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A novel approach and corresponding compounds to treat gut diseases where retinoic acid plays a role in disease homeostasis and progression

Background

The burden of inflammatory bowel disease (IBD) is rapidly increasing globally, with an estimated 7 million cases of IBD globally. Crohn's disease and ulcerative colitis are the two main types of IBD characterized by chronic inflammation of the gastrointestinal tract. While several therapeutic options exist many patients fail to respond to therapy or experience remission. Although the etiology of IBD is still unclear gut microbiota alterations are known to contribute to the pathogenesis of IBD. Therapies that alter the gut microbiome are being developed despite limited understanding of how the microbiomes contribute to disease. A better understanding of the role of the gut microbiome in IBD will enhance therapeutic development.

Retinoic acid (RA) plays a key role in the mucosal immune response and is crucial for maintaining homeostatsis at the intestinal barrier. RA is the activated form of vitamin A that may mitigate IBD severity through various immunoregulatory mechanisms. RA has been shown to help restore and/or reprogram the impaired Treg/Th7 lineage that is usually linked to the pathogenesis of IBD. All trans retinoic acid (ATRA) an active metabolite of vitamin A, also plays a crucial role in the progression of acute colitis through inhibiting NF-κB activation, suggesting that ATRA represents a novel therapeutic approach for the management of IBD. Interestingly, RA has been found to not only mitigate inflammation but also counteract IBD-related consequences such as necrotizing colitis and tumorigenesis. Conversely, mechanisms lowering vitamin A, as in deficiency, and RA have been linked to increased tumor burden in ulcerative colitis patients due to clearance of CD8+ Cytotoxic T-Lymphocytes (CTLs), whereas RA normalization induced protective CD8+ T-cell activities. Colitis-associated dysbiosis also has been implicated in systemic negative impacts on RA signaling. It has been proposed that dysbiosis can suppress normal host related RA synthesis. Thus, maintaining adequate vitamin A and its metabolites in the gut is crucial for GI health and factors altering this balance may predispose individuals to pathogenic processes.

Technology Overview

The lab has identified an important enzymatic metabolic pathway associated with a human pathogenic bacteria present in the gut and associated with multiple pathologies such as Crohn's disease, intestinal (inflammatory bowel diseases, IBD) as well as liver diseases. The researchers have discovered that this bacterium can specifically metabolize both retinol, the precursor of ATRA as well as ATRA in a manner that phenocopies mammalian CYP26s enzymes. This surprising finding reveals a new mechanism whereby host RA levels can be affected. Such bacterial strains may play a role in retinoic acid imbalance and disease progression. A pathogenic dysregulation of RA in the gut may result in lowering immune defense to favor other bacteria (Campylobacter jejuni, Salmonella, Shigella, Escherichia coli, Yersinia enterocolitica, Clostridium difficile, and Mycobacterium tuberculosis) all of which are suppressed by RA and thereby facilitate the initiation and progression of bacterial colitis.

Goals:

• Demonstrate that Retinoic acid metabolizing bacteria plays an important role in modifying the gut Biome and favors dysbiosis.
• Demonstrate that bacterial RA metabolism is responsible for the dysregulation of the gut immune system and favor pathogens to proliferate leading to several gut diseases such as colitis.
• Demonstrate that the bacterial RA metabolizing enzyme plays an important role in bacteria associated/regulated RA metabolism in the gut. 
• Demonstrate that blocking RA metabolizing enzyme in bacteria (RAMB) can restore gut microbiome and prevent dysbiosis and disease progression.
• Develop specific bacteria RA metabolizing enzyme inhibitors for prevention and treatment of gut diseases or use active RA isomers that are not metabolized by RAMB to restore RA balance in affected tissues. We have generated a substantial library of proprietary compounds designed to block RA metabolism which we will assess against the bacterial RA metabolizing enzymes.

Methods for proof of concept and early treatment method:

Animal models such as mice can be used to measure the effect of RA metabolizing bacteria (RAMB) on the gut RA levels, gut microbiome and disease progression. Two IBD models of interest could be used in this study, the DSS and TNBS models. In these two models, specific microbial signatures associated with two IBD subtypes were consistent between the animal models and human IBD patients, suggesting that the animal models can partially recapitulate the microbiota in human diseases.

• The effect on RA levels and gene regulation in the gut of normal mice exposed to high RAMB in their diet will be measured. Long term effect on gut disease (IBD) progression and dysbiosis will also be monitored. Ultimately germ-free mice could also be used.
• Transgenic mice such as RARE-LacZ can also be used to measure the effect on RAMEB on gut RA levels.
• Gene silencing (CRISPR or other methods) of the RA metabolizing enzyme in bacteria will be used for target validation 
• Specific RAMB enzyme inhibitors will be selected in vitro and used in vivo (mice) to block and restore RA levels in the gut after high RAMB diet.
• The researchers have also identified an active RA analogue that is not metabolized by the RAMB demonstrating that we can use this enzyme, which they have expressed and purified, to screen for therapeutic agents. This active analogue is a potent and safe RAR ligand that could potentially be developed for an indication such as colitis or IBD. 

Stage of Development

arget validation: Proof of concept compound screening. 

Research in discovery stage. 

Benefits

The benefits of this research will lead to a novel and unique approach and corresponding compounds to treat gut diseases where RA metabolism is a key player in disease homeostasis and progression.

• New inhibitors or other RA analogs not metabolized by RAMB will provide treatment to RA deficiency associated gut diseases.
• The researchers believe that their discoveries may lead to new approaches to manage gut microbiota without complex manipulation of bacterial constituents of the gut flora.

Applications

Use of specific RAMB enzymes inhibitor or non-metabolized RA analogues to normalize RA levels and signalling in the gut while suppressing growth of pathogenic bacterial strains which opportunistically grow in low RA environments (eg. Vitamin A deficiency). This can be beneficial for treating diseases where low RA levels in the GI tract are etiologically linked such as:

• Gastrointelsetional diseases such as Inflammatory bowel diseases and colitis
• Non-GI diseases such as Alzheimer’s, Type I diabetes, Multiple sclerosis, and lupus

Opportunity

Develop and commercialize therapies to reduce pathogenic bacterial load in the gut and restore RA balance to prevent or treat colitis related disease.

Patents

• US Patent 10,874,634, “Compounds and methods for inhibiting CYP26 enzymes”
• US Patent 11,364,220, “Compounds and methods for inhibiting CYP26 enzymes”
• Pending Canadian Patent Application Serial No. 3,047,433, “Compounds and Methods for Inhibiting Cyp26 Enzymes”

IP Status

Patented

Seeking

• Seeking investment
• University spinout
• Licensing
• Commercial partner

Posted

November 9, 2022