Microbiomes: A New Paradigm for Drug Discovery?

Focus: Drugs From Gut Bacteria

You may have read a few articles about the impact of the microbiomes and their impact on diets, digestion and nutrition but now there is the potential of discovering new therapies from bacteria in your gut. We are not talking about faecal transplant therapy (FMT) but new drugs isolated from gut bacteria. The human microbiome (or microbiota) loosely defined consists of all the trillions of microbial cells, primarily bacteria and their genes harbored by each person in their gut. Rapidly advancing analytical  techniques such as sequencing are advancing our knowledge of microbiota  bringing prospects for new drugs and personalized medicine. As vast amounts of sequencing data from individual bacterial genes become available there is the prospect of  manipulating the microbiome to create drugs and come up with links to chronic GI diseases such as Colitis and Crohn’s disease.

Although research is at an early stage the clinical indications are growing: C.difficile, preterm labor, IBD, Obesity, Chronic Fatigue Syndrome, Acne, and Diabetic Foot Ulcers. The agriculture market also has potential for environmental challenges and insect control. In summary, how does the human microbiota interact with the human host and gut flora to impact health and disease.

Several companies are focused in this area with discovery platforms and many have venture backed funding.

On a BIO Therapeutic Panel Andres Hurtado-Lorenzo PhD, Director of Translational Research  of Crohn’s and Colitis Foundation moderated a panel of three executives, Collen Cutliffe PhD CEO of Whole Biome,  Len Nedwin PhD CEO of Second Genome Inc. and Heather A. Wasserman PhD Senior Director of Eli Lilly and Company. Later we also attended a presentation by Yug Varma CEO of Phi Therapeutics, Inc.

The individual WEB sites of these companies have a wealth of information on this “hot field”.

Research is still at an early stage with few clinical stage products but here are some promising concepts and developments in the search for new drug candidates:

  • Identify specific bacterial strains and related proteins correlated to a healthy gut.What does the bacteria make? How does it act on microbiome?
  • Identify small molecules and peptides that modulate microbe/microbe and microbe/human interactions. Identify biomarkers that influence a disease state.
  •  What happens when you put bacteria back into the person?
  • What is genetic profile of an individual’s microbiome?
  • Big data metagenomics capabilities are needed.
  • Possible to get good bacterial samples for testing with periodontal disease.
  • 12 classes of probiotics are approved.
  • Bacteria are naturally occurring so what are IP issues?

PHI Therapeutics is an early stage Company out of UCSF (University of California San Francisco) with a microbiome editing platform that is unique in its ability to perform additive and subtractive fountains on the microbiome. Pathogens can be “killed and replaced” to attain microbiome equilibrium and target a specific pathogen unlike the broad treatment approach of antibiotics that creates antimicrobial resistance. The Company was awarded an NIH SBIR grant to develop a panel of candidates with an initial focus on bacterial skin diseases like acne. The available US acne market is $3.6B but most current drugs have serious side effects. The core technology of the company utilizes and engineered bacterial phage (PHT-101) which targets and kills the Propionibacterium acne. Other skin products are envisioned in the pipeline such as atopic dermatitis. A provisional patent has been filed and a Series A financing is being pursued.

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