Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm

Journal of Cheminformatics
Michael A SkinniderNathan A Magarvey

Abstract

Natural products represent a prominent source of pharmaceutically and industrially important agents. Calculating the chemical similarity of two molecules is a central task in cheminformatics, with applications at multiple stages of the drug discovery pipeline. Quantifying the similarity of natural products is a particularly important problem, as the biological activities of these molecules have been extensively optimized by natural selection. The large and structurally complex scaffolds of natural products distinguish their physical and chemical properties from those of synthetic compounds. However, no analysis of the performance of existing methods for molecular similarity calculation specific to natural products has been reported to date. Here, we present LEMONS, an algorithm for the enumeration of hypothetical modular natural product structures. We leverage this algorithm to conduct a comparative analysis of molecular similarity methods within the unique chemical space occupied by modular natural products using controlled synthetic data, and comprehensively investigate the impact of diverse biosynthetic parameters on similarity search. We additionally investigate a recently described algorithm for natural product retrobiosyn...Continue Reading

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Citations

Apr 23, 2020·Frontiers in Pharmacology·Emmanuelle LautiéJean A Boutin
Dec 25, 2019·Proceedings of the National Academy of Sciences of the United States of America·Nishanth J MerwinNathan A Magarvey
Oct 20, 2020·Protein Science : a Publication of the Protein Society·Diego A Alonzo, T Martin Schmeing
Nov 6, 2020·Briefings in Bioinformatics·Lan HuangJianxin Wang
Jun 3, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Artem A MitrofanovStepan N Kalmykov
Nov 12, 2021·Journal of Agricultural and Food Chemistry·Sebastian BayerAngela Bassoli

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Methods Mentioned

BETA
glycosylation
glycosylations

Software Mentioned

LEMONS Development
RDKit
Chemistry Development Kit
LEMONS ( Library for the Enumeration of MOdular Natural Struct...
GRAPE
GARLIC
LEMONS
Chemistry Development Kit ( CDK )

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