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Natural products used as a chemical library for protein-protein interaction targeted drug discovery

Authors
 Xuemei Jin  ;  Kyungro Lee  ;  Nam Hee Kim  ;  Hyun Sil Kim  ;  Jong In Yook  ;  Jiwon Choi  ;  Kyoung Tai No 
Citation
 Journal of Molecular Graphics & Modelling, Vol.79 : 46-58, 2018 
Journal Title
 Journal of Molecular Graphics & Modelling 
ISSN
 1093-3263 
Issue Date
2018
Keywords
Drug discovery ; FDA-approved drugs ; Molecular descriptors ; Molecular docking ; Molecular fingerprint ; Natural products ; Protein-protein interaction inhibitors ; XIAP
Abstract
Protein-protein interactions (PPIs), which are essential for cellular processes, have been recognized as attractive therapeutic targets. Therefore, the construction of a PPI-focused chemical library is an inevitable necessity for future drug discovery. Natural products have been used as traditional medicines to treat human diseases for millennia; in addition, their molecular scaffolds have been used in diverse approved drugs and drug candidates. The recent discovery of the ability of natural products to inhibit PPIs led us to use natural products as a chemical library for PPI-targeted drug discovery. In this study, we collected natural products (NPDB) from non-commercial and in-house databases to analyze their similarities to small-molecule PPI inhibitors (iPPIs) and FDA-approved drugs by using eight molecular descriptors. Then, we evaluated the distribution of NPDB and iPPIs in the chemical space, represented by the molecular fingerprint and molecular scaffolds, to identify the promising scaffolds, which could interfere with PPIs. To investigate the ability of natural products to inhibit PPI targets, molecular docking was used. Then, we predicted a set of high-potency natural products by using the iPPI-likeness score based on a docking score-weighted model. These selected natural products showed high binding affinities to the PPI target, namely XIAP, which were validated in an in vitro experiment. In addition, the natural products with novel scaffolds might provide a promising starting point for further medicinal chemistry developments. Overall, our study shows the potency of natural products in targeting PPIs, which might help in the design of a PPI-focused chemical library for future drug discovery.
Full Text
https://www.sciencedirect.com/science/article/pii/S1093326317304667
DOI
10.1016/j.jmgm.2017.10.015
Appears in Collections:
5. Research Institutes (연구소) > Oral Cancer Research Institute (구강종양연구소) > 1. Journal Papers
2. College of Dentistry (치과대학) > Dept. of Oral Pathology (구강병리학교실) > 1. Journal Papers
Yonsei Authors
Kim, Nam Hee(김남희) ORCID logo https://orcid.org/0000-0002-3087-5276
Kim, Hyun Sil(김현실) ORCID logo https://orcid.org/0000-0003-3614-1764
Yook, Jong In(육종인) ORCID logo https://orcid.org/0000-0002-7318-6112
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URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/161988
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