect, described herein, is a method of making a modified IL-2 polypeptide comprising a. synthesizing two or more fragments of the modified IL-2 polypeptide, b. ligating the fragments; and c. folding the ligated fragments. Examples of methods synthesizing IL-2 polypeptides can also be found in, for example, at least PCT Publication No WO2021140416A2, US Patent Application Publication No US20190023760A1, and Asahina et al., Angew. Chem. Int. Ed. 2015, 54, 8226-8230, each of which is incorporated by reference as if set forth herein in its entirety.
In some embodiments, the two or more fragments of the modified IL-2 polypeptide are synthesized chemically. In some embodiments, the two or more fragments of the modified IL-2 polypeptide are synthesized by solid phase peptide synthesis. In some embodiments, the two or more fragments of the modified IL-2 polypeptide are synthesized on an automated peptide synthesizer.
In some embodiments, the modified IL-2 polypeptide is ligated from 2, 3, 4, 5, 6, 7, 8, 9, 10, or more peptide fragments. In some embodiments, the modified peptide is ligated from 2 peptide fragments. In some embodiments, the modified IL-2 polypeptide is ligated from 3 peptide fragments. In some embodiments, the modified IL-2 polypeptide is ligated from 4 peptide fragments. In some embodiments, the modified IL-2 polypeptide is ligated from 2 to 10 peptide fragments.
In some embodiments, the two or more fragments of the modified IL-2 polypeptide are ligated together. In some embodiments, three or more fragments of the modified IL-2 polypeptide are ligated in a sequential fashion. In some embodiments, three or more fragments of the modified IL-2 polypeptide are ligated in a one-pot reaction.
In some embodiments, ligated fragments are folded. In some embodiments, folding comprises forming one or more disulfide bonds within the modified IL-2 polypeptide. In some embodiments, the ligated fragments are subjected to a folding process. In some embodiments, the ligated fragments are folding using methods well known in the art. In some embodiments, the ligated polypeptide or the folded polypeptide are further modified by attaching one or more polymers thereto. In some embodiments, the ligated polypeptide or the folded polypeptide are further modified by PEGylation.
In some embodiments, the modified IL-2 polypeptide is synthetic.
In some embodiments, the modified IL-2 polypeptide is recombinant. In one aspect, described herein is a host cell comprising a modified IL-2 polypeptide. In some embodiments, the host cell is a prokaryotic cell or a eukaryotic cell. In some embodiments, the host cell is a mammalian cell, an avian cell, and an insect cell. In some embodiments, the host cell is a CHO cell, a COS cell, or a yeast cell.
In one aspect, described herein is a method of producing a modified IL-2 polypeptide, wherein the method comprises expressing the modified IL-2 polypeptide in a host cell. In some embodiments, the host cell is a prokaryotic cell or a eukaryotic cell. In some embodiments, the host cell is a mammalian cell, an avian cell, and an insect cell. In some embodiments, the host cell is a CHO cell, a COS cell, or a yeast cell.

VI. SEQ IDs

TABLE 5

SEQ ID NO / Identifier	Substitutions	Sequence
1 (WT-IL-2)	None (WT IL-2)	APTSSSTKKTQLQLEHLLLDLQMILNGINNYK NPKLTRMLTFKFYMPKKATELKHLQCLEEEL KPLEEVLNLAQS KNFHLRPRDLISNINVIVLEL KGSETTFMCEYADETATIVEFLNRWITFCQSII STLT
2 (Aldesleukin)	A1Del, C125S	PTSSSTKKTQLQLEHLLLDLQMILNGINNYKN PKLTRMLTFKFYMPKKATELKHLQCLEEELK PLEEVLNLAQSKNFHLRPRDLISNINVIVLELK GSETTFMCEYADETATIVEFLNRWITFSQSIIS TLT
3	M23Nle, Y31H, K35R, M39Nle, T41Hse, M46Nle N71Hse, Q74P, N88D, M104Hse, C125S X=Nle, Z=Hse N-terminus with glutaric acid and 0.5 kDa azido PEG	APTSSSTKKT QLQLEHLLLD LQXILNGINN HKNPRLTRXL ZFKFYXPKKA TELKHLQCLE EELKPLEEVL ZLAPSKNFHL RPRDLISDIN VIVLELKGSE TTFZCEYADE TATIVEFLNR WITFSQSIIS TLT
4	M23Nle, Y31H, K35R, M39Nle, T41Hse, M46Nle, N71Hse, Q74P M104Hse, C125S X=Nle, Z=Hse N-terminus with glutaric acid and 0.5 kDa azido PEG	APTSSSTKKT QLQLEHLLLD LQXILNGINN HKNPRLTRXL ZFKFYXPKKA TELKHLQCLE EELKPLEEVL ZLAPSKNFHL RPRDLISNIN VIVLELKGSE TTFZCEYADE TATIVEFLNR WITFSQSIIS TLT
5	M23Nle, Y31H, K35R, M39Nle, T41Hse, M46Nle, V69A, N71Hse, Q74P, N88D, M104Hse, C125S X=Nle, Z=Hse N-terminus with glutaric acid and 0.5 kDa azido PEG	APTSSSTKKT QLQLEHLLLD LQXILNGINN HKNPRLTRXL ZFKFYXPKKA TELKHLQCLE EELKPLEEAL ZLAPSKNFHL RPRDLISDIN VIVLELKGSE TTFZCEYADE TATIVEFLNR WITFSQSIIS TLT
6	M23Nle, Y31H, K35R, M39A, T41Hse, M46Nle N71Hse, Q74P, M104Hse, C125S X=Nle, Z=Hse N-terminus with glutaric acid and 0.5 kDa azido PEG	APTSSSTKKT QLQLEHLLLD LQXILNGINN HKNPRLTRAL ZFKFYXPKKA TELKHLQCLE EELKPLEEVL ZLAPSKNFHL RPRDLISNIN VIVLELKGSE TTFZCEYADE TATIVEFLNR WITFSQSIIS TLT
7	M23A, Y31H, K35R, M39Nle, T41Hse, M46Nle, N71Hse, Q74P M104Hse, C125S X=Nle, Z=HseN-terminus with glutaric acid and 0.5 kDa azido PEG	APTSSSTKKT QLQLEHLLLD LQAILNGINN HKNPRLTRXL ZFKFYXPKKA TELKHLQCLE EELKPLEEVL ZLAPSKNFHL RPRDLISDIN VIVLELKGSE TTFZCEYADE TATIVEFLNR WITFSQSIIS TLT
8	M23Nle, Y31H, K35R, M39Nle, T41Hse, M46A, N71Hse, Q74P, M104Hse, C125S X=Nle, Z=HseN-terminus with glutaric acid and 0.5 kDa azido PEG	APTSSSTKKT QLQLEHLLLD LQXILNGINN HKNPRLTRXL ZFKFYAPKKA TELKHLQCLE EELKPLEEVL ZLAPSKNFHL RPRDLISNIN VIVLELKGSE TTFZCEYADE TATIVEFLNR WITFSQSIIS TLT
9	Y31H, K35R, V69A, N71R, Q74P, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPRLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEAL RLAPSKNFHL RPRDLISNIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
10	N29S, Y31H, K35R, T37A, K48E, V69A, N71R, Q74P, N88D, I89V, C125S, Q126T	APTSSSTKKT QLQLEHLLLD LQMILNGISN HKNPRLARML TFKFYMPEKA TELKHLQCLE EELKPLEEAL RLAPSKNFHL RPRDLISDVN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSTSIIS TLT
11	L18R, Q22E, C125S, Q126T	APTSSSTKKT QLQLEHLRLD LEMILNGINN YKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAQSKNFHL RPRDLISNIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSTSIIS TLT
12	L18R, Q22E, L80F, R81D, L85V, I86V, N88D, I92F, C125S, Q126T	APTSSSTKKT QLQLEHLRLD LEMILNGINN YKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAQSKNFHF DPRDVVSDIN VFVLELKGSE TTFMCEYADE TATIVEFLNR WITFSTSIIS TLT
13	Y31H, K35R, V69A, N71R, Q74P, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPRLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEAL RLAPSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
14	Y31H, K35R, Q74P, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPRLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAPSKNFHL RPRDLISNIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
15	Y31H, K35R, N71R, Q74P, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPRLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL RLAPSKNFHL RPRDLISNIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
16	L18R, Q22E, L80F, R81D, L85V, I86V, I92F, C125S	APTSSSTKKT QLQLEHLRLD LEMILNGINN YKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAQSKNFHF DPRDVVSNIN VFVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
17	L18R, L80F, R81D, L85V, I86V, I92F, C125S, Q126T	APTSSSTKKT QLQLEHLRLD LQMILNGINN YKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAQSKNFHF DPRDVVSNIN VFVLELKGSE TTFMCEYADE TATIVEFLNR WITFSTSIIS TLT
18	L80F, R81D, L85V, I86V, I92F, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN YKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAQSKNFHF DPRDVVSNIN VFVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
19	C125S, Q126T	APTSSSTKKT QLQLEHLLLD LQMILNGINN YKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAQSKNFHL RPRDLISNIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSTSIIS TLT
20	Y31H, V69A, N71R, Q74P, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEAL RLAPSKNFHL RPRDLISNIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
21	Y31H, V69A, Q74P, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEAL NLAPSKNFHL RPRDLISNIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
22	N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN YKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAQSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
23	Y31H, N71R, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL RLAQSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
24	Y31H, N71R, C125S, Q126T	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL RLAQSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSTSIIS TLT
25	Y31H, K35R, V69A, N71R, Q74P, C125S, Q126T	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPRLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEAL RLAPSKNFHL RPRDLISNIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSTSIIS TLT
26	Y31H, K35R, N71R, Q74P, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPRLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL RLAPSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
27	Y31H, K35R, N71R, Q74P, C125S, Q126T	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPRLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL RLAPSKNFHL RPRDLISNIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSTSIIS TLT
28	Y31H, K35R, Q74P, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPRLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAPSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
29	Y31H, K35R, Q74P, C125S, Q126T	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPRLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAPSKNFHL RPRDLISNIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSTSIIS TLT
30	Y31H, V69A, Q74P, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEAL NLAPSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
31	V69A, Q74P, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN YKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEAL NLAPSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
32	V69A, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN YKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEAL NLAQSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
33	Q74P, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN YKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAPSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
34	Y31H, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAQSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
35	Y31H, Q74P, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAPSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
36	Y31H, V69A, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEAL NLAQSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
37	Y31H, V69A, N71R, Q74P, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN HKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEAL RLAPSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
38	V69A, N71R, Q74P, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN YKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEAL RLAPSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
39	N71R, N88D, C125S	APTSSSTKKT QLQLEHLLLD LQMILNGINN YKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL RLAQSKNFHL RPRDLISDIN VIVLELKGSE TTFMCEYADE TATIVEFLNR WITFSQSIIS TLT
40	M23Nle, K35R, M39Nle, T41Hse, M46Nle, V69A, N71Hse, Q74P, N88D, M104Hse, C125S X=Nle, Z=Hse	APTSSSTKKT QLQLEHLLLD LQXILNGINN YKNPRLTRXL ZFKFYXPKKA TELKHLQCLE EELKPLEEAL ZLAPSKNFHL RPRDLISDIN VIVLELKGSE TTFZCEYADE TATIVEFLNR WITFSQSIIS TLT
41	M23Nle, M39Nle, T41Hse, F42(4-NH2)-Phe, M46Nle, N71Hse, N88D, M104Hse, C125S B=(4-NH2)-Phe X=Nle, Z=Hse	APTSSSTKKT QLQLEHLLLD LQXILNGINN YKNPKLTRXL ZBKFYXPKKA TELKHLQCLE EELKPLEEVL ZLAQSKNFHL RPRDLISDIN VIVLELKGSE TTFZCEYADE TATIVEFLNR WITFSQSIIS TLT
42	M23Nle, M39Nle, T41Hse, M46Nle, N71Hse, N88D, M104Hse, C125S X=Nle, Z=Hse	APTSSSTKKT QLQLEHLLLD LQXILNGINN YKNPKLTRXL ZFKFYXPKKA TELKHLQCLE EELKPLEEVL ZLAQSKNFHL RPRDLISDIN VIVLELKGSE TTFZCEYADE TATIVEFLNR WITFSQSIIS TLT
43	M23Nle, M39Nle, T41Hse, M46Nle, N71Hse, N88Dgp, M104Hse, C125S X=Nle, Z=Hse Dgp=D with a O-(2-aminoethyl)-O′-(2-aminoethyl)octaethylene glycol	APTSSSTKKT QLQLEHLLLD LQXILNGINN YKNPKLTRXL ZFKFYXPKKA TELKHLQCLE EELKPLEEVL ZLAQSKNFHL RPRDLIS(Dgp)IN VIVLELKGSE TTFZCEYADE TATIVEFLNR WITFSQSIIS TLT

