Latin American Natural Product Database (LANaPDB): An Update
Natural product (NP) databases are crucial tools in computer-aided drug design (CADD). Over the past decade, there has been a worldwide effort to assemble information regarding natural products (NPs) isolated and characterized in certain geographical regions. In 2023, it was published LANaPDB, and to our knowledge, this is the first attempt to gather and standardize all the NP databases of Latin America. Herein, we present and analyze in detail the contents of an updated version of LANaPDB, which includes 619 newly added compounds from Colombia, Costa Rica, and Mexico. The present version of LANaPDB has a total of 13 578 compounds, coming from ten databases of seven Latin American countries. A chemoinformatic characterization of LANaPDB was carried out, which includes the structural classification of the compounds, calculation of six physicochemical properties of pharmaceutical interest, and visualization of the chemical space by employing and comparing two different fingerprints (MACCS keys (166-bit) and Morgan2 (2048-bit)). Furthermore, additional analyses were made, and valuable information not included in the first version of LANaPDB was added, which includes structural diversity, molecular complexity, synthetic feasibility, commercial availability, and reported and