肠道微生物群介导的药物代谢计算分析。

Sammie Chum, Alberto Naveira Montalvo, Soha Hassoun
{"title":"肠道微生物群介导的药物代谢计算分析。","authors":"Sammie Chum, Alberto Naveira Montalvo, Soha Hassoun","doi":"10.1101/2024.12.20.629788","DOIUrl":null,"url":null,"abstract":"<p><p>The gut microbiota, an extensive ecosystem harboring trillions of bacteria, plays a pivotal role in human health and disease, influencing diverse conditions from obesity to cancer. Among the microbiota's myriad functions, the capacity to metabolize drugs remains relatively unexplored despite its potential implications for drug efficacy and toxicity. Experimental methods are resource-intensive, prompting the need for innovative computational approaches. We present a computational analysis, termed MDM, aimed at predicting gut microbiota-mediated drug metabolism. This computational analysis incorporates data from diverse sources, e.g., UHGG, MagMD, MASI, KEGG, and RetroRules. An existing tool, PROXIMAL2, is used iteratively over all drug candidates from experimental databases queried against biotransformation rules from RetroRules to predict potential drug metabolites along with the enzyme commission number responsible for that biotransformation. These potential metabolites are then categorized into gut MDM metabolites by cross referencing UHGG. The analysis' efficacy is validated by its coverage on each of the experimental databases in the gut microbial context, being able to recall up to 74% of experimental data and producing a list of potential metabolites, of which an average of about 65% are relevant to the gut microbial context. Moreover, explorations into ranking metabolites, iterative applications to account for multi-step metabolic pathways, and potential applications in experimental studies showcase its versatility and potential impact beyond raw predictions. Overall, this study presents a promising computational framework for further research and applications gut MDM, drug development and human health.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11702676/pdf/","citationCount":"0","resultStr":"{\"title\":\"Computational Analysis of the Gut Microbiota-Mediated Drug Metabolism.\",\"authors\":\"Sammie Chum, Alberto Naveira Montalvo, Soha Hassoun\",\"doi\":\"10.1101/2024.12.20.629788\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The gut microbiota, an extensive ecosystem harboring trillions of bacteria, plays a pivotal role in human health and disease, influencing diverse conditions from obesity to cancer. Among the microbiota's myriad functions, the capacity to metabolize drugs remains relatively unexplored despite its potential implications for drug efficacy and toxicity. Experimental methods are resource-intensive, prompting the need for innovative computational approaches. We present a computational analysis, termed MDM, aimed at predicting gut microbiota-mediated drug metabolism. This computational analysis incorporates data from diverse sources, e.g., UHGG, MagMD, MASI, KEGG, and RetroRules. An existing tool, PROXIMAL2, is used iteratively over all drug candidates from experimental databases queried against biotransformation rules from RetroRules to predict potential drug metabolites along with the enzyme commission number responsible for that biotransformation. These potential metabolites are then categorized into gut MDM metabolites by cross referencing UHGG. The analysis' efficacy is validated by its coverage on each of the experimental databases in the gut microbial context, being able to recall up to 74% of experimental data and producing a list of potential metabolites, of which an average of about 65% are relevant to the gut microbial context. Moreover, explorations into ranking metabolites, iterative applications to account for multi-step metabolic pathways, and potential applications in experimental studies showcase its versatility and potential impact beyond raw predictions. Overall, this study presents a promising computational framework for further research and applications gut MDM, drug development and human health.</p>\",\"PeriodicalId\":519960,\"journal\":{\"name\":\"bioRxiv : the preprint server for biology\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2025-03-07\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11702676/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"bioRxiv : the preprint server for biology\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1101/2024.12.20.629788\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"bioRxiv : the preprint server for biology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1101/2024.12.20.629788","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
Computational Analysis of the Gut Microbiota-Mediated Drug Metabolism.

The gut microbiota, an extensive ecosystem harboring trillions of bacteria, plays a pivotal role in human health and disease, influencing diverse conditions from obesity to cancer. Among the microbiota's myriad functions, the capacity to metabolize drugs remains relatively unexplored despite its potential implications for drug efficacy and toxicity. Experimental methods are resource-intensive, prompting the need for innovative computational approaches. We present a computational analysis, termed MDM, aimed at predicting gut microbiota-mediated drug metabolism. This computational analysis incorporates data from diverse sources, e.g., UHGG, MagMD, MASI, KEGG, and RetroRules. An existing tool, PROXIMAL2, is used iteratively over all drug candidates from experimental databases queried against biotransformation rules from RetroRules to predict potential drug metabolites along with the enzyme commission number responsible for that biotransformation. These potential metabolites are then categorized into gut MDM metabolites by cross referencing UHGG. The analysis' efficacy is validated by its coverage on each of the experimental databases in the gut microbial context, being able to recall up to 74% of experimental data and producing a list of potential metabolites, of which an average of about 65% are relevant to the gut microbial context. Moreover, explorations into ranking metabolites, iterative applications to account for multi-step metabolic pathways, and potential applications in experimental studies showcase its versatility and potential impact beyond raw predictions. Overall, this study presents a promising computational framework for further research and applications gut MDM, drug development and human health.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
相关文献
二甲双胍通过HDAC6和FoxO3a转录调控肌肉生长抑制素诱导肌肉萎缩
IF 8.9 1区 医学Journal of Cachexia, Sarcopenia and MusclePub Date : 2021-11-02 DOI: 10.1002/jcsm.12833
Min Ju Kang, Ji Wook Moon, Jung Ok Lee, Ji Hae Kim, Eun Jeong Jung, Su Jin Kim, Joo Yeon Oh, Sang Woo Wu, Pu Reum Lee, Sun Hwa Park, Hyeon Soo Kim
具有疾病敏感单倍型的非亲属供体脐带血移植后的1型糖尿病
IF 3.2 3区 医学Journal of Diabetes InvestigationPub Date : 2022-11-02 DOI: 10.1111/jdi.13939
Kensuke Matsumoto, Taisuke Matsuyama, Ritsu Sumiyoshi, Matsuo Takuji, Tadashi Yamamoto, Ryosuke Shirasaki, Haruko Tashiro
封面:蛋白质组学分析确定IRSp53和fastin是PRV输出和直接细胞-细胞传播的关键
IF 3.4 4区 生物学ProteomicsPub Date : 2019-12-02 DOI: 10.1002/pmic.201970201
Fei-Long Yu, Huan Miao, Jinjin Xia, Fan Jia, Huadong Wang, Fuqiang Xu, Lin Guo
来源期刊
自引率
0.00%
发文量
0
期刊最新文献
Infection characteristics among Serratia marcescens capsule lineages. Functional redundancy between penicillin-binding proteins during asymmetric cell division in Clostridioides difficile. Pyruvate and Related Energetic Metabolites Modulate Resilience Against High Genetic Risk for Glaucoma. Computational Analysis of the Gut Microbiota-Mediated Drug Metabolism. Jointly representing long-range genetic similarity and spatially heterogeneous isolation-by-distance.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1