Development of novel endolysins targeting Cutibacterium acnes to treat acne vulgaris

Topaz Biosciences, Inc., Emeryville CA

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Abstract

PROJECT SUMMARY Acne vulgaris (acne) affects up to 50 million people in the U.S. annually and can have significant negative consequences on psychosocial functioning including higher rates of anxiety, low self-esteem, and depression. Cutibacterium acnes plays a central role in acne pathogenesis. Topical and oral antibiotics to target C. acnes remain part of first-line treatments for acne, but extensive use of antibiotics poses significant issues including exacerbation of antibiotic resistance as well as collateral damage to the healthy commensals in the gut and skin microbiomes. Given these drawbacks, novel antimicrobial agents that can provide alternatives to antibiotics and selectively target C. acnes without damaging beneficial bacteria are needed. Endolysins are phage-encoded enzymes that can degrade bacterial cell walls. Exogenously added endolysins can quickly lyse their target bacteria and because they bind very specific epitopes in target cell walls, they can have lytic specificity down to a single bacterial species. Given these properties, endolysins hold enormous potential as high-specificity skin microbiome modulators. However, the diversity of endolysins known to target C. acnes is very low and these enzymes suffer from low specificity, weak activity and poor solubility. As such, previous efforts to discover C. acnes endolysins with commercially-relevant properties have failed. In Phase I of this program, we leveraged our proprietary metagenomics platform and a synthetic biology-based approach to discover novel, soluble endolysins that target C. acnes and further improve them for high activity and specificity, overcoming this long-standing discovery bottleneck. In total, we developed 13 engineered enzymes that meet our target activity profile, including CUT-001 and CUT-002. We further developed base hydrogel formulations of CUT-001 and CUT-002 that have strong activity, good long-term stability, and was non-toxic / non-irritating in in vitro and in vivo safety tests. In Phase II of this program, we propose to develop a final CUT-002 hydrogel formulation, prototype a hydrocolloid patch incorporating CUT- 002, and develop an optimized CUT-002 bioreactor fermentation process. Successful completion of Phase II activities will result in a) two alternative product formulations/formats that meet our target product profile and can be advanced to clinical testing and b) cost-effective production of our lead enzyme at scale to support clinical testing and commercialization.