Abstract
BackgroundNatural product-likeness of a molecule, i.e. similarity of this molecule to the structure space covered by natural products, is a useful criterion in screening compound libraries and in designing new lead compounds. A closed source implementation of a natural product-likeness score, that finds its application in virtual screening, library design and compound selection, has been previously reported by one of us. In this note, we report an open-source and open-data re-implementation of this scoring system, illustrate its efficiency in ranking small molecules for natural product likeness and discuss its potential applications.ResultsThe Natural-Product-Likeness scoring system is implemented as Taverna 2.2 workflows, and is available under Creative Commons Attribution-Share Alike 3.0 Unported License at http://www.myexperiment.org/packs/183.html. It is also available for download as executable standalone java package from http://sourceforge.net/projects/np-likeness/under Academic Free License.ConclusionsOur open-source, open-data Natural-Product-Likeness scoring system can be used as a filter for metabolites in Computer Assisted Structure Elucidation or to select natural-product-like molecules from molecular libraries for the use as leads in drug discovery.
Highlights
Natural product-likeness of a molecule, i.e. similarity of this molecule to the structure space covered by natural products, is a useful criterion in screening compound libraries and in designing new lead compounds
Besides that, PubMed abstracts reporting isolation of new Natural products (NPs) were text-mined for natural product’s name and the names were converted into SMILES using Chemical Identifier Resolver [18] and the resultant set of 3610 non-redundant NPs was used as our test set
We have presented an open-source, open-data implementation of a Natural-Product-likeness scorer originally described by Ertl et al Workflows for curation, training and scoring are implemented in the open-source workflow tool Chemistry Development Kit (CDK)-Taverna and published at myexperiment.org
Summary
Natural product-likeness of a molecule, i.e. similarity of this molecule to the structure space covered by natural products, is a useful criterion in screening compound libraries and in designing new lead compounds. A closed source implementation of a natural product-likeness score, that finds its application in virtual screening, library design and compound selection, has been previously reported by one of us. We report an open-source and open-data re-implementation of this scoring system, illustrate its efficiency in ranking small molecules for natural product likeness and discuss its potential applications. The class of NPs termed secondary metabolites that are involved in defence or signalling, are of particular importance because they were optimised during evolution to have effective interactions with biological receptors. They are good starting points for designing new drugs [1]. We focus only on identifying structural features typical of natural products, and based on their presence, rank molecules of interest according to their NP-likeness
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