Chemical Space, Scaffolds, and Halogenated Compounds of CMNPD: A Comprehensive Chemoinformatic Analysis

• Published in: Journal of chemical information and modeling 2021-07, Vol.61 (7), p.3323-3336
• Main Authors: Liu, Ningfeng, Lai, Junyong, Lyu, Chuanyu, Qiang, Bo, Wang, Heyu, Jin, Hongwei, Zhang, Liangren, Liu, Zhenming
• Format: Article
• Language: English
• Subjects: Bromides; Bromination; Chemical Information; Drugs; Halogens; Microorganisms; Natural products; Scaffolds
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.1c00162

The comprehensive marine natural products database (CMNPD) is a new free access and comprehensive database developed originally by Lyu’s team of our research group, including more than 30 000 marine natural products (MNPs) reported from the 1960s. In this article, we aimed to present CMNPD’s value in drug discovery and to present several characteristics of MNPs based on our new comprehensive data. We used chemoinformatic analysis methods to report the molecular properties, chemical space, and several scaffold assessments of CMNPD compared with several databases. Then, we reported the characteristics of MNPs from the aspect of halogens, comparing MNPs with terrestrial natural products (TNPs) and drugs. We found that CMNPD had a low proportion (2.91%) of scaffolds utilized by drugs, and high similarities between CMNPD and NPAtlas (a microbial natural products database), which are worth further investigation. The proportion of bromides in MNPs is outstandingly higher (11.0%) in contrast to other halogens. Furthermore, the results showed great differences in halogenated structures between MNPs and drugs, especially brominated substructures. Finally, we found that many marine species (2.52%) reported only halogenated compounds. It can be concluded from these results that CMNPD is a promising source for drug discovery and has many scientific issues relative to MNPs that need to be further investigated.