In Table 5 above, Nle is a norleucine residue and Hse is a homoserine residue.
Although the present disclosure and its advantages have been described in detail, it should be understood that various changes, substitutions and alterations can be made herein without departing from the spirit and scope of the disclosure as defined in the appended claims.
The present disclosure is further illustrated in the following Examples which are given for illustration purposes only and are not intended to limit the disclosure in any way.

Example 1: Synthesis of Modified IL-2 Polypeptides - General Procedures

Preparation IL-2 Linear Protein (Representative Protocols)

General strategy: A modified IL-2 polypeptide as described herein, such as a modified IL-2 polypeptide having an amino acid sequence of, for example, SEQ ID NO: 3, or any of SEQ ID NOs: 3-8 or 40-43, or a synthetic version of any one of SEQ ID NOs: 9-39, or a modified IL-2 polypeptide otherwise described herein, can be synthesized by ligating individual peptide segments prepared by solid phase peptide synthesis (SPPS). Individual peptides are synthesized on an automated peptide synthesizer using the methods described below.
Materials and solvents: Fmoc-amino acids with suitable side chain protecting groups for Fmoc-SPPS, resins polyethylene glycol derivatives used for peptide functionalization and reagents were commercially available and were used without further purification. HPLC grade CH₃CN was used for analytical and preparative RP-HPLC purification.
Loading of protected ketoacid derivatives (segment 1-3) on amine-based resin: 5 g of Rink-amide MBHA or ChemMatrix resin (1.8 mmol scale) was swollen in DMF for 30 min. Fmoc-deprotection was performed by treating the resin twice with 20% piperidine in DMF (v/v) at r.t. for 10 min. followed by several washes with DMF. Fmoc-AA-protected-α-ketoacid (1.8 mmol, 1.00 equiv.) was dissolved in 20 mL DMF and pre-activated with HATU (650 mg, 1.71 mmol, 0.95 equiv.) and DIPEA (396 µL, 3.6 mmol, 2.00 equiv.). The reaction mixture was added to the swollen resin. It was let to react for 6 h at r.t. under gentle agitation. The resin was rinsed thoroughly with DMF. Capping of unreacted amines on the resin was performed by addition of a solution of acetic anhydride (1.17 mL) and DIPEA (2.34 mL) in DMF (20 mL). It was let to react at r.t. for 15 min under gentle agitation. The resin was rinsed thoroughly with DCM followed by diethyl ether and dried. The loading of the resin was determined by UV quantification of dibenzofulvene to be 0.25 mmol/g.
Protected ketoacid used
Loading of Fmoc-Thr(tBu)-OH on Wang resin (segment4): Preloading of Fmoc-Thr-OH was performed on a Wang resin. 4 g of resin (loading: 0.56 mmol/g, 2.24 mmol scale) was swollen in DMF for 15 min. The resin was treated with 20% (v/v) piperidine in DMF at r.t. for 20 min. The resin was washed several times with DMF. Fmoc-Thr(tBu)-OH (638 mg, 1.68 mmol, 0.75 equiv) and HATU (638 mg, 1.68 mmol, 0.75 equiv) were dissolved in DMF (12 mL). Pre-activation was performed at r.t. for 3 min by addition of DIPEA (585 µL, 3.36 mmol, 1.5 equiv). The reaction mixture was added to the swollen resin. It was let to react overnight at r.t. under gentle agitation. The resin was rinsed thoroughly with DMF. Capping of unreacted amines on the resin was initiated by addition of a solution of acetic anhydride (1.27 mL) and DIPEA (2.34 mL) in DMF (12 mL). It was let to react at r.t. for 15 min under gentle agitation. The resin was rinsed thoroughly with DCM and dried. The loading of the resin was measured (0.34 mmol/g).
Solid-phase peptide synthesis (SPPS): The peptide segments were synthesized on an automated peptide synthesizer using Fmoc-SPPS chemistry. The following Fmoc-amino acids with side-chain protecting groups were used: Fmoc-Ala-OH, Fmoc-Arg(Pbf)-OH, Fmoc-Asn(Trt)-OH, Fmoc-Asp(OtBu)-OH, Fmoc-Cys(Acm)-OH, Fmoc-Gln(Trt)-OH, Fmoc-Glu(OtBu)-OH, Fmoc-Gly-OH, Fmoc-His(Trt)-OH, Fmoc-Ile-OH, Fmoc-Leu-OH, Fmoc-Lys(Boc)-OH, Fmoc-Nle-OH, Fmoc-Phe-OH, Fmoc-Pro-OH, Fmoc-Ser(tBu)-OH, Fmoc-Thr(tBu)-OH, Fmoc-Trp(Boc)-OH, Fmoc-Tyr(tBu)-OH, Fmoc-Val-OH, Fmoc or Boc-Opr-OH (Opr = 5-(S)-oxaproline). Fmoc-pseudoproline dipeptides were incorporated in the synthesis if necessary. Fmoc deprotections were performed with 20% piperidine in DMF (2 × 8 min) or 25% piperidine in DMF containing 0.1 M Cl-HOBt (2 × 8 min) or 20% piperidine in DMF containing 0.1 M Cl-HOBt (2 × 8 min) and monitored by UV at 304 nm with a feedback loop to ensure complete Fmoc removal. Couplings were performed with Fmoc-amino acid (3.0 - 5.0 equiv to resin substitution), HCTU or HATU (2.9 - 4.9 equiv) as coupling reagents and DIPEA or NMM (6 - 10 equiv) in DMF at r.t. or at 50° C. After pre-activation for 3 min, the solution containing the reagents was added to the resin and allowed to react for 30 min or 2 h depending on the amino acid. In some cases, double couplings were required. In some cases, the resin was treated with 20% acetic anhydride in DMF for capping any unreacted free amine.
Resin cleavage and side chain deprotection of the peptides: Once the peptide synthesis was completed, the peptides were cleaved from the resin using a cleavage cocktail at room temperature for 2 h. The resin was filtered off, and the filtrate was concentrated and treated with cold diethyl ether, triturated and centrifuged. The ether layer was carefully decanted, the residue was suspended again in diethyl ether, triturated and centrifuged. Ether washings were repeated twice. The resulting crude peptide was dried under vacuum and stored at -20° C. An aliquot of the solid obtained was solubilized in 1:1 CH₃CN/H₂O with 0.1% TFA (v/v) and analyzed by analytical RP-HPLC using C18 column (4.6×150 mm) at 60° C. The molecular weight of the product was identified using MALDI-TOF or LC-MS.
Ligation of IL-2 segments 1 and 2 and photodeprotection: IL-2 Seg1 (1.2 equiv) and IL-2 Seg2 (1 equiv) were dissolved in DMSO:H₂O (9:1, v/v) containing 0.1 M oxalic acid (20 mM peptide concentration) and allowed to react at 60° C. for 22 h. The ligation vial was protected from light by wrapping it in aluminum foil. The progress of the KAHA ligation was monitored by HPLC using a C18 column (4.6 × 150 mm) at 60° C. with CH₃CN/H₂O containing 0.1% TFA as mobile phase, with a gradient of 5 to 95% CH₃CN in 7 min. After completion of the ligation the mixture was diluted with CH₃CN/H₂O (1:1) containing 0.1% TFA and irradiated at a wavelength of 365 nm for 1 h. The completion of photolysis reaction was confirmed by injecting a sample on HPLC using previously described method. The solution was then purified by preparative HPLC.
Ligation of IL-2 segments 3 and 4 and Fmoc deprotection: IL2-Seg3 (1.2 equiv) and IL2-Seg4 (1 equiv) were dissolved in DMSO/H₂O (9.8:0.2) containing 0.1 M oxalic acid (15 mM) and allowed to react for 20 h at 60° C. The progress of the KAHA ligation was monitored by HPLC using a C18 column (4.6 × 150 mm) at 60° C. using CH₃CN/H₂O containing 0.1 %TFA as mobile phase, with a gradient of 30 to 70 % CH₃CN in 7 min. After completion of ligation, the reaction mixture was diluted with DMSO (6 mL), 5% of diethylamine (300 µL) was added and the reaction mixture was shaken for 7 min at room temperature. To prepare the sample for purification, it was diluted with DMSO (4 mL) containing TFA (300 µL).
Final ligation: IL2-Seg12 (1.2 equiv) and IL2-Seg34 (1 equiv) were dissolved in DMSO/H₂O (9:1) or (9.8:0.2) containing 0.1 M oxalic acid (15 mM peptide concentration) and the ligation was allowed to proceed for 24 h at 60° C. The progress of the KAHA ligation was monitored by analytical HPLC using a C18 column (4.6 ×250 mm) at 60° C. and CH₃CN/H₂O containing 0.1 %TFA as mobile phase, with a gradient of 30 to 95 % CH₃CN in 14 min. After completion of ligation, the reaction mixture was diluted with DMSO followed by further dilution with a mixture of (1:1) CH₃CN:H₂O containing 0.1 % TFA (7 mL). The sample was purified by injecting on a preparative HPLC.
Acm deprotection: IL2 linear protein with 2x Acm was dissolved in AcOH/H₂O (1:1) (0.25 mM protein concentration) and AgOAc (1% m/v) was added to the solution. The mixture was shaken for 2.5 h at 50° C. protected from light. After completion of reaction as ascertained by HPLC, the sample was diluted with CH₃CN:H₂O (1:1) containing 0.1 % TFA, and purified by preparative HPLC.
Purification of the peptides: Peptide segments, ligated peptides and linear proteins were purified by RP-HPLC. Different gradients were applied for the different peptides. The mobile phase was MilliQ-H₂O with 0.1% TFA (v/v) (Buffer A) and HPLC grade CH₃CN with 0.1% TFA (v/v) (Buffer B). Preparative HPLC was performed on a (50× 250 mm) or on a C18 column (50×250 mm) at a flow rate of 40 mL/min at 40° C. or 60° C.
Characterization of the peptides: Peptide segments, ligated peptides and linear proteins were analyzed by RP-HPLC. The mobile phase was MilliQ-H₂O with 0.1% TFA (v/v) (Buffer A) and HPLC grade CH₃CN with 0.1% TFA (v/v) (Buffer B). Analytical HPLC was performed on C4 column (3.6 µm, 150 × 4.6 mm) at r.t. or C18 column (3.6 µm, 150 × 4.6 mm) with a flow rate of 1 mL/min at 60° C. Peptides and proteins were characterized by high resolution Fourier-transform mass spectrometry (FTMS) using a SolariX (9.4 T magnet) spectrometer (Bruker, Billerica,USA) equipped with a dual ESI/MALDI-FTICR source, using 4-hydroxy-α-cyanocinnamic acid (HCCA) as matrix.

