Fragment Library of Natural Products and Compound Databases for Drug Discovery

Natural products and semi-synthetic compounds continue to be a significant source of drug candidates for a broad range of diseases, including the current pandemic caused by COVID-19. Besides being attractive sources of bioactive compounds for further development or optimization, natural products are excellent candidates of unique substructures for fragment-based drug discovery inspired on natural products. To this end, fragment libraries are required that can be incorporated into automated drug design pipelines. However, it is still scarce to have public fragment libraries based on extensive collections of natural products. Herein we report the generation and analysis of a fragment library of natural products derived from a database with more than 400,000 compounds. We also report fragment libraries of food chemical databases and other compound data sets of interest in drug discovery, including compound libraries relevant for COVID-19 drug discovery. The fragment libraries were characterized in terms of contents and diversity.<br><br>Sopporting information contains: <br>COCONUT_COMPOUNDS.csv, FooDB_COMPOUNDS.csv, DCM_COMPOUNDS.csv, CAS_COMPOUNDS.csv, 3CLP_COMPOUNDS.csv. All datasets contain the curated structures and the following information: identicator number (ID), simplified molecular input line entry system (Smiles), Average Molecular Weight (AMW), number of carbons, oxygens, nitrogens, heavy atoms, aliphatic rings, aromatic rings, heterocycles, bridgehead atoms, fraction of sp3 carbon atoms and chiral carbons, and a list of fragments generated from each compound. FRAGMENTS_COCONUT.csv, FRAGMENTS_FooDB.csv, FRAGMENTS_DCM.csv, FRAGMENTS_CAS.csv, FRAGMENTS_3CLP.csv. All libraries contain structures generated (Fragments) from each compound library (Dataset) and the following information: number of compounds that contain that fragment in a dataset (Count) and fraction of them (Proportion), average Molecular Weight (AMW), number of carbons, oxygens, nitrogens, heavy atoms, aliphatic rings, aromatic rings, heterocycles, bridgehead atoms, fraction of sp3 carbon atoms and chiral carbons. <br>