Chemoinformatic Characterization of NAPROC-13: A Database for Natural Product 13 C NMR Dereplication

• Published in: Journal of natural products (Washington, D.C.) D.C.), 2024-09, Vol.87 (9), p.2216-2229
• Main Authors: Avellaneda-Tamayo, Juan F, Agudo-Muñoz, Naicolette A, Sánchez-Galán, Javier E, López-Pérez, José L, Medina-Franco, José L
• Format: Article
• Language: English
• Subjects: Biological Products - chemistry; Carbon-13 Magnetic Resonance Spectroscopy; Cheminformatics - methods; Molecular Structure
• ISSN: 0163-3864; 1520-6025
• DOI: 10.1021/acs.jnatprod.4c00530

Natural products (NPs) are secondary metabolites of natural origin with broad applications across various human activities, particularly the discovery of bioactive compounds. Structural elucidation of new NPs entails significant cost and effort. On the other hand, the dereplication of known compounds is crucial for the early exclusion of irrelevant compounds in contemporary pharmaceutical research. NAPROC-13 stands out as a publicly accessible database, providing structural and C NMR spectroscopic information for over 25 000 compounds, rendering it a pivotal resource in natural product (NP) research, favoring open science. This study seeks to quantitatively analyze the chemical content, structural diversity, and chemical space coverage of NPs within NAPROC-13, compared to FDA-approved drugs and a very diverse subset of NPs, UNPD-A. Findings indicated that NPs in NAPROC-13 exhibit properties comparable to those in UNPD-A, albeit showcasing a notably diverse array of structural content, scaffolds, ring systems of pharmaceutical interest, and molecular fragments. NAPROC-13 covers a specific region of the chemical multiverse (a generalization of the chemical space from different chemical representations) regarding physicochemical properties and a region as broad as UNPD-A in terms of the structural features represented by fingerprints.