EXAMPLE 2 - Synthesis of Composition A and A1 Variants of IL-2 (SEQ ID NO: 3)

Synthesis of IL-2 (1-39)-Leu-α-Ketoacid of Composition A (Segment 1A)

Peptide synthesis: IL2 (1-39)-Leu- α -ketoacid segment 1A (See residues 1-40 of SEQ ID NO: 3) was synthesized on a 0.2 mmol scale on Rink-Amide MBHA resin pre-loaded with Fmoc-Leu-protected-α -ketoacid (0.8 g) with a substitution capacity of ~0.25 mmol/g. Automated Fmoc-SPPS of segment 1A was performed following the general procedure “Solid-phase peptide synthesis (SPPS)”. Insertion of the conjugation handle was performed as follow. The first manual coupling reaction was performed at r.t. for 30 min by addition of glutaric anhydride (CAS RN 108-55-4, 114.10 mg, 5 equiv.) and DIPEA (242 µL, 7 equiv.) in DMF to the resin. Secondly, coupling with commercially available O-(2-Aminoethyl)-O′-(2-azidoethyl) nonaethylene glycol (Compound 2, 421 mg, equiv) in DMF was performed at r.t. for 3 hours by addition of DIPEA (276 µL, 8 equiv) and HATU (300 mg, 3.95 equiv) in DMF to the resin. The resin was washed with DCM and dried under vacuum. The mass of the dried peptidyl resin was 1.6 g. The crude peptide was precipitated following the procedure “Resin cleavage and side-chain deprotection of the peptides” using a cocktail of 95:2.5:2.5 TFA/DODT/H₂O v/v/v (10 mL/g resin) at r.t. for 2.0 hours.
O-(2-Aminoethyl)-O′-(2-azidoethyl) nonaethylene glycol (Compound 2).
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 60° C., gradient: 30 to 80%B in 25 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 1A as a white solid in 97% purity. The isolated yield based on the resin loading was 260 mg (25%). HRMS (ESI): C₂₂₈H₃₉₄N₆₄O₇₂; Average isotope calculated 5182.9193 Da [M+H]⁺; found: 5182.9111 Da [M+H]⁺.

Synthesis of Opr-IL2 (42-69) Photoprotected-Leu- α -Ketoacid of Composition A (Segment 2A)

Peptide synthesis: Opr-IL2(42-69)-Leu-photoprotected-α-ketoacid segment 2A (see 41-70 of SEQ ID NO: 3) was synthesized on a 0.2 mmol scale on Rink-Amide MBHA resin pre-loaded with Fmoc-Leu-photoprotected- α -ketoacid (0.8 g) with a substitution capacity of ~0.25 mmol/g. Automated Fmoc-SPPS of segment 2A was performed following the general procedure “Solid-phase peptide synthesis (SPPS)”. The resin was washed with DCM and dried under vacuum. The mass of the dried peptidyl resin was 1.8 g. The crude peptide was precipitated following the procedure “Resin cleavage and side-chain deprotection of the peptides” using a cocktail of 95:2.5:2.5 TFA/DODT/H₂O v/v/v (15 mL/g resin) at r.t. for 2.0 hours.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 60° C., gradient: 10 to 60%B in 30 min. The fractions containing the purified product were pooled and lyophilized to segment 2A as a white solid in 97% purity. The isolated yield based on the resin loading was 203 mg (20%). HRMS (ESI): C₁₈₄H₂₈₆N₄₀O₅₂S; Average isotope calculated: 3922.0742 Da [M+H]⁺; found: 3922.0680 Da [M+H]⁺.

Synthesis of Fmoc-Opr IL2 (72-102)-Phe-α-Ketoacid of Composition A (Segment 3A)

Peptide synthesis: Fmoc-Opr IL2 (72-102)-Phe-α-ketoacid segment 3A (See residues 71-103 of SEQ ID NO: 3) was synthesized on a 0.2 mmol scale on Rink-Amide ChemMatrix resin pre-loaded with Fmoc-Phe-photoprotected-α-ketoacid (0.8 g) with a substitution capacity of -0.286 mmol/g. Automated Fmoc-SPPS of segment 3A was performed following the general procedure “Solid-phase peptide synthesis (SPPS)”. The resin was washed with DCM and dried under vacuum. The mass of the dried peptidyl resin was 2.17 g. The crude peptide was precipitated following the procedure “Resin cleavage and side-chain deprotection of the peptides” using a cocktail of 95:2.5:2.5 TFA/DODT/H₂O v/v/v (10 mL/g resin) at r.t. for 2.0 hours.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 40° C., 2-step gradient: 10 to 30%B in 10 min followed by 30 to 80%B in 30 min. The fractions containing the purified product were pooled and lyophilized to segment 3A as a white solid in 98% purity. The isolated yield based on the resin loading was 200 mg (17.6%). HRMS (ESI): C₁₈₄H₂₈₃N₄₅O₅₃; Average isotope calculated 3973.0891 Da [M+H]⁺; found: 3973.0995 Da [M+H]⁺.

