Live microbial therapeutics: an enhanced treatment paradigm for classical homocystinuria

Project Summary The goal of this proposal is to continue the development of a synthetic live bacterial therapeutic for homocystinuria (HCU), an inborn metabolic disorder leading to accumulation of homocysteine (Hcy), an intermediary of the amino acid methionine. This condition is estimated to occur at an estimated prevalence of 1 in 100,000 to 200,000. The condition may evade clinical detection until specific hallmarks manifest, including lens detachment from the center of the eye or increased incidence of stroke and other thrombotic conditions. Petri Bio’s approach is intended to break down methionine in the gut to subsequently reduce systemic levels of Hcy. Current treatment strategies for pyridoxine non-responsive HCU typically attempt to lower plasma and tissue levels of Hcy by a combination of restricting dietary intake of the Hcy precursor methionine and dietary supplementation with trimethylglycine, more commonly referred to as betaine. Both strategies are of limited efficacy due to a lack of adherence to the diet, and unpleasant side effects from taking betaine (e.g., diarrhea, nausea, odor). Petri Bio, Inc. employs prokaryotic strains compatible with the human gut microbiome to serve as expression vectors for therapeutic proteins capable of targeted modulation of metabolic pathways, such as the methionine cycle. In a search for enzymes capable of impacting methionine levels, we carried out an in silico screen for potential methionase enzymes in microbial genomic datasets. During the Phase I program, leading candidate enzymes were subsequently cloned, expressed, and tested in vitro for methionine catalysis capabilities. The best performing enzymes were engineered for expression in a bacterial strain which is known to readily engraft into the human gut microbiome. These strains were tested in a genetic model system of HCU and mitigated systemic levels of Hcy as intended. During Phase II, strains will be additionally optimized and scaled up to develop a commercial-scale fermentation method. Safety, toxicology, and maximum tolerable dose testing will be undertaken in a range of standardized tests (both in vitro and in vivo). The lead strain will then be tested for efficacy in the HCU model employed in Phase I as well as in a murine model of HCU to measure metabolic effectiveness as well as mitigation of cognitive deficits due to HCU. Pending successful completion of Phase II, the data will be submitted to the FDA in a pre-IND meeting, the next step towards eventual clinical evaluation and availability to patients.