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Intestinal inflammatory pharmaceutics

Curator: Larry H. Bernstein, MD, FCAP


AbbVie Invests in Synthetic Microbes for Treatment of Intestinal Disorders

Aaron Krol


February 10, 2016 | This morning, AbbVie announced a partnership with Synlogic of Cambridge, Mass., to create microbiome-based therapies for the treatment of inflammatory bowel disease (IBD). The two companies have sketched out a suggested three-year timeline for preclinical research and development, after which AbbVie will take over advancing any drug candidates into clinical trials.

Drugs inspired by the microbes that live in the human gut are a hot topic in biotech. Companies like Seres Health and Vedanta Biosciences are pursuing the idea from a variety of angles, from making traditional small molecule drugs that interact with the microbiome, to creating probiotics or microbial cocktails that restore a healthy balance to the gut ecosystem. IBD, including Crohn’s disease and ulcerative colitis, is an especially popular target for these companies, thanks to strong suggestions that bacterial populations can affect the course of the disease. Already, Second Genome and Coronado Biosciences have taken prospective treatments into the clinic (though the latter has been dealt serious setbacks in Phase II trials).

But even among this peculiar batch of startups, Synlogic’s approach to drug design is exquisitely odd. The company calls its products “synthetic biotics”―in fact, they’re genetically engineered bacteria whose DNA contains intricately designed “gene circuits,” built to start producing therapeutic molecules when and only when the patient needs them.

“We are not looking at correcting the dysregulation of microbes in the gut, like other microbiome companies,” CEO José-Carlos Gutiérrez-Ramos tells Bio-IT World. “We have one bacterium, and it’s engineered to do different functions.”

Synlogic was founded in 2013 by two synthetic biologists at MIT, Timothy Lu and Jim Collins. (Bio-IT World has previously spoken with Lu about his academic work on bacterial gene circuits.) Gutiérrez-Ramos joined almost two years later, leaving a position as the head of Pfizer’s BioTherapeutics R&D group, where he had plenty of opportunity to turn emerging biotechnology ideas into drug candidates ready for submission to the FDA.

Still, synthetic biotics are a good deal more unusual than the biologic drugs he worked on at Pfizer.

His new company doesn’t quite spin functions for its microbes out of whole cloth. All the genes the company uses are copied either from the human genome, or from the bacteria living inside us. But by recombining those genes into circuits, Gutiérrez-Ramos believes Synlogic can finely control whether and when genes are expressed, giving its synthetic biotics the same dosage control as a traditional drug. Meanwhile, choosing the right bacterium to engineer―the current favorite is a strain called E. coli Nissle―ensures the biotics do not form stable colonies in the gut, but can be cleared out as soon as a patient stops treatment.

“We’re pharma guys,” he says. “What we want is to have pharmacologically well-defined products.”

The Molecular Circuit Board

Even before the partnership with AbbVie, Synlogic had a pipeline of drug candidates in development, all meant to treat rare genetic disorders caused by single mutations that shut down the activity of a crucial gene. In principle, there seems to be no reason that bacteria carrying the right genes couldn’t pick up the slack. “We know the patient is missing a function that is typically performed by the liver, or the kidney, or the pancreas,” says Gutiérrez-Ramos. “What we do is shift that function from an organ to a stable fraction of the microbiome.”

The approach is in some ways analogous to gene therapy, where a corrected version of a broken gene is inserted into a patient’s own DNA. “We don’t use that word, but the fact is it’s a non-somatic gene therapy,” Gutiérrez-Ramos says. “And if something goes wrong, you can control it just by stopping treatment.” The most advanced synthetic biotic in Synlogic’s pipeline targets urea cycle disorder, exactly the sort of disease that might otherwise be addressed by gene therapy: patients are missing a single enzyme that helps remove nitrogen from the body and prevent it from forming ammonia in the bloodstream. Synlogic will meet with the FDA this March to discuss whether and how this first product can be tested in humans.