Synthesis of IL-2 Opr- IL2(105-133) of Composition A (Segment 4A)

Peptide synthesis: Opr-IL2(105-133) segment 4A (See residues 104-133 of SEQ ID NO: 3) was synthesized on a 0.1 mmol scale on Wang resin pre-loaded with Fmoc-Thr-OH (0.294 g) with a substitution capacity of -0.34 mmol/g. Automated Fmoc-SPPS of segment 4A was performed following the general procedure “Solid-phase peptide synthesis (SPPS)”. The resin was washed with DCM and dried under vacuum. The mass of the dried peptidyl resin was 725 mg. The crude peptide was precipitated following the procedure “Resin cleavage and side-chain deprotection of the peptides” using a cocktail of 92.5:2.5:2.5:2.5 TFA/TIPS/DODT/H₂O v/v/v/v (10 mL/g resin) at r.t. for 2 hours.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 40° C., gradient: 10 to 50%B in 40 min. The fractions containing the purified product were pooled and lyophilized to segment 4A as a white solid in 90.8% purity. The isolated yield based on the resin loading was 40 mg (8%). HRMS (ESI): C₁₅₈H₂₄₁N₃₇O₅₂S; Average isotope calculated 1175.2449 Da [M+H]⁺³; found: 1175.2440 [M+H]⁺³.

KAHA Ligation for the Preparation of IL2-Seg12 of Composition A (Segment 12A)

Ligation and photodeprotection: The segment 12A was obtained following the general procedure “Ligation of IL-2 segments 1 and 2 and photodeprotection” with 34 mg (6.56 µmol; 1.1 equiv.) of segment 1A and 19 mg (4.9 µmol; 1.0 equiv.) of segment 2A dissolved in 241 µL of 9.5:0.5 v/v DMSO/H₂O solution containing 0.1 M oxalic acid.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 40° C., 2-step gradient: 10 to 40%B in 5 min followed by 40 to 70%B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 12A as a white solid in 98% purity. The isolated yield was 55% (25.5 mg). HRMS (ESI): C₄₀₀H₆₆₇N₁₀₃O₁₁₉S; Average isotope calculated: 8855.2806 Da [M+H]⁺; found: 8855.9008 Da [M+H]⁺.

KAHA Ligation for the Preparation of IL2-Seg34 of Composition A (Segment 34A)

Ligation: The segment 34A was obtained following the general procedure “Ligation of IL-2 segments 3 and 4 and Fmoc deprotection” with 69 mg (17.5 µmol; 1.1 equiv.) of segment 3A and 59 mg (16.6 µmol; 1.0 equiv.) of segment 4A dissolved in 1100 µL of 9.9:0.1 DMSO/H₂O v/v containing 0.1 M oxalic acid.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 40° C., gradient: 20 to 60%B in 40 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 34A as a white solid in 95% purity. The isolated yield was 33% (42.3 mg). HRMS (ESI): C₃₂₆H₅₁₄N₈₂O₁₀₁S; Average isotope calculated 7229.7437 Da [M+H]⁺; found: 7229.7618 Da [M+H]⁺.

Final KAHA Ligation for the Preparation of IL2 Linear Protein of Composition A (Segment 1234A)

Ligation: The segment 1234A was obtained following the general procedure “Final ligation” with 45 mg (5.1 µmol; 1.2 equiv.) of segment 12A and 31 mg (16.6 µmol; 1.0 equiv.) of segment 34A dissolved in 220 µL of 9.5:0.5 DMSO/H₂O v/v containing 0.1 M oxalic acid.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 40° C., gradient: 30 to 80%B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain Acm protected segment 1234A as a white solid in 95% purity. The isolated yield was 26% (18 mg).
Acm deprotection: The deprotection of cysteine residues was performed following the general procedure “Acm deprotection” with 18 mg of Acm protected segment 1234A as starting material.
Purification: C18 column (5 µm, 20 × 250 mm), flow rate 10 mL/min at 40° C., 2-step gradient: 10 to 30%B in 5 min followed by 30 to 95%B in 20 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 1234A as a white solid in 97% purity. The isolated yield was 17% (11.6 mg). HRMS (ESI): C₇₁₉H₁₁₇₁N₁₈₃O₂₁₆S₂; Average isotope calculated: 15898.5963 Da [M+H]⁺; found: 15898.6118 Da [M+H]⁺.

Folding of IL-2 Linear Protein of Composition A

Rearrangement of linear protein: IL2-Seg1234-A linear protein (11.7 mg, 0.736 µmol) was dissolved in aqueous 6 M Gu·HCl containing 0.1 M Tris and 30 mM reduced glutathione (15 µM protein concentration) and the mixture was gently shaken at 50° C. for 2 hours.
Folding of the linear rearranged protein (method 1): After completion of rearrangement reaction, the sample was cooled to room temperature and diluted with 0.1 M Tris and 1.5 mM oxidized glutathione, pH 8.0 (5 µM protein concentration). The folding was allowed to proceed for 20 hours at room temperature. Then, the sample was acidified with TFA to pH 3 and purified by preparative HPLC using a C4 column (20 × 250 mm) kept at room temperature with a two-step gradient of 5 to 40 to 95% acetonitrile with 0.1% TFA in 60 min, at a flow rate of 10.0 mL/min, using CH₃CN/H₂O with 0.1% TFA (v/v) as mobile phase. The fractions containing the product were pooled and lyophilized to give pure folded protein Composition A as a white powder in 98% purity (2.2 mg, 19% yield for folding and purification steps).
The purity and identity of the pure protein was confirmed by analytical RP-HPLC, MALDI-TOF and analytical size exclusion. HRMS (ESI): C₇₁₉H₁₁₆₉N₁₈₃O₂₁₆S₂; Average isotope calculated: 15896.5806 Da [M+ H]⁺; found: 15896.6322 Da [M+H]⁺

Synthesis of IL-2 Protein Composition A1

IL-2 composition A folded protein (39.76 mg, 1 equiv.) were first dissolved in 8 mL of 10 mM sodium acetate buffer, 8.4% Sucrose, 0.02% polysorbate80 pH 5.0. The solution was supplemented with 22 mL 50 mM sodium acetate buffer pH 5.0 and 30 kDa DBCO-polyethylene glycol polymer (392.05 mg, 5 equiv) and the reaction was gently mixed at 25° C. for 17 hours. The reaction mixture was loaded 10 mL at a time on a HiTrap Capto S ImpAct column (5 mL) and purified at a flow rate of 2.5 mL/min with a gradient of 20 CV from 50 mM sodium acetate buffer pH 5.0 to 50 mM sodium acetate buffer with 1 M NaCl. The fractions containing the IL-2 composition A1 PEGylated protein were pooled together and dialyzed against 10 mM sodium acetate buffer, 8.4% Sucrose, 0.02% polysorbate80 pH 5.0 to obtain 12.26 mg of protein fraction IL-2 composition A1 PEGylated protein as determined by BCA (31% yield for PEGylation and purifications steps). The purity and identity of the pure PEGylated protein was confirmed by analytical RP-HPLC, MALDI-TOF and analytical size exclusion.

EXAMPLE 3 Synthesis of Composition B and B1 Variants of IL-2

For this variant, except segment 3, all the other segments are the same as the ones used for Composition A.

Synthesis of Fmoc-Opr IL2 (72-102)-Phe-α-Ketoacid of Composition B (Segment 3B)

Fmoc-Opr IL2 (72-102)-Phe-α-ketoacid segment 3B (See residues 71-103 of SEQ ID NO: 4) was synthesized by automated Fmoc-SPPS synthesis in analogy to the procedures described for the synthesis of segment 3A to yield segment 3B as a white solid in >98% purity. The isolated yield based on the resin loading was 18% (200 mg). HRMS (ESI): C₁₈₄H₂₈₄N₄₆O₅₂; Average isotope calculated 3972.1051 Da [M+H]⁺; found: 3972.1054 Da [M+H]⁺.

Synthesis of IL2-Seg34 of Composition B by KAHA Ligation

Ligation: The segment 34B was obtained following the general procedure “Ligation of IL-2 segments 3 and 4 and Fmoc deprotection” with 37 mg (9.3 µmol; 1.2 equiv.) of segment 3B and 27 mg (7.8 µmol; 1.0 equiv.) of segment 4A dissolved in 517 µL of 9.8:0.2 DMSO/H₂O v/v containing 0.1 M oxalic acid.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 40° C., 2-step gradient: 10 to 40% %B in 5 min followed by 40 to 80% %B in 35 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 34B as a white solid in >99% purity. The isolated yield was 22% (12.6 mg). HRMS (ESI): C₃₂₆H₅₁₅N₈₃O₁₀₀S; Average isotope calculated 7228.7597 Da [M+ H]⁺; found: 7228.7738 Da [M+H]⁺.

Final KAHA Ligation for the Preparation of IL2 Linear Protein of Composition B (Segment 1234B)

Ligation: The segment 1234B was obtained following the general procedure “Final ligation” with 34 mg (3.8 µmol; 1.2 equiv.) of segment 12A and 23 mg (3.2 µmol; 1.0 equiv.) of segment 34B dissolved in 214 µL of 9.5:0.5 DMSO/H₂O v/v containing 0.1 M oxalic acid.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 40° C., 2-step gradient: 10 to 40% %B in 5 min followed by 40 to 80% %B in 35 min. The fractions containing the purified product were pooled and lyophilized to obtain Acm protected segment 1234B as a white solid in 96% purity. The isolated yield was 52% (26.8 mg). HRMS (ESI): C₇₂₅H₁₁₈₂N₁₈₆O₂₁₇S₂; Average isotope calculated 16039.6865 Da [M+H]⁺; found: 16039.6389 Da [M+H]⁺.
Acm deprotection: The deprotection of cysteine residues was performed following the general procedure “Acm deprotection” with 26.8 mg of Acm protected segment 1234B as starting material.
Purification: C18 column (5 µm, 20 × 250 mm), flow rate 10 mL/min at 40° C., 2-step gradient: 10 to 30%B in 5 min followed by 30 to 95%B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 1234B as a white solid in 97% purity. The isolated yield was 55% (14.5 mg). HRMS (ESI): C₇₁₉H₁₁₇₂N₁₈₄O₂₁₅S₂; Average isotope calculated: 15897.6117 Da [M+H]⁺; found: 15897.6195 Da [M+H]⁺.

