WO2021155281A1

WO2021155281A1 - Compositions and methods for treatment of celiac disease

Info

Publication number: WO2021155281A1
Application number: PCT/US2021/015895
Authority: WO
Inventors: Randall J. Mrsny; Tahir Mahmood; Weijun Feng; Sally Postlethwaite; Bittoo KANWAR; James Andrew Whitney
Original assignee: Applied Molecular Transport Inc.
Priority date: 2020-01-31
Filing date: 2021-01-29
Publication date: 2021-08-05

Abstract

The present disclosure provides carrier-payload complexes and methods of using the same. Carrier-payload complexes described herein can comprise a carrier coupled to a heterologous payload (e.g., IL-22), wherein the carrier is capable of transporting the payload across intact polarized epithelial cells. Such carrier-payload complex can be part of a pharmaceutical composition that can be orally administered to a subject (e.g., a human or a rodent) for treatment of a disease in the subject, e.g., celiac disease.

Description

COMPOSITIONS AND METHODS FOR TREATMENT OF CELIAC DISEASE

CROSS-REFERENCE

[0001] This application claims the benefit of U.S. Provisional Application No. 62/968,841, filed January 31, 2020, which application is incorporated herein by reference in its entirety.

SEQUENCE LISTING

[0001.1] The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on January 26, 2021, is named 40566-752_601_SL.txt and is 35,344 bytes in size.

BACKGROUND

[0002] The gut epithelium has thwarted efforts to orally administer large therapeutic molecules such as proteins because proteins cannot diffuse across the intact epithelial barrier or cross the barrier through the tight junctions. Once taken up by an epithelial cell, a therapeutic protein can enter the destructive lysosomal trafficking pathway, or can be released back into the intestinal lumen. This inability to be readily transported across the intestinal epithelium can be a limiting factor in developing commercially viable oral formulations, particularly for polypeptide-based therapeutics for the prevention and/or treatment of disease (e.g., celiac disease). Parenteral administration such as intravenous or subcutaneous administration can be a solution, but these administration routes can often create considerable side effects, lower the therapeutic efficacy, and reduce patient convenience that can negatively affect compliance. [0003] Celiac disease is a chronic autoimmune disease that can be triggered by exposure to gluten in genetically predisposed individuals. The pathogenesis of celiac disease can be a T-cell driven process initiated by gluten, leading to increased intestinal permeability and villous atrophy celiac disease can cause mucosal tissue damage of the small intestine, including villous atrophy, crypt hyperplasia, and inflammation, leading to malabsorption, diarrhea, bloating, constipation, abdominal pain, and weight loss. Over the past two decades, celiac disease has emerged as a major health problem. The estimated global prevalence of celiac disease is approximately 1.4% of the general population and is potentially higher in Europe where wheat and cereal consumption remains high celiac disease is currently treated with a strict gluten-free diet (GFD) without wheat, rye, or barley. About 40% of celiac disease patients are not controlled on a GFD regime and would be interested in exploring alternative treatments. Refractory celiac disease is defined by persistent symptoms despite strict GFD adherence for at least six to twelve months. [0004] Since there are currently no pharmacological therapies approved for the treatment of celiac disease, new treatment options for this disease are needed.

INCORPORATION BY REFERENCE

[0005] All references disclosed herein are hereby incorporated by reference in their entirety for all purposes.

SUMMARY

[0006] Provided herein are compositions for treatment of inflammatory and autoimmune diseases to address the need for novel treatment strategies. In various instances, the disease to be treated is celiac disease. A composition for treatment of celiac disease can comprise, consist essentially of, or consist of a carrier-payload complex comprising a carrier coupled to a heterologous payload. Such carrier can be cholix-derived carrier. The payload can be an interleukin-22 (IL-22).

[0007] In various cases, the carrier-payload complex can translocate from the intestinal lumen to the gastrointestinal (GI) mucosa (e.g., lamina propria) where the payload can interact with immune cells. Such transepithelial delivery of payload into the lamina propria can be facilitated by the Cholix-derived carrier that is capable of shuttling a payload across a polarized epithelium (e.g., a polarized intestinal epithelium) by utilizing endogenous transport mechanisms.

[0008] Further provided herein are methods for treating celiac disease in a subject. Such methods can comprise administering to the subject a pharmaceutical composition comprising a carrier-payload complex comprising a carrier coupled to a heterologous payload, wherein the carrier-payload complex is present in an effective amount for treating Celiac disease in the subject. The subject can be a human. In other cases, the subject is a rat, a mouse, or another rodent. In some instances, the carrier-payload complex used to treat celiac disease in the subject can comprise an amino acid sequence set forth in SEQ ID NO: 10 or 11, or an amino acid sequence having at least 90%, 95% or 99% sequence identity thereto.

