Description and Analysis of Glycosidic Residues in the Largest Open Natural Products Database

Abstract

Natural products (NPs), biomolecules produced by living organisms, inspire the pharmaceutical industry and research due to their structural characteristics and the substituents from which they derive their activities. Glycosidic residues are frequently present in NP structures and have particular pharmacokinetic and pharmacodynamic importance as they improve their solubility and are often involved in molecular transport, target specificity, ligand–target interactions, and receptor binding. The COlleCtion of Open Natural prodUcTs (COCONUT) is currently the largest open database of NPs, and therefore a suitable starting point for the detection and analysis of the diversity of glycosidic residues in NPs. In this work, we report and describe the presence of circular, linear, terminal, and non-terminal glycosidic units in NPs, together with their importance in drug discovery.

MORTAR - A Rich Client Application for in silico Molecule Fragmentation

“…The comparatively high number of hydroxy groups detected in absolute numbers as opposed to the molecule frequency means that natural products usually have multiple substituents of this type (3.3 on average, dividing the frequency by the molecule frequency). One type of structures that may be responsible for this trend is glycosidic moieties that occur frequently in natural products [30]. The results of this proof of concept analysis using MORTAR are in general agreement with an analogous systematic study of functional group frequencies in natural products conducted by Ertl et al [28].…”

MORTAR – A Rich Client Application for in silico Molecule Fragmentation

“…The comparatively high number of hydroxy groups detected in absolute numbers as opposed to the molecule frequency means that natural products usually have multiple substituents of this type (3.3 on average, dividing the frequency by the molecule frequency). One type of structure that may be responsible for this trend is glycosidic moieties that occur frequently in natural products [30]. The results of this proof-ofconcept analysis using MORTAR are in general agreement with an analogous systematic study of functional group frequencies in natural products conducted by Ertl et al [28].…”

Substituents of life: The most common substituent patterns present in natural products

“…Recently also an open source procedure for in silico deglycosylation has been made available [20]. It is well known that the presence of sugar units, influencing mostly molecule solubility and transport properties, is one of the most typical structural features of NPs [14], in our study, however, we were interested in identifying other, smaller substituents typical for NPs. After molecular preprocessing the substituents were extracted.…”

“…The only study focusing on the analysis of substituents in NPs is according to our knowledge a recent publication about sugar substitution patterns in NPs [14] where authors studied the presence of circular, linear, terminal, and non-terminal glycosidic units in NPs, together with their importance in drug discovery.…”