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Chen Z, Yan D, Zhang M, Han W, Wang Y, Xu S, Tang K, Gao J, Cao Z. MetNC: Predicting Metabolites in vivo for Natural Compounds. Front Chem 2022; 10:881975. [PMID: 35646826 PMCID: PMC9135178 DOI: 10.3389/fchem.2022.881975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/11/2022] [Indexed: 12/02/2022] Open
Abstract
Natural compounds (NCs) undergo complicated biotransformation in vivo to produce diverse forms of metabolites dynamically, many of which are of high medicinal value. Predicting the profiles of chemical products may help to narrow down possible candidates, yet current computational methods for predicting biotransformation largely focus on synthetic compounds. Here, we proposed a method of MetNC, a tailor-made method for NC biotransformation prediction, after exploring the overall patterns of NC in vivo metabolism. Based on 850 pairs of the biotransformation dataset validated by comprehensive in vivo experiments with sourcing compounds from medicinal plants, MetNC was designed to produce a list of potential metabolites through simulating in vivo biotransformation and then prioritize true metabolites into the top list according to the functional groups in compound structures and steric hindrance around the reaction sites. Among the well-known peers of GLORYx and BioTransformer, MetNC gave the highest performance in both the metabolite coverage and the ability to short-list true products. More importantly, MetNC seemed to display an extra advantage in recommending the microbiota-transformed metabolites, suggesting its potential usefulness in the overall metabolism estimation. In summary, complemented to those techniques focusing on synthetic compounds, MetNC may help to fill the gap of natural compound metabolism and narrow down those products likely to be identified in vivo.
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Affiliation(s)
- Zikun Chen
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Deyu Yan
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Mou Zhang
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wenhao Han
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yuan Wang
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shudi Xu
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Kailin Tang
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jian Gao
- International Human Phenome Institutes, Shanghai, China
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- *Correspondence: Zhiwei Cao, ; Jian Gao,
| | - Zhiwei Cao
- Dept. of Gastroenterology, Shanghai Tenth People’s Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- School of Life Sciences, Fudan University, Shanghai, China
- *Correspondence: Zhiwei Cao, ; Jian Gao,
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