[0009] In various aspects, provided herein is a method of treating celiac disease in a subject, the method comprising administering to the subject having celiac disease a pharmaceutical composition comprising a carrier-payload complex comprising a carrier coupled to a heterologous payload, wherein the carrier-payload complex is present in an effective amount for treating celiac disease in the subject. In some aspects, the subject is a human, a rat, or a mouse.

In some aspects, the pharmaceutical composition is orally administered to the subject. In some aspects, the pharmaceutical composition is formulated in a capsule. In some aspects, the pharmaceutical composition is formulated in a tablet. In some aspects, the pharmaceutical composition further comprises at least one pharmaceutically acceptable excipient. In some aspects, the carrier comprises a non-toxic cholix variant. In some aspects, the carrier comprises an amino acid sequence set forth in SEQ ID NO: 4 or 5, or an amino acid sequence having at least 90%, 95% or 99% sequence identity thereto. In some aspects, the heterologous payload is an IL-22. In some aspects, the IL-22 comprises the amino acid sequence set forth in SEQ ID NO: 7. In some aspects, the carrier is coupled to the heterologous payload via a spacer. In some aspects, the spacer comprises the amino acid sequence set forth in SEQ ID NO: 9. In some aspects, the carrier-payload complex comprises an amino acid sequence set forth in SEQ ID NO: 10 or 11, or an amino acid sequence having at least 90%, 95% or 99% sequence identity thereto. In some aspects, the carrier-payload complex consists of the amino acid sequence set forth in SEQ ID NO: 10 or 11.

[0010] In various aspects, provided herein is a pharmaceutical composition for use in treatment of celiac disease, wherein the pharmaceutical composition comprises a carrier-payload complex comprising an amino acid sequence set forth in SEQ ID NO: 10 or 11, or an amino acid sequence having at least 90%, 95% or 99% sequence identity thereto.

DETAILED DESCRIPTION

[0011] While various embodiments of the invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions may occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed.

Carrier-Payload Complexes

[0012] Provided herein are carrier-payload complexes capable of transporting one or more heterologous payload molecules (e.g., one or more therapeutic payloads) across epithelial cells (e.g., polarized gut epithelial cells) and into the lamina propria via transcytosis. The carrier- payload complexes can comprise a carrier coupled to a heterologous payload. The carrier can be capable of transporting the heterologous payload across polarized epithelial cells (e.g., polarized gut epithelial cells) using endogenous trafficking pathways. Utilization of endogenous trafficking pathways, as opposed to use of passive diffusion, can allow the carrier to shuttle the heterologous payload rapidly and efficiently across epithelial cells without impairing the barrier function of these cells or the biological activity of the heterologous payload.

[0013] A carrier herein may be derived from a polypeptide secreted by a bacterium. Such a carrier may be derived from a polypeptide secreted from Vibrio Cholerae or Pseudomonas aeruginosa. The polypeptide secreted by Vibrio Cholerae can be a Cholix polypeptide. A carrier derived from a Cholix polypeptide can be naturally occurring or non-naturally occurring. For example, a non-naturally occurring Cholix polypeptide can consist of the amino acid sequence set forth in SEQ ID NO: 1 (an example of a Cholix^{1 634}) (TABLE 1). A carrier derived from a Cholix polypeptide can be a truncated and/or mutated variant of a polypeptide derived from Cholix. Mutation(s) can include one or more substitution(s), deletion(s), and/or addition(s). For example, a carrier herein can comprise a V1L substitution. A carrier provided herein can have a reduced (e.g., at least 50% reduced) or ablated ADP ribosylation activity (e.g., ribosylation of elongation factor 2) relative to a naturally-occurring Cholix variant. A carrier can comprise a modification at an N-terminus, such as an N-terminal methionine (“M”).

[0014] A truncated Cholix carrier can consist of, consist essentially of, or comprise amino acid residues 1-266 of SEQ ID NO: 1. Thus, the carrier can consist of, consist essentially of, or comprise the amino acid sequence set forth in SEQ ID NO: 2 (an example of Cholix^{1 266}). In some instances, a carrier comprises SEQ ID NO: 2 with a V1L substitution. Such sequence is provided herein as SEQ ID NO: 3. Any of these carriers can include one or more amino acids at its N-terminus for expression in various microorganisms (e.g., bacteria), e.g., an N-terminal methionine. Such carrier can consist of, consist essentially of, or comprise an amino acid sequence set forth in SEQ ID NO: 4 or 5 (examples of an M+Cholix^{1 266}).

[0015] Also contemplated herein are carrier-payload complexes comprising carriers having high sequence identity to the carrier sequences herein. Such high sequence identity can include, at least 90%, 95%, 96%, 97%, 98% or 99% sequence identity.