Gutierrez Ramos

The new IBD program with AbbVie, however, adds a whole new level of complexity. Executives from the two companies have been in discussions for around six months, and both agree that no single mechanism will be enough to provide significant relief for patients. Crohn’s and ulcerative colitis are painful autoimmune diseases that involve both a weakening of the epithelial lining in the stomach, and a buildup of inflammatory molecules. The development plan that AbbVie and Synlogic have agreed on includes three separate methods of attack to relieve these symptoms.

“One approach AbbVie is very interested in is for our synthetic biotics to produce substances that could tighten the epithelial barrier,” says Gutiérrez-Ramos. “Another approach is to degrade pro-inflammatory molecules”―the same tack taken by AbbVie’s current leading IBD drug, Humira, which targets the inflammatory protein TNFα. “Finally, we can produce anti-inflammatory molecules.”

Uniquely, synthetic biotics can perform all three functions at once; it’s just a matter of inserting the right genes. But that alone might not be a decisive advantage over some sort of combination therapy. The biggest selling point of Synlogic’s microbes is not the genes they can be engineered to express―what you might call the “output” of their gene circuits―but the input, the DNA elements called “inducible promoters” that decide when those genes should be activated.

The core idea is that patients will have a constant population of synthetic biotics in their bodies, taken daily―but those microbes will only generate their therapeutic payloads when needed. In IBD, Gutiérrez-Ramos explains, “it’s not that the patient is always inflamed, but they have flares. Our vision, and AbbVie’s vision, is that the bacteria that you take every day sense when the flare is coming, and then trigger the genetic output.”

This would be a major improvement over a drug like Humira, which after all is constantly inhibiting a part of the immune system. Patients taking Humira, or one of the many other immunosuppressant drugs for IBD, are at a constantly heightened risk of infection; tuberculosis is a particular specter for these patients. If Synlogic can find a genetic “on-switch” that responds to a reliable indicator of IBD flares, it could potentially create a much more precisely administered treatment, while still giving patients the simple dosing schedule of one pill every day.

The company has leads on two inducible promoters that might do the trick: one that reacts to nitric oxide, and another tied to reactive oxygen species. Of course, there’s no guarantee that either will respond sensitively to IBD flares in a real clinical setting. “This is an early time for the technology,” says Gutiérrez-Ramos. “We have demonstrated this in animals, but we have to demonstrate it in humans.”

Although it’s far too early to say if synthetic biotics will become an ordinary part of the pharma toolkit, AbbVie’s decision to invest in the technology offers the means to test this approach on a large scale. Synlogic expects to raise its own funding for trials of its rare disease products, which the FDA does not expect to enroll huge numbers of patients, but IBD is a problem of a very different order.

“We are very honored to work with truly the leader in treatment of inflammatory bowel disease,” says Gutiérrez-Ramos. With the backing of big pharma, it will be possible to trial microbiome-based therapies for the kinds of common, chronic diseases that are the biggest drain on our healthcare system. What’s more, the AbbVie partnership is an important signal of the industry’s faith in synthetic biology as an approach to treating disease.




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Curator/ Author: Aviral Vatsa, PhD, MBBS

In continuation with the previous posts that dealt with short history and chemistry of nitric oxide (NO), here I will try to highlight the pathways involved in NO chemical signalling.

NO is a very small molecule, with a short half life (<5 sec). It diffuses rapidly to its surroundings and is metabolised to nitrites and nitrates. It can travel short distances, a few micrometers, before it is oxidised. Although it was previously believed that NO can only exert its effect for a very short time as other nitrogen oxides were believed to be biologically inert. Recent data suggests that other NO containing compounds such as S- or N-nitrosoproteins and iron-nitrosyl complexes can be reduced back to produce NO. These NO containing compounds can serve as storage and can reach distant tissues via blood circulation, remote from their place of origin. Hence NO can have both paracrine and ‘endocrine’ effects.

Intracellularly the oxidants present in the cytosol determine the amount of bioacitivity that NO performs. NO can travel roughly 100 microns from NOS enzymes where it is produced. NOS enzymes on the other hand are localised to specific sub-cellular areas, which have relevant proteins in the vicinity as targets for signalling.

