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Understanding the properties of gut metabolites can provide guidance for the design of gut-targeted drugs. In the present work we analyze a large set of gut metabolites, both shared with serum or present only in gut, and compare them with oral systemic drugs. We find patterns specific for these two subsets of metabolites that could be used to design drugs targeting the gut. In addition, we develop and openly share a Super Learner model to predict gut permanence, in order to aid in the design of molecules with appropriate profiles to remain in the gut, resulting in molecules with putatively reduced secondary effects and better pharmacokinetics.<\/jats:p>","DOI":"10.1186\/s13321-023-00768-y","type":"journal-article","created":{"date-parts":[[2023,10,13]],"date-time":"2023-10-13T04:02:57Z","timestamp":1697169777000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Analysis of metabolites in human gut: illuminating the design of gut-targeted drugs"],"prefix":"10.1186","volume":"15","author":[{"given":"Alberto","family":"Gil-Pichardo","sequence":"first","affiliation":[]},{"given":"Andr\u00e9s","family":"S\u00e1nchez-Ruiz","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8249-4547","authenticated-orcid":false,"given":"Gonzalo","family":"Colmenarejo","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,10,13]]},"reference":[{"issue":"7164","key":"768_CR1","doi-asserted-by":"publisher","first-page":"804","DOI":"10.1038\/nature06244","volume":"449","author":"PJ Turnbaugh","year":"2007","unstructured":"Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI (2007) The human microbiome project. 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