[0016] The term “percent (%) sequence identity,” as used herein in the context of amino acid sequences is the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in a selected sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN, ALIGN-2 or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full-length of the sequences being compared. [0017] A carrier contemplated herein can be coupled to a heterologous payload. In some instances, such heterologous payload is a therapeutic payload. The therapeutic payload can be an interleukin. The interleukin can be a human interleukin-22 (IL-22). The IL-22 can consist of, consist essentially of, or comprise amino acids 34-179 of SEQ ID NO: 6 (IL-22^{1 179}). Thus, the IL-22 can consist of, consist essentially of, or comprise the amino acid sequence set forth in SEQ ID NO: 7 (IL-22^{34 179}). An IL-22 can include a methionine at its N-terminus, e.g., when such IL- 22 protein is bacterially expressed. Such IL-22 can consist of, consist essentially of, or comprise an amino acid sequence set forth in SEQ ID NO: 8 (M+IL-22^{34 179}).

[0018] A carrier can be coupled to a therapeutic payload covalently or non-covalently and directly or indirectly. In instances where the carrier is covalently coupled to the payload, the carrier can be coupled to such payload via a spacer. The spacer can comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or more amino acids. In some instance, a spacer consists of, consists essentially of, or comprises the amino acid sequence set forth in SEQ ID NO: 9 ((G₄S)₃).

[0019] Thus, in various embodiments, a carrier-payload complex consists of the amino acid sequence set forth in SEQ ID NO: 10 or 11 (examples of M+Cholix^{1 266}-(G₄S)₃-IL-22^{34 179}) (TABLE 1). Other carrier-payload complexes can consist of or comprise SEQ ID NOs: 12 or 13 (e.g., when expressed in a mammalian cell such as CHO cell). Such carrier-payload complexes are capable of transporting the IL-22 payload with SEQ ID NO: 7 across intact, polarized gut epithelial cells and into the lamina propria.

TABLE 1 - Exemplary Amino Acid Sequences

[0020] Further provided herein are pharmaceutical compositions comprising a carrier-payload complex and one or more pharmaceutically acceptable carriers and/or excipients. In some cases, the carrier-payload complex of such pharmaceutical composition comprises or consists of the amino acid sequence set forth in SEQ ID NO: 10 or SEQ ID NO: 11. A pharmaceutical composition herein can be formulated for administration to a subject. In some instances, a pharmaceutical composition is formulated for oral administration to a subject. Such oral formulation can be a capsule or a tablet. A unit dose may comprise from about 0.01 mg to about 100 g of the delivery construct. [0021] In some embodiments, the pharmaceutical compositions comprising a carrier-payload complex comprises an enteric coating. The enteric coating may be relatively stable at a relatively low pH (such as in the stomach) and break down at a neutral or high pH. The enteric coating may be stable in a first (e.g., upper) region of the gastrointestinal tract and break down in a second (e.g., lower) region. The enteric coating may release the contents in the intestinal tract. Methods of Treatment

[0022] Provided herein are methods for treating a disease in a subject in need thereof. Such methods can comprise administering a pharmaceutical composition comprising a carrier-payload complex disclosed herein to a subject (e.g., a human) in need thereof to treat the disease.

[0023] Diseases that can be treated using the carrier-payload complexes of this disclosure include autoimmune diseases and inflammatory diseases. In various instances, the disease is hepatitis, obesity, fatty liver disease, liver inflammation, pancreatitis, Crohn’s disease, ulcerative colitis, celiac disease, pouchitis, proctitis, multiple sclerosis, systemic lupus erythematosus, graft versus host disease (GvHD), gastrointestinal GvHD, rheumatoid arthritis, or psoriasis. In some cases, the disease is gastrointestinal GvHD.

[0024] The term “treatment,” as used herein, refers to an intervention performed with the intention of preventing the development or altering the pathology of a disease. Accordingly, “treatment” refers to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) the targeted pathological condition or disease, or ameliorate one or more undesired symptoms of the disease. Those subjects in need of treatment include those already with the disease as well as those in which the disease is to be prevented. In treatment of an inflammatory or autoimmune disease, for example, a therapeutic agent, such as a carrier-payload complex described herein, may directly decrease or increase the magnitude of response of a pathological component of the disease, or render the disease more susceptible to treatment by other therapeutic agents, e.g., cell therapies, immune therapies, anti inflammatory agents, etc.

[0025] In various embodiments, the disease that can be treated using the carrier-payload complexes described herein is celiac disease. Celiac disease is a chronic, autoimmune disease that can be triggered by exposure to gluten in genetically predisposed individuals. The pathogenesis of celiac disease can be a T-cell driven process initiated by gluten, leading to increased intestinal permeability and villous atrophy. Gluten and gluten peptides can increase intestinal permeability via the zonulin signaling pathway to allow an influx of these peptides by crossing the intestinal epithelium. Tissue transglutaminase (TTG) can deamidate gluten, allowing high affinity binding to HLA DQ2/ DQ8+ antigen-presenting cells (APC), which can turn on CD4⁺ T cells to produce pro-inflammatory cytokines. Celiac disease can cause mucosal tissue damage of the small intestine, including villous atrophy, crypt hyperplasia, and inflammation, leading to malabsorption, diarrhea, bloating, constipation, abdominal pain, and weight loss. The risk of small bowel lymphoma in celiac disease can be increased.