NO signalling occurs primarily via three mechanisms (according to Martínez-Ruiz et al):

  1. Classical: This occurs via soluble guanylyl cyclase (sGC). Once NO is produced by NOS it diffuses to sGC intracellularly or even in other cells. SGC is highly sensitive for NO, even nanomolar amounts of NO activates sGC, thus making it a potent target for NO in signalling pathways. sGC in turn increases the conversion of GTP to cGMP. cGMP further mediates the regulation of contractile proteins and gene expression pathways via cGMP-activated protein kinases (PKGs). cGMPs cause confirmational changes in PKGs. Signalling by cGMP is terminated by the action of phosphodiestrases (PDEs). PDEs have become major therapeutic targets in the upcoming exciting research projects.
  2. Less classical: Within the mitochondria NO can compete with O2 and inhibit cytochrome c oxidase (CcO) enzyme. This is a reversible inhibition that depends on O2and NO concentrations and can occur at physiological levels of NO. Various studies have demonstrated that endogenously generated NO can inhibit respiration or that NOS inhibitors can increase respiration at cellular, tissue or whole animal level. Although the exact mechanism of CcO inhibition of NO is still debated, NO-CcO interaction is considered important signalling step in a variety of functions such as inhibition of mitochondrial oxidative phosphorylation, apoptosis and reactive oxygen species (ROS) generation. Interestingly, at higher concentration (~1nM) NO can cause irreversible inhibition of cellular oxidation by reversible and/or irreversible damage to the mitochondrial iron–sulfur centers,In addition to the above mentioned pathways, NO (along with AMP, ROS and O2), can also activate AMP- activated protein kinase (AMPK), an enzyme that plays a central role in regulating intracellular energy metabolism. NO can also regulate hypoxia inducible factor (HIF), an O2-dependent transcription factor that plays a key role in cell adaptation to hypoxia .
  3. Non- classical: S-nitrosylation or S-nitrosation is the covalent insertion of NO into thiol groups such as of cysteine residues of proteins. It is precise, reversible, and spatiotemporally restricted post translational modification. This chemical activity is dependent upon the reactivity between nitrosylating agent (a small molecule) and the target (protein residue). It might appear that this generic interaction results in non-specific, wide spread chemical activity with various proteins. However, three factors might determine the regulation of specificity of s-nitrosylation for signalling purposes:
  • Subcellular compartmentalisation: high concentrations of nitrosylating agents are required in the vicinity of target residues, thus making it a specific activity.
  • Site specificity: certain cysteine residues are more reactive in specific protein microenvironments than others, thus favouring their modification. As a result under physiological conditions only a specific number of cysteine residues would be modified, but under higher NO levels even the slow reacting ones would be modified. Increased impetus in research in this area to determine protein specificity to s-nitrosylation provides huge potential in discovering new therapeutic targets.
  • Denitrosylation: different rates of denitrosylation result in s-nitrosylation specificity.

Other modifications in non classical NO mechanisms include S-glutathionylation and tyrosine nitration

Peroxynitrite: It is one of the important reactive nitrogen species that has immense biological relevance. NO reacts with superoxide to form peroxynitrite. Production of peroxynitrite depletes the bioactivty of NO in physiological systems. Peroxynitrite can diffuse through membranes and react with cellular components such as mitochondrial proteins, DNA, lipids, thiols, and amino acid residues. Peroxynitrite can modify proteins such as haemoglobin, myoglobin and cytochrome c. it can alter calcium homeostasis and promote mitochondrial signalling of cell death. However, NO itself in low concentrations have protective action on mitochondrial signalling of cell death.

More details about various aspects of NO signalling can be obtained from the following references.

The post is based on the following Sources:

  2. 2012;122:55-68 (DOI: 10.1159/000338150)
  3. J Am Coll Cardiol. 2006;47(3):580-581. doi:10.1016/j.jacc.2005.11.016


In addition, other aspects of NO involvement in biological systems in humans are covered in the following posts on this site:

  1. Nitric Oxide and Platelet Aggregation
  2. Inhaled NO in Pulmonary Artery Hypertension and Right Sided Heart Failure
  3. Cardiovascular Disease (CVD) and the Role of agent alternatives in endothelial Nitric Oxide Synthase (eNOS) Activation and Nitric Oxide Production
  4. Nitric Oxide in bone metabolism

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