Phenotypic high-throughput screening identifies modulators of gut microbial choline metabolism

Abstract

Anaerobic metabolism of dietary choline to trimethylamine (TMA) by the human gut microbiome is a disease-associated pathway. The host's impaired ability to oxidize TMA to trimethylamine-N-oxide (TMAO) results in trimethylaminuria (TMAU), while elevated serum TMAO levels have been positively correlated with cardiometabolic disease. Small molecule inhibition of gut bacterial choline metabolism attenuates the development of disease in mice, highlighting the therapeutic potential of modulating this metabolism. Inhibitors previously developed to target this pathway are often designed to mimic choline, the substrate of the key TMA-generating enzyme choline–trimethylamine lyase (CutC). Here, we use a growth-based phenotypic high-throughput screen and medicinal chemistry to identify distinct chemical scaffolds that can modulate anaerobic microbial choline metabolism and lower TMAO levels in vivo. These results illustrate the potential of using phenotypic screening to rapidly discover new inhibitors of gut microbial metabolic activities.

Competing Interest Statement

E.P.B., A.Y.M.W., W.J.S-E. and M.B. are inventors on an unpublished U.S. provisional patent application submitted by President and Fellows of Harvard College that covers choline–TMA inhibitors. W.J.S-E. is currently affiliated with Facultad de Ciencias Exactas y Naturales, Departamento de Biotecnología, Laboratorio de Biotecnología Microbiana, Universidad Nacional de Asunción, San Lorenzo, Paraguay, Departamento de Análisis de Microbiomas, GeneBiome E.A.S, Luque, Paraguay, and Departamento de Investigación Aplicada de Microbiomas, MicroBios S.A, Montevideo, Uruguay. M.B. is an employee of Bayer SAS, France and A.W. is an employee of Takeda Pharmaceuticals USA, Inc. All work for this manuscript was performed when the authors were at the institutions listed in the author list.