1. Expanding the drug discovery space with predicted metabolite–target interactions
- Author
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Andrea Nuzzo, Channa Jayawickreme, Ellen L. Berg, Joel Tocker, James R. Brown, and Somdutta Saha
- Subjects
0301 basic medicine ,Databases, Factual ,Metabolite ,Anti-Inflammatory Agents ,Medicine (miscellaneous) ,Ligands ,Inflammatory bowel disease ,Machine Learning ,chemistry.chemical_compound ,0302 clinical medicine ,Drug Discovery ,Data Mining ,Molecular Targeted Therapy ,Protein Interaction Maps ,Biology (General) ,Cells, Cultured ,media_common ,Drug discovery ,Drug development ,030220 oncology & carcinogenesis ,Host-Pathogen Interactions ,Metabolome ,General Agricultural and Biological Sciences ,Signal Transduction ,Drug ,Cellular signalling networks ,QH301-705.5 ,media_common.quotation_subject ,Computational biology ,Biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,Protein–protein interaction ,03 medical and health sciences ,Gastrointestinal Agents ,medicine ,Humans ,Metabolomics ,Genetic association ,Bacteria ,Gene Expression Profiling ,Inflammatory Bowel Diseases ,medicine.disease ,digestive system diseases ,Gastrointestinal Microbiome ,030104 developmental biology ,chemistry ,Transcriptome ,Human Microbiome Project - Abstract
Metabolites produced in the human gut are known modulators of host immunity. However, large-scale identification of metabolite–host receptor interactions remains a daunting challenge. Here, we employed computational approaches to identify 983 potential metabolite–target interactions using the Inflammatory Bowel Disease (IBD) cohort dataset of the Human Microbiome Project 2 (HMP2). Using a consensus of multiple machine learning methods, we ranked metabolites based on importance to IBD, followed by virtual ligand-based screening to identify possible human targets and adding evidence from compound assay, differential gene expression, pathway enrichment, and genome-wide association studies. We confirmed known metabolite–target pairs such as nicotinic acid–GPR109a or linoleoyl ethanolamide–GPR119 and inferred interactions of interest including oleanolic acid–GABRG2 and alpha-CEHC–THRB. Eleven metabolites were tested for bioactivity in vitro using human primary cell-types. By expanding the universe of possible microbial metabolite–host protein interactions, we provide multiple drug targets for potential immune-therapies., Using computational approaches, Nuzzo et al. identify 983 potential metabolite–human target interactions from the Inflammatory Bowel Disease (IBD) cohort dataset of the Human Microbiome Project 2 (HMP2) and public databases. These predicted interactions can further the understanding of host–microbiome interactions and assist in drug discovery for IBD and other diseases.
- Published
- 2021
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