Fragment Libraries from Large and Novel Synthetic Compounds and Natural Products: A Comparative Chemoinformatic Analysis
We report comprehensive fragment libraries obtained from large natural product databases and compare their chemical space coverage and diversity with those of synthetic fragment libraries. Specifically, we obtained 2,583,127 fragments derived from the recently updated collection of open natural product (COCONUT) data set with more than 695,133 unique (nonduplicate) natural products and 74,193 fragments derived from the Latin America Natural Product Database (LANaPDB) with 13,578 unique natural products from Latin America. The content, chemical space coverage, and chemical diversity of the natural product libraries were compared to the recently developed CRAFT library, which contains 1214 fragments based on distinct heterocyclic scaffolds and natural product-derived chemicals. The fragment libraries herein obtained and curated are freely available at https://github.com/DIFACQUIM/Fragment-libraries-from-large-synthetic-compounds-and-natural-products-collections.git.
Authors
- Wemenes J. Lima Silva
- Temitayo Omowumi Alegbejo Price (ORCID: https://orcid.org/0000-0002-8750-0635)
- Flávio da Silva Emery (ORCID: https://orcid.org/0000-0002-8652-7123)
- Carolina Horta Andrade (ORCID: https://orcid.org/0000-0003-0101-1492)
- Osvaldo Sánchez López
- Kamilla M. Alves
- Ana L. Chávez‐Hernández (ORCID: https://orcid.org/0000-0002-6202-1769)
- José L. Medina‐Franco (ORCID: https://orcid.org/0000-0003-4940-1107)
- Verónica Ramírez-Cid
- Raul Marques Novais
Institutions
- Universidade de São Paulo (BR)
- Mechanical Design (Czechia) (CZ)
- Institute of Informatics of the Slovak Academy of Sciences (SK)
- Artificial Intelligence in Medicine (Canada) (CA)
- Universidade Federal de Goiás (BR)
- Universidad Nacional Autónoma de México (MX)
Publication Details
- Journal
- ACS Omega
- Published
- 2025-04-16
- DOI
- https://doi.org/10.1021/acsomega.5c01420
- Citations
- 2
- Primary Topic
- Computational Drug Discovery Methods
- Type
- article
- Field-Weighted Citation Impact
- 3.01
Funders
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
- Consejo Nacional de Ciencia y Tecnología
- Conselho Nacional de Desenvolvimento Científico e Tecnológico
- Fundação de Amparo à Pesquisa do Estado de Goiás
- National Institutes of Health