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Abstract

Chemistry

Visualizing and Analyzing the Chemical Space of Natural Product Databases for Drug Discovery

Published: September 6th, 2024

DOI:

10.3791/66349

1Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 2DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México

Abstract

Chemical space is a multidimensional descriptor space that encloses all possible molecules, and at least 1 x 1060 organic substances with a molecular weight below 500 Da are thought to be potentially relevant for drug discovery. Natural products have been the primary source of the new pharmacological entities marketed during the past forty years and continue to be one of the most productive sources for the creation of innovative medications. Chemoinformatics-based computational tools accelerate the drug development process for natural products. Methods including estimating bioactivities, safety profiles, ADME, and natural product likeness measurement have been used. Here, we go over recent developments in chemoinformatic tools designed to visualize, characterize, and expand the chemical space of natural compound data sets using various molecular representations, create visual representations of such spaces, and investigate structure-property relationships within chemical spaces. With an emphasis on drug discovery applications, we evaluate the open-source databases BIOFACQUIM and PeruNPDB as proof of concept.

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