Folding of IL-2 Linear Protein of Composition B

Rearrangement of linear protein: IL2-Seg1234-B linear protein (14.5 mg, 0.913 µmol) was dissolved in aqueous 6 M Gu-HCl containing 0.1 M Tris and 30 mM reduced glutathione (61 mL, 15 µM protein concentration) and the mixture was gently shaken at 50° C. for 2 hours.
Folding of the linear rearranged protein: After completion of rearrangement reaction, the sample was cooled to room temperature and diluted with 0.1 M Tris and 1.5 mM oxidized glutathione, pH 8.0 (122 mL, 5 µM protein concentration). The folding was allowed to proceed for 20 hours at room temperature. Then, the sample was acidified with TFA to pH 3 and purified by preparative HPLC using a C4 column (20 × 250 mm) kept at room temperature with a two-step gradient of 10 to 30%B in 5 min followed by 30 to 95%B in 30 min, at a flow rate of 10.0 mL/min. The fractions containing the product were pooled and lyophilized to give pure folded IL2-Seg1234-B protein as as a white powder in >98% purity. (3.9 mg, 27% yield for folding and purification steps). HRMS (ESI): C₇₁₉H₁₁₇₀N₁₈₄O₂₁₅S₂; Average isotope calculated: 15895.5966 Da [M+H]⁺; found: 15895.5669 Da [M+H]⁺.

Synthesis of IL-2 Protein Composition B1

To a solution of IL2-Seg1234-B (2 mg, 0.126 µmol, 1 equiv.) in 1:1 CH₃CN:H₂O (50 mM protein concentration) was added a 30 kDa DBCO-polyethylene glycol polymer (11.7 mg, 0.403 µmol, 3.2 equiv) and the reaction was gently mixed at 25° C. for 20 hours. The reaction mixture was diluted with 1:1 CH₃CN/H₂O + 0.1% TFA and purify on preparative HPLC, using a C4 column (20 × 250 mm) with a two-step gradient of 10 to 30%B in 5 min followed by 30 to 95%B in 30 min, flow rate: 10.0 mL/min. The fractions containing the PEGylated IL2-Seg1234-B1 protein were pooled together and lyophilized to obtain 2.5 mg of IL2-Seg1234-B1 PEGylated protein as a white powder in 98% purity. (29% yield for PEGylation and purifications steps). The purity and identity of the pure PEGylated protein was confirmed by analytical RP-HPLC, MALDI-TOF, SEC-HPLC and SDS-page.

Example 4 Synthesis of Composition C and C1 Variants of IL-2

For this variant, except segment 2, all the other segments are the same as the ones used for Composition A.

Synthesis of IL-2 Fmoc-Opr IL2 (42-69)-Leu-α-Ketoacid of Composition C(Segment 2C)

Opr-IL2(42-69)-Leu-photoprotected-a-ketoacid segment 2C (See residues 41-70 of SEQ ID NO: 5) was synthesized by automated Fmoc-SPPS synthesis in analogy to the procedures described for the synthesis of segment 2A to yield segment 2C as a white solid in 94% purity. The isolated yield based on the resin loading was 19.7% (153.7 mg). MALDI-TOF was used to confirm the desired product mass was obtained.

Synthesis of IL2-Seg12 of Composition C by KAHA Ligation (Segment 12C)

Ligation and photodeprotection: The segment 12C was obtained following the general procedure “Ligation of IL-2 segments 1 and 2 and photodeprotection” with 90 mg of segment 1A (17.4 µmol; 1.1 equiv.) and 56 mg (14.5 µmol; 1.0 equiv.) of segment 2C dissolved in 1157 µL of 9.5:0.5 v/v DMSO/H₂O solution containing 0.1 M oxalic acid.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 40° C., 2-step gradient: 10 to 40%B in 5 min followed by 40 to 70%B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 12C as a white solid in >99% purity. The isolated yield was 36% (46.7 mg).

Final KAHA Ligation for the Preparation of IL2 Linear Protein of Composition C (Segment 1234C)

Ligation: The segment 1234C was obtained following the general procedure “Final ligation” with 46.7 mg (5.24 µmol; 1.2 equiv.) of segment 12C and 32 mg (4.41 µmol; 1.0 equiv.) of segment 34A dissolved in 683 µL of 9.5:0.5 DMSO/H₂O v/v containing 0.1 M oxalic acid.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 60° C., gradient: 30 to 80% %B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain Acm protected segment 1234C as a white solid. The isolated yield was 34% (24.5 mg).
Acm deprotection: The deprotection of cysteine residues was performed following the general procedure “Acm deprotection” with 24.5 mg of Acm protected segment 1234C as starting material.
Purification: C18 column (5 µm, 20 × 250 mm), flow rate 10 mL/min at 40° C., 2-step gradient: 10 to 30%B in 5 min followed by 30 to 95%B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 1234C as a white solid in 94% purity. The isolated yield was 69% (16.6 mg). HRMS (ESI): C₇₁₇H₁₁₆₇N₁₈₃O₂₁₆S₂; Average isotope calculated: 15870.5650 Da [M+H]⁺; found: 15870.6232 Da [M+H]⁺.

Folding of IL-2 Linear Protein of Composition C

Rearrangement of linear protein: IL2-Seg1234-C linear protein (16.6 mg, 1.04 µmol) was dissolved in aqueous 6 M Gu-HCl containing 0.1 M Tris and 30 mM reduced glutathione (69 mL, 15 µM protein concentration) and the mixture was gently shaken at 50° C. for 2 hours.
Folding of the linear rearranged protein: After completion of rearrangement reaction, the sample was cooled to room temperature and diluted with 0.1 M Tris and 1.5 mM oxidized glutathione, pH 8.0 (140 mL, 5 µM protein concentration). The folding was allowed to proceed for 20 hours at room temperature. Then, the sample was acidified with TFA to pH 3 and purified by preparative HPLC using a C4 column (20 × 250 mm) kept at room temperature with a two-step gradient of 10 to 30%B in 5 min followed by 30 to 95%B in 30 min, at a flow rate of 10.0 mL/min. The fractions containing the product were pooled and lyophilized to give pure folded IL2-Seg1234-C protein as as a white powder in >99% purity (3.4 mg, 20.5% yield for folding and purifications steps). HRMS (ESI): C₇₁₇H₁₁₆₅N₁₈₃O₂₁₆S₂; Average isotope calculated: 15868.5493 Da [M+H]⁺; found: 15868.5979 Da [M+H]⁺.

Synthesis of IL-2 Protein Composition C1

To a solution of IL2-Seg1234-C (2 mg, 1 equiv.) in 1:1 CH₃CN:H₂O (50 µM protein concentration) was added a 30 kDa DBCO-polyethylene glycol polymer (11.0 mg, 3 equiv) and the reaction was gently mixed at 25° C. for 20 hours. The reaction mixture was diluted with 1:1 CH₃CN/H₂O + 0.1% TFA and purify on preparative HPLC, using a C4 column (20 × 250 mm) with a two-step gradient 10 to 30%B in 5 min followed by 30 to 95%B in 30 min, at a flow rate of 10.0 mL/min. The fractions containing the PEGylated IL2-Seg1234-C1 protein were pooled together and lyophilized to obtain 1.4 mg of IL2-Seg1234-C1 PEGylated protein as a white powder in >99% purity. (25% yield for PEGylation and purifications steps). The purity and identity of the pure PEGylated protein was confirmed by analytical RP-HPLC and MALDI-TOF.

Example 5: Synthesis of Composition D and D1 Variants of IL-2

For this variant, except segment 1, all the other segments are the same as the ones used for Composition B.

Synthesis of IL-2 (1-39)-Leu-α-Ketoacid of Composition D (Segment ID)

IL2 (1-39)-Leu-α-ketoacid segment 1D (See residues 1-40 of SEQ ID NO: 6) was synthesized by automated Fmoc-SPPS synthesis in analogy to the procedures described for the synthesis of segment 1A to yield segment 1D as a white solid in 98% purity. The isolated yield based on the resin loading was 20% (209 mg). MALDI-TOF was used to confirm the desired product mass was obtained.

Synthesis of IL2-Seg12 of Composition D by KAHA Ligation (Segment 12D)

Ligation and photodeprotection: The segment 12D was obtained following the general procedure “Ligation of IL-2 segments 1 and 2 and photodeprotection” with 60 mg (11.7 µmol; 1.1 equiv.) of segment 1D and 38 mg (9.7 µmol; 1.0 equiv.) of segment 2A dissolved in 780 µL of 9.5:0.5 v/v DMSO/H₂O solution containing 0.1 M oxalic acid.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 40° C., 2-step gradient: 10 to 40%B in 5 min followed by 40 to 70%B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 12D as a white solid. The isolated yield was 54% (46.2 mg). HRMS (ESI): C₃₉₇H₆₆₁N₁₀₃O₁₁₉S; m/z calculated: 8812.8698 Da [M+H]⁺; found: 8812.8833 Da [M+H]⁺.

