Oxygen-containing fragments in natural products

• Published in: Journal of computer-aided molecular design Vol. 27; no. 2; pp. 125 - 160
• Main Authors: Titarenko, Zoya, Vasilevich, Natalya, Zernov, Vladimir, Kirpichenok, Michael, Genis, Dmitry
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-02-2013; Springer Nature B.V
• Subjects: Algorithms; Animal Anatomy; Atomic properties; Atoms & subatomic particles; Biological Products - chemistry; CAD; Chemical compounds; Chemistry; Chemistry and Materials Science; Clusters; Computer aided design; Computer Applications in Chemistry; Databases, Factual; Design engineering; Drug Design; Fragments; Histology; Humans; Models, Molecular; Molecular Structure; Morphology; Natural products; Oxygen; Oxygen - chemistry; Physical Chemistry; Similarity; Structure-Activity Relationship; Distinctive set of fragments; NP-likeness score; Natural products; Oxygen-containing structural fragments; NP-likeness
• ISSN: 0920-654X; 1573-4951
• DOI: 10.1007/s10822-012-9629-z

An analysis of the chemical environment of the oxygen atoms in the DNP database compared to the CMC and SCD databases was performed. Some structural clusters were identified which are predominant among the natural products and can be considered as distinctive features of NPs. Fifty-three oxygen-containing structural fragments that are distinctive for the DNP (distinctive set of fragments DSF) in comparison with the SCD have been identified. A new descriptor Mc was introduced for describing the ratio of atoms involved in the DSF to the total number of heavy atoms. A significant difference in the Mc values among the reference databases allowed the use of a specific cluster of the DSF as a tool for performing similarity searches for oxygen-containing NP molecules, or for evaluation or comparison of databases according to their NP-likeness. An example illustrating that the suggested approach could allow not only estimating the NP-likeness, but also serve as a tool for designing new NP-like compounds is provided. The suggested approach for NP-likeness evaluation moves away from the traditional ideas of scaffolds, cycles, linkers and substituents.