[0026] In some embodiments, provided herein are pharmaceutical compositions that can be used in a method to treat celiac disease in a subject. Such compositions can comprise a carrier- payload complex comprising, consisting essentially of, or consisting of the amino acid sequence set forth in SEQ ID NO: 10 or SEQ ID NO: 11. In some instances, such carrier-payload complex can treat celiac disease in the subject by providing sufficient IL-22 concentrations in local GI and/or mucosal GI tissue (e.g., lamina propria). The IL-22 payload can interact with immune cells in the immune cell rich environment of the lamina propria. In some cases, IL-22 delivery to specific locations within the GI tract and/or the GI mucosa of a subject using the carrier-payload complex described herein can lead to repair of damaged epithelial barrier, which is the protective lining along the gastrointestinal tract.

[0027] The delivery construct may be provided in a therapeutically effective amount. The therapeutically effective amount may be from about 0.01 mg/kg to about 1000 mg/kg.

[0028] In some cases, the subject to be treated for celiac disease can be a human, a mouse, a rat, or another mammal. In some instances, the subject suffering from celiac disease is a human. [0029] All of the articles and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the articles and methods of this disclosure have been described in terms of embodiments, it will be apparent to those of skill in the art that variations can be applied to the articles and methods without departing from the spirit and scope of the disclosure. All such variations and equivalents apparent to those skilled in the art, whether now existing or later developed, are deemed to be within the spirit and scope of the disclosure as defined by the appended claims. All patents, patent applications, and publications mentioned in the specification are indicative of the levels of those of ordinary skill in the art to which the disclosure pertains. All patents, patent applications, and publications are herein incorporated by reference in their entirety for all purposes and to the same extent as if each individual publication was specifically and individually indicated to be incorporated by reference in its entirety for any and all purposes. The disclosure illustratively described herein suitably can be practiced in the absence of any element(s) not specifically disclosed herein. The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention that in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the disclosure claimed. Thus, it should be understood that although the present disclosure has been specifically disclosed by embodiments and optional features, modification and variation of the concepts herein disclosed can be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this disclosure as defined by the appended claims.

Claims

CLAIMS WHAT IS CLAIMED IS:

1. A method of treating celiac disease in a subject, the method comprising administering to the subject having celiac disease a pharmaceutical composition comprising a carrier-payload complex comprising a carrier coupled to a heterologous payload, wherein the carrier-payload complex is present in an effective amount for treating celiac disease in the subject.

2. The method of claim 1, wherein the subject is a human.

3. The method of claim 1 or 2, wherein the pharmaceutical composition is orally administered to the subject.

4. The method of claim 3, wherein the pharmaceutical composition is formulated in a capsule.

5. The method of claim 3, wherein the pharmaceutical composition is formulated in a tablet.

6. The method of any one of claims 1-5, wherein the pharmaceutical composition further comprises at least one pharmaceutically acceptable excipient.

7. The method of any one of claims 1-6, wherein the carrier comprises a non-toxic cholix variant.

8. The method of any one of claims 1-7, wherein the carrier comprises an amino acid sequence set forth in SEQ ID NO: 4 or 5, or an amino acid sequence having at least 90%, 95%, or 99% sequence identity thereto.

9. The method of any one of claims 1-8, wherein the heterologous payload is an IL-22.

10. The method of claim 9, wherein the IL-22 comprises the amino acid sequence set forth in SEQ ID NO: 7.

11. The method of claim 9, wherein the IL-22 consists of the amino acid sequence set forth in SEQ ID NO: 7.

12. The method of any one of claims 1-11, wherein the carrier is coupled to the heterologous payload via a spacer.

13. The method of claim 12, wherein the spacer comprises the amino acid sequence set forth in SEQ ID NO: 9.

14. The method of any one of claims 1-13, wherein the carrier-payload complex comprises an amino acid sequence set forth in SEQ ID NO: 10 or 11, or an amino acid sequence having at least 90%, 95% or 99% sequence identity thereto.

15. The method of claim 14, wherein the carrier-payload complex consists of the amino acid sequence set forth in SEQ ID NO: 10 or 11.

16. A pharmaceutical composition for use in treatment of celiac disease, wherein the pharmaceutical composition comprises a carrier-payload complex comprising an amino acid sequence set forth in SEQ ID NO: 10 or 11, or an amino acid sequence having at least 90%, 95% or 99% sequence identity thereto.