Final KAHA Ligation for the Preparation of IL2 Linear Protein of Composition D (Segment 1234D)

Ligation: The segment 1234D was obtained following the general procedure “Final ligation” with 35.2 mg (5.24 µmol; 1.2 equiv.) of segment 12D and 26 mg (3.62 µmol; 1.0 equiv.) of segment 34B dissolved in 270 µL of 9.5:0.5 DMSO/H₂O v/v containing 0.1 M oxalic acid.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 60° C., gradient: 30 to 80% %B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain Acm protected segment 1234D as a white solid. The isolated yield was 26% (15 mg).
Acm deprotection: The deprotection of cysteine residues was performed following the general procedure “Acm deprotection” with 15 mg (0.95 µmol) of Acm protected segment 1234D as starting material.
Purification: C18 column (5 µm, 20 × 250 mm), flow rate 10 mL/min at 40° C., 2-step gradient: 10 to 30%B in 5 min followed by 30 to 95%B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 1234D as a white solid in 94% purity. The isolated yield was 80% (12 mg). HRMS (ESI): C₇₁₆H₁₁₆₆N₁₈₄O₂₁₅S₂; Average isotope calculated: 15855.5653 Da [M+H]⁺; found: 15855.5300 Da [M+H]⁺.

Folding of IL-2 Linear Protein of Composition D

Rearrangement of linear protein: IL2-Seg1234-D linear protein (9 mg, 0.568 µmol) was dissolved in aqueous 6 M Gu-HCl containing 0.1 M Tris and 30 mM reduced glutathione (38 mL, 15 µM protein concentration) and the mixture was gently shaken at 50° C. for 2 hours.
Folding of the linear rearranged protein: After completion of rearrangement reaction, the sample was cooled to room temperature and diluted with 0.1 M Tris and 1.5 mM oxidized glutathione, pH 8.0 (76 mL, 5 µM protein concentration). The folding was allowed to proceed for 44 hours at room temperature. Then, the sample was acidified with TFA to pH 3 and purified by preparative HPLC using a Shiseido ProteonAvi C4 column (20 × 250 mm) kept at room temperature with a two-step gradient of 10 to 30%B in 5 min followed by 30 to 95%B in 30 min, at a flow rate of 10.0 mL/min.. The fractions containing the product were pooled and lyophilized to give folded IL2-Seg1234-D as a white solid in >98% purity (0.3 mg, 3% yield for folding and purification steps).

Synthesis of IL-2 Protein Composition DI

To a solution of IL2-Seg1234-D (0.3 mg, 1 equiv.) in 1:1 CH₃CN:H₂O (50 µM protein concentration) was added a 30 kDa DBCO-polyethylene glycol polymer (1.8 mg, 3.2 equiv) and the reaction was gently mixed at 25° C. for 20 hours. The reaction mixture was diluted with 1:1 CH₃CN/H₂O + 0.1% TFA and purify on preparative HPLC, using a C4 column (20 × 250 mm) with a two-step gradient of 10 to 30%B in 5 min followed by 30 to 95%B in 30 min, at a flow rate of 10.0 mL/min. The fractions containing the PEGylated IL2-Seg1234-D1 protein were pooled together and lyophilized to obtain 0.1 mg of IL2-Seg1234-D1 PEGylated protein as a white powder in >98% purity. (11% yield for PEGylation and purifications steps).
The purity and identity of the pure PEGylated protein was confirmed by analytical RP-HPLC, MALDI-TOF.

Example 6: Synthesis of Composition E and E1 Variants of IL-2

Synthesis of IL-2 (1-39)-Leu-α-Ketoacid of Composition E (Segment 1E)

IL2 (1-39)-Leu-α-ketoacid segment 1E (See residues 1-40 of SEQ ID NO: 7) was synthesized by automated Fmoc-SPPS synthesis in analogy to the procedures described for the synthesis of segment 1A to yield segment 1E as a white solid in 97% purity. The isolated yield based on the resin loading was 17% (180 mg). HRMS (ESI): C₂₂₅H₃₈₈N₆₄O₇₂; Average isotope calculated 5140.87247 Da [M+H]⁺; found: 5141.8699 Da [M+H]⁺.

Synthesis of IL2-Seg12 of Composition E by KAHA Ligation (Segment 12E)

Ligation and photodeprotection: The segment 12E was obtained following the general procedure “Ligation of IL-2 segments 1 and 2 and photodeprotection” with 60 mg (11.7 µmol; 1.1 equiv.) of segment 1E and 38 mg (9.7 µmol; 1.0 equiv.) of segment 2A dissolved in 780 µL of 9.5:0.5 v/v DMSO/H₂O solution containing 0.1 M oxalic acid.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 40° C., 2-step gradient: 10 to 40%B in 5 min followed by 40 to 70%B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 12E as a white solid. The isolated yield was 55% (33.4 mg). HRMS (ESI): C₃₉₇H₆₆₁N₁₀₃O₁₁₉S; m/z calculated: 8812.8698 Da [M+H]⁺; found: 8812.8833 Da [M+H]⁺.

Final KAHA Ligation for the Preparation of IL2 Linear Protein of Composition E (Segment 1234E)

Ligation: The segment 1234E was obtained following the general procedure “Final ligation” with 17.5 mg (1.98 µmol; 1.2 equiv.) of segment 12E and 12 mg (1.66 µmol; 1.0 equiv.) of segment 34B dissolved in 256 µL of 9.5:0.5 DMSO/H₂O v/v containing 0.1 M oxalic acid.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 60° C., gradient: 30 to 80% %B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain Acm protected segment 1234E as a white solid. The isolated yield was 22% (6.6 mg). MALDI-TOF was used to confirm the desired product mass was obtained.
Acm deprotection: The deprotection of cysteine residues was performed following the general procedure “Acm deprotection” with 6.6 mg (0.37 µmol) of Acm protected segment 1234E as starting material.
Purification: C18 column (5 µm, 20 × 250 mm), flow rate 10 mL/min at 40° C., 2-step gradient: 10 to 30%B in 5 min followed by 30 to 95%B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 1234E as a white solid in 94% purity. The isolated yield was 98% (5.8 mg). HRMS (ESI): C₇₁₆H₁₁₆₆N₁₈₄O₂₁₅S₂; Average isotope calculated: 15855.5653 Da [M+H]⁺; found: 15855.5479 Da [M+H]⁺.

Folding of IL-2 Linear Protein of Composition E

Rearrangement of linear protein: IL2-Seg1234-E linear protein (5.8 mg, 0.366 µmol) was dissolved in aqueous 6 M Gu-HCl containing 0.1 M Tris and 30 mM reduced glutathione (24 mL, 15 µM protein concentration) and the mixture was gently shaken at 50° C. for 2 hours.
Folding of the linear rearranged protein: After completion of rearrangement reaction, the sample was cooled to room temperature and diluted with 0.1 M Tris and 1.5 mM oxidized glutathione, pH 8.0 (48 mL, 5 µM protein concentration). The folding was allowed to proceed for 20 hours at room temperature. Then, the sample was acidified with TFA to pH 3 and purified by preparative HPLC using a C4 column (20 × 250 mm) kept at room temperature with a two-step gradient of 10 to 30%B in 5 min followed by 30 to 95%B in 30 min, at a flow rate of 10.0 mL/min. The fractions containing the product were pooled and lyophilized to give folded IL2-Seg1234-E as a white solid in >98% purity (0.6 mg, 10% yield for folding and purification steps).

Synthesis of IL-2 Protein Composition E1

To a solution of IL2-Seg1234-E (0.6 mg, 1 equiv.) in 1:1 CH₃CN:H₂O (50 µM protein concentration) was added 30 kDa DBCO-mPEG (3 mg, 2.7 equiv) and the reaction was gently mixed at 25° C. for 20 hours. The reaction mixture was diluted with 1:1 CH₃CN/H₂O + 0.1% TFA and purify on preparative HPLC, using a Shiseido Proteonavi C4 column (20 × 250 mm) with a two-step gradient of 10 to 30%B in 5 min followed by 30 to 95%B in 30 min, at a flow rate of 10.0 mL/min. The fractions containing the PEGylated IL2-Seg1234-E1 protein were pooled together and lyophilized to obtain 0.2 mg of IL2-Seg1234-E1 PEGylated protein as a white powder in >98% purity. (12% yield for PEGylation and purifications steps). The purity and identity of the pure PEGylated protein was confirmed by analytical RP-HPLC, MALDI-TOF.

Example 7: Synthesis of Composition F

For this variant, except segment 2, all the other segments are the same as the ones used for Composition B.

Synthesis of Opr-IL2(42-69)-Leu-Photoprotected-α-Ketoacid of Composition F (Segment 2F)

Opr-IL2(42-69)-Leu-photoprotected-α-ketoacid segment 2F (See residues 1-40 of SEQ ID NO: 8) was synthesized by automated Fmoc-SPPS synthesis in analogy to the procedures described for the synthesis of segment 2A to yield segment 2F as a white solid in 99% purity. The isolated yield based on the resin loading was 35% (269 mg). HRMS (ESI): C₁₈₁H₂₈₀N₄₀O₅₂S; m/z calculated: 3880.0273 Da [M+H]⁺; found: 3880.0207 Da [M+H]⁺.

Synthesis of IL2-Seg12 of Composition F by KAHA Ligation (Segment 12F)

Ligation and photodeprotection: The segment 12F was obtained following the general procedure “Ligation of IL-2 segments 1 and 2 and photodeprotection” with 34 mg (6.6 µmol; 1.1 equiv.) of segment 1A and 19 mg (4.9 µmol; 1.0 equiv.) of segment 2F dissolved in 385 µL of 9.5:0.5 v/v DMSO/H₂O solution containing 0.1 M oxalic acid.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 40° C., 2-step gradient: 10 to 40%B in 5 min followed by 40 to 70%B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 12F as a white solid in 96% purity. The isolated yield was 59% (25.5 mg). MALDI-TOF was used to confirm the desired product mass was obtained.

