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Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products

  • Jun Shang
    Jun Shang
    College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
    State Key Laboratory of Agricultural Microbiology and Agricultural Bioinformatics, Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
    State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
    More by Jun Shang
  • Ben Hu
    Ben Hu
    State Key Laboratory of Agricultural Microbiology and Agricultural Bioinformatics, Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
    More by Ben Hu
  • Junmei Wang
    Junmei Wang
    Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
    More by Junmei Wang
  • Feng Zhu
    Feng Zhu
    College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
    More by Feng Zhu
  • Yu Kang
    Yu Kang
    College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
    More by Yu Kang
  • Dan Li
    Dan Li
    College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
    More by Dan Li
  • Huiyong Sun
    Huiyong Sun
    College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
    More by Huiyong Sun
  • De-Xin Kong*
    De-Xin Kong
    State Key Laboratory of Agricultural Microbiology and Agricultural Bioinformatics, Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
    *E-mail: [email protected] (D.-X.K.).
    More by De-Xin Kong
  • , and 
  • Tingjun Hou*
    Tingjun Hou
    College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
    State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
    *E-mail: [email protected] (T.H.).
    More by Tingjun Hou
Cite this: J. Chem. Inf. Model. 2018, 58, 6, 1182–1193
Publication Date (Web):May 24, 2018
https://doi.org/10.1021/acs.jcim.8b00125
Copyright © 2018 American Chemical Society

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    Abstract

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    This is a new golden age for drug discovery based on natural products derived from both marine and terrestrial sources. Herein, a straightforward but important question is “what are the major structural differences between marine natural products (MNPs) and terrestrial natural products (TNPs)?” To answer this question, we analyzed the important physicochemical properties, structural features, and drug-likeness of the two types of natural products and discussed their differences from the perspective of evolution. In general, MNPs have lower solubility and are often larger than TNPs. On average, particularly from the perspective of unique fragments and scaffolds, MNPs usually possess more long chains and large rings, especially 8- to 10-membered rings. MNPs also have more nitrogen atoms and halogens, notably bromines, and fewer oxygen atoms, suggesting that MNPs may be synthesized by more diverse biosynthetic pathways than TNPs. Analysis of the frequently occurring Murcko frameworks in MNPs and TNPS also reveals a striking difference between MNPs and TNPs. The scaffolds of the former tend to be longer and often contain ester bonds connected to 10-membered rings, while the scaffolds of the latter tend to be shorter and often bear more stable ring systems and bond types. Besides, the prediction from the naïve Bayesian drug-likeness classification model suggests that most compounds in MNPs and TNPs are drug-like, although MNPs are slightly more drug-like than TNPs. We believe that MNPs and TNPs with novel drug-like scaffolds have great potential to be drug leads or drug candidates in drug discovery campaigns.

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jcim.8b00125.

    • Table S1 information of the 60 physicochemical properties; Table S2 statistics of numbers (N) and percentages (P) of the compounds satisfying different numbers of Ro5 rules; Figure S1 unique and common chain assemblies of MNPs and TNPs; Figure S2 unique and common ring assemblies of MNPs and TNPs; Figure S3 (A) unique and (B) common RECAP fragments of MNPs and TNPs; Figure S4 unique and common Murcko frameworks of MNPs and TNPs (PDF)

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