Final KAHA Ligation for the Preparation of IL2 Linear Protein of Composition F (Segment 1234F)

Ligation: The segment 1234F was obtained following the general procedure “Final ligation” with 25.5 mg (2.89 µmol; 1.2 equiv.) of segment 12F and 17.5 mg (2.42 µmol; 1.0 equiv.) of segment 34B dissolved in 373 µL of 9.5:0.5 DMSO/H₂O v/v containing 0.1 M oxalic acid.
Purification: C18 column (5 µm, 50 × 250 mm), flow rate 40 mL/min at 60° C., gradient: 30 to 80% %B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain Acm protected segment 1234F as a white solid. The isolated yield was 31% (12 mg). MALDI-TOF was used to confirm the desired product mass was obtained.
Acm deprotection: The deprotection of cysteine residues was performed following the general procedure “Acm deprotection” with 12 mg (0.75 µmol) of Acm protected segment 1234F as starting material.
Purification: C18 column (5 µm, 20 × 250 mm), flow rate 10 mL/min at 40° C., 2-step gradient: 10 to 30%B in 5 min followed by 30 to 95%B in 30 min. The fractions containing the purified product were pooled and lyophilized to obtain segment 1234F as a white solid in 94% purity. The isolated yield was 73% (8.7 mg). HRMS (ESI): C₇₁₆H₁₁₆₆N₁₈₄O₂₁₅S₂; Average isotope calculated: 15855.5653 Da [M+H]⁺; found: 15855.6061 Da [M+H]⁺.

Folding of IL-2 Linear Protein of Composition F

Rearrangement of linear protein: IL2-Seg1234-F linear protein (8.7 mg, 0.549 µmol) was dissolved in aqueous 6 M Gu-HCl containing 0.1 M Tris and 30 mM reduced glutathione (37 mL, 15 µM protein concentration) and the mixture was gently shaken at 50° C. for 2 hours.
Folding of the linear rearranged protein: After completion of rearrangement reaction, the sample was cooled to room temperature and diluted with 0.1 M Tris and 1.5 mM oxidized glutathione, pH 8.0 (80 mL, 5 µM protein concentration). The folding was allowed to proceed for 44 hours at room temperature. Then, the sample was acidified with TFA to pH 3 and purified by preparative HPLC using a C4 column (20 × 250 mm) kept at room temperature with a two-step gradient of 10 to 30%B in 5 min followed by 30 to 95%B in 30 min, at a flow rate of 10.0 mL/min. The fractions containing the product were pooled and lyophilized to give pure folded IL2-Seg1234-F (0.2 mg, 2% yield for folding and purification steps). The purity and identity of the pure folded protein was confirmed by analytical RP-HPLC and MALDI-TOF.

Example 8: Selective Activation of STAT5 by Unconjugated and PEGylated IL-2 Variants

Engagement of the IL-2R results in the phosphorylation of signal transducer and activator of transcription 5 (STAT5) and this can be used as a readout to assess selectivity for T cell subsets. Primary pan T-cells were obtained from healthy donor buffy coat by peripheral blood mononuclear cells (PBMC) purification using ficoll gradient centrifugation followed by negative isolation with magnetic beads and then cryopreserved until further use. Pan T-cells were thawed and incubated overnight in T-cell medium (RPMI 10% FCS, 1% Glutamine, 1% NEAA, 25)µM βMeoH, 1% NaPyruvate) followed by two washing steps with PBS. Cells were resuspended in PBS and distributed at 200,000 cells per well followed by incubation for 40 min at 37° C./5% CO₂ with either aldesleukin, unconjugated IL-2 polypeptide (Composition A), PEGylated IL-2 polypeptide (Composition A1), or another indicated variant provided herein. After incubation, cells were fixed and permeabilized using the Transcription Factor Phospho Buffer kit followed by a surface and intracellular immunostaining for CD4, CD8, CD25, FoxP3 and pSTAT5 to enable cell subset identification and measure of levels of STAT5 phosphorylation. The FACS measurement was done either with a NovoCyte or a Quanteon Flow Cytometer from Acea. Tregs were classified as CD4+CD25+FoxP3+ cells and Teff as CD8+ T cells. EC50 results of STAT5 phosphorylation assay from the indicated variants in various immune cell types is shown below in Table 6. More detailed information about the data found in Table 6 below can be found in FIG. 4C and FIG. 4D.

TABLE 6

SEQ ID NO / Identifier	Treg EC50 (nM)	CD4 conv EC50 (nM)	CD8 EC50 (nM)	CD8 naïve EC50 (nM)	CD8 memory EC50 (nM)
Aldesleukin	0.019		9.069	477
9	0.05	2.14	588.57	822.42
10	2.55		650.00
11	3.96		650.00
12	200.00		650.00
16	0.03	1.31	1.68	1.81
17	1000.00	1000.00	10000.00	10000.00
18	0.08	15.86	23.51	21.14
19	9.78	477.33	10000.00	10000.00
13	0.65	4156.82	8650.00	8411.76
14	0.29	29.14	372.06	444.40
15	0.01	2.52	28.38	29.80
20	0.03	1.20	227.40	311.90
21	0.07	4.81	150.89	203.80
22	9.99	1750.00	3769.23	3769.23
23	0.49	1000.00	1821.00	1882.29
24	18.28	4000.00	10000.00	10000.00
25	0.43	2285.71	10000.00	10000.00
26	0.67	2636.36	4272.73	4272.73
27	5.94	4000.00	10000.00	10000.00
28	1.02	1000.00	4000.00	4000.00
29	9.32	2285.71	10000.00	10000.00
30	10.70	7000.00	10000.00	10000.00
31	16.98	7000.00	10000.00	10000.00
32	94.88	7000.00	10000.00	10000.00
33	2.53	4000.00	1000.00	1000.00
34	2.44	1000.00	1000.00	1000.00
35	15.66	7000.00	10000.00	10000.00
36	11.70	4000.00	10000.00	10000.00
37	1.11	5500.00	10000.00	10000.00
38	0.40	8875.00	10000.00	10000.00
39	91.89	5500.00	10000.00	10000.00
40	0.79	914.38	1000.00	1000.00
41	2.76	1000.00	1000.00	1000.00
42	8.71	6294.50	4460.00	10000.00
43	100.00		1000.00
Composition B (SEQ ID NO: 4 + 0.5 kDa azido PEG)	0.01	0.73	3.13	4.19
Composition D (SEQ ID NO: 6 + 0.5 kDa azido PEG)	0.70	32.95	69.16	795.40
Composition E (SEQ ID NO: 7 + 0.5 kDa azido PEG)	0.90	59.06	188.92	306.10
Composition C (SEQ ID NO: 5 + 0.5 kDa azido PEG)	1.28	2296.20	2472.92	5646.83
Composition A (SEQ ID NO: 3 + 0.5 kDa azido PEG)	2.03	1067.90	4095.72	3867.39	424.18
Composition A1 (SEQ ID NO: 3 + 30 kDa PEG)	16.78	4739.35	5786.34	6683.42	361.95
Composition F (SEQ ID NO: 8 + 0.5 kDa azido PEG)	0.62	79.45	292.37	504.42

Both the unconjugated (Composition A) and PEGylated IL-2 polypeptide (Composition A1), activated STAT5 selectively in Tregs (FIG. 4B) with little effect on STAT5 activation in Teff cells (FIG. 4A). On the other hand, aldesleukin non-selectively activated STAT5 in both Tregs and Teff cells. The potency of STAT5 activation for the PEGylated IL-2 polypeptide (Composition A1) was lower than for the unconjugated IL-2 polypeptide (Composition A), suggesting that the PEGylation leads to a slight reduction in activity.
Additionally, both the unconjugated and PEGylated IL-2 polypeptide activated STAT5 in Tregs from mouse and cynomolgus monkeys with comparable potency to that for human Tregs, thus demonstrating cross-reactivity to mouse and cynomolgus IL-2R (Table 7).

TABLE 7

	Treg human	Treg mouse	Treg cyno
Aldesleukin	0.025 (+-0.023) n=146	0.016 (+-0.012) n=2	0.06 n=1
Composition A	3.72 (+-6.64) n=33	4.16 (+/4.09) n=2	1.19 n=1
Composition A1	23.95 (+-20.3) n=22	45.45 (+-23.3) n=2	9.17 (+/-1.3) n=3

Example 9: Binding Affinity of PEGylated IL-2 Polypeptide (Composition A1) to Α and Β Subunits of the IL-2 Receptor

The binding affinities of PEGylated IL-2 polypeptide (Composition A1) and SEQ ID NO: 2 (aldesleukin) to the IL-2R alpha and beta subunits was measured using bio-layer interferometry (BLI) technology. Biotinylated IL-R2α and β (R&D, cat AVI10305-050 and AVI10459-050) were individually loaded onto Streptavidin Biosensors SAX2 and the sensor immersed into 1x Octet® kinetic buffer to set the baseline. The sensors were incubated in the analyte solution for 300 s followed by an incubation in kinetics buffer for 600 s to measure the dissociation. Octet® Analysis studio was used to calculate Kd values. Composition A1 had a higher affinity for the alpha subunit than aldesleukin (2.37 versus 12.23 nM, respectively) whereas binding to the beta subunit was abolished (FIG. 5 ). Composition A1 therefore represents an α-enhanced, β-dead IL-2 polypeptide.

Example 10: Pharmacokinetic/Pharmacodynamic Studies in Mice for Composition A1

Single-dose pharmacokinetic/pharmacodynamic (PK/PD) studies were performed in C57BL/6 mice receiving 5 daily subcutaneous (sc) injections of 0.3 mg/kg protein equivalents of aldesleukin or a single subcutaneous injection of 0.1 or 0.3 mg/kg of PEGylated IL-2 polypeptide Composition A1. Blood was sampled at various timepoints in K₂EDTA, plasma was generated by centrifugation and stored at -80° C. until PK analysis and cell pellets were freshly subjected to staining for flow cytometry analysis.
Cell pellets were treated with 1 × Lyse/Fix buffer (BD Bioscience, 558050) during 10 min. After washing, cells were stained with anti-CD3, ant-CD335, and anti-CD25 antibodies for 30 min at 4° C. Cells were then permeabilized using cold BD Perm Buffer III and stained with antibodies against Ki67, Siglec-F, CD4, CD8, FoxP3, CD62L, CD44 or pSTAT5. The FACS (fluorescence activated cell sorting) measurement was done with a Fortessa X-20 Flow Cytometer from BD. For each cell subset, the percentage of pSTAT5 positive cells, and percentage of Ki67 positive cells, cell counts and cell frequency was determined.
Concentrations of Composition A1 in plasma were determined using a qualified human IL-2 LegendPlex bead assay (Biolegend, #740717, #740368, #740758). PK data were subjected to a non-compartmental PK analysis by using the Phoenix WinNonlin software version 6.3. The linear/log trapezoidal rule was applied in obtaining the PK parameters. The PK profile of the modified IL-2 polypeptide (FIG. 6 ) peaked at 6 hours and concentration declined with a long half-life between 26 and 30 hours by virtue of the PEGylation. PK parameters (Table 8) showed a dose proportional increase in exposure. This PK profile is superior to the wild-type polypeptide whose half-life in mouse is reported to be within minutes.

TABLE 8

Dosing route	SC	SC
Dose of Composition A1 (mg/kg)	0.1	0.3
Cmax (ng/mL)	617	1685
Tmax (h)	6	6
T½ (h)	29.5	25.5
AUC0-inf (ng.h/mL)	12835	33843
MRT0-inf (h)	19.1	18.5

The immuno PD profiles of aldesleukin and PEGylated IL-2 polypeptide Composition A1 were assessed concurrently in the same study and monitored for 14 days. A single dose treatment with the PEGylated IL-2 polypeptide led to a strong and sustained STAT5 phosphorylation in the Treg population (CD3+, CD4+, CD25Hi, FoxP3+) with no or minimal effect on CD8+ Teff cells(CD3+, CD8+, CD4-) and NK cells (CD3-, CD49b+) (FIG. 7 ). In contrast, a 5-dose treatment with aldesleukin led to a more modest STAT5 phosphorylation profile in Treg cells and also no effect on CD8+ T eff cells and NK cells (FIG. 7 ). The activation of the IL-2 receptor signaling pathway in Treg cells upon treatment with Composition A1 translated into a pronounced and sustained upregulation of the proliferation marker Ki67, not observed on CD8+ Teff cells and NK cells. In contrast, the 5-dose treatment with aldesleukin led to limited Ki67 upregulation in Tregs (FIG. 7 ). The increased proliferation activity of the Treg subpopulation upon treatment with Composition A1 led to a very pronounced increase in Treg cell numbers compared to baseline, superior to the one observed upon 5-daily doses of aldesleukin. Cell expansion was selective to the Treg subpopulation and CD8+ Teff and NK cells remained comparably unchanged (FIG. 7 ).

Example 11: Composition A1 Suppresses Keyhole Limpet Hemocyanin-Induced Delayed Type Hypersensitivity

Delayed type hypersensitivity (DTH) represents a local T effector recall response to a previously encountered antigen. Here, mice are first sensitized to keyhole limpet hemocyanin (KLH) by immunization s.c. with KLH and then rechallenged several days later with an intradermal injection of the same antigen into the ear resulting in local tissue inflammation and swelling. Adult Balb/c mice were randomly allocated to experimental groups (n=10/group) and allowed to acclimatize for one week. On Day 0, animals were administered with an emulsion of 100 µg KLH in complete Freund’s adjuvant (CFA) by s.c. injection between the shoulder blades. Composition A1 was administered at 0.3 mg/kg s.c. on either day 0; days 0 and 3; days 0, 3 and 5 or days 0, 3, 5 and 8 (See FIG. 8A). Vehicle was administered s.c. on days 0, 3, 5 and 8. Following baseline measurements of right and left ear thickness using digital calipers, on Day 7, all animals were challenged with an intra-dermal injection of 10 µg KLH in sodium chloride 0.9% into the right ear. The contralateral (left) ear was administered with an equal volume of sodium chloride 0.9%. Ear thickness was measured at 24, 48, 72 and 96 hours using digital calipers. In the vehicle-treated group, ear inflammation peaked 48 hours post-challenge and then slowly resolved (FIG. 8A). A single administration of Composition A1 strongly suppressed ear inflammation at all time points compared to vehicle. Multiple dosing resulted in an earlier and shallower peak of inflammation at 24 hrs post-challenge followed by a rapid resolution almost back to baseline. In each instance of Composition A1 administration, the ear swelling difference as measured by area under the curve (AUC) was significantly less than vehicle control (See FIG. 8B and FIG. 8C). Composition A1 therefore potently suppresses antigen-driven tissue inflammation.

Claims

What is claimed is:

1. A modified interleukin-2 (IL-2) polypeptide, comprising:

a modified IL-2 polypeptide, wherein the modified IL-2 polypeptide comprises up to seven natural amino acid substitutions, wherein the seven natural amino acid substitutions comprise amino acid substitutions at residues Y31, K35, and Q74; wherein residue position numbering of the modified IL-2 polypeptide is based on SEQ ID NO:1 as a reference sequence.

2. The modified IL-2 polypeptide of claim 1, wherein the modified IL-2 polypeptide comprises 3, 4, 5, or 6 natural amino acid substitutions relative to the sequence set forth in SEQ ID NO: 1.

3. (canceled)

4. The modified IL-2 polypeptide of claim 1, comprising at least one unnatural amino acid substitution is selected from:

a) a homoserine (Hse) residue located in any one of residues 36-45;

b) a homoserine residue located in any one of residues 61-81; and

c) a homoserine residue located in any one of residues 94-114.

5. (canceled)

6. The modified IL-2 polypeptide of claim 1, wherein the modified IL-2 polypeptide comprises Hse41, Hse71, Hse104, or a combination thereof.

7. The modified IL-2 polypeptide of claim 1, wherein the modified IL-2 polypeptide comprises each of Hse41, Hse71, and Hse104.

8. The modified IL-2 polypeptide of claim 1, wherein the modified IL-2 polypeptide comprises a norleucine (Nle) substitution at residue 23, residue 39, or residue 46, or any combination thereof.

9. (canceled)

10. (canceled)

11. The modified IL-2 polypeptide of claim 1, wherein the modified IL-2 polypeptide comprises at least one amino acid substitution selected from Y31H, K35R, Q74P, and N88D.

12. (canceled)

13. The modified IL-2 polypeptide of claim 1, wherein the modified IL-2 polypeptide comprises Y31H, K35R, and Q74P amino acid substitutions.

14. (canceled)

15. The modified IL-2 polypeptide of claim 13, comprising an N88D substitution.

16. (canceled)

17. The modified IL-2 polypeptide of claim 1, further comprising a C125S substitution.

18. (canceled)

19. (canceled)

20. The modified IL-2 polypeptide of claim 1, wherein the modified IL-2 polypeptide comprises a V69A substitution.

21. The modified IL-2 polypeptide of claim 1, wherein the modified IL-2 polypeptide does not comprise any natural amino acid substitutions at residues E15, N29, N30, T37, K48, V69, N71, I89, or I92.

22. The modified IL-2 polypeptide of claim 1, wherein the modified IL-2 polypeptide does not comprise a V69A or K48E substitution.

23. (canceled)

24. The modified IL-2 polypeptide of claim 1, wherein the modified IL-2 polypeptide is synthetic.

25. A The modified IL-2 polypeptide of claim 1,

wherein the modified IL-2 polypeptide exhibits a binding affinity for the IL-2 receptor alpha subunit (IL-2Rα) which is between about 0.1 nM and about 100 nM, and wherein the modified IL-2 polypeptide exhibits a binding affinity for the IL-2 receptor beta subunit (IL-2Rβ) which is at least about 1000 nM.

26. The modified IL-2 polypeptide claim 1, wherein the modified IL-2 polypeptide exhibits a binding affinity for IL-2Rβ which is at least about 1000 nM, at least about 2000 nM, at least about 3000 nM, at least about 5000 nM, or at least about 10000 nM .

27. The modified IL-2 polypeptide of claim 1, wherein the modified IL-2 polypeptide exhibits a binding affinity for IL-2Rα which is at most about 100 nM, at most about 75 nM, at most about 50 nM, at most about 40 nM, at most about 30 nM, at most about 20 nM, at most about 10 nM, or at most about 5 nM.

28-33. (canceled)

34. The modified IL-2 polypeptide of claim 1, wherein the modified IL-2 polypeptide comprises the sequence set forth in SEQ ID NO: 3.

35-41. (canceled)

42. The modified IL-2 polypeptide of claim 1, wherein the modified IL-2 polypeptide comprises a conjugation handle attached to the N-terminal residue.

43. The modified IL-2 polypeptide of claim 42, wherein the N-terminal residue has a structure of

attached to the N-terminal amine, wherien each n is independently an integer from 1-30, and wherein X is the conjugation handle.

44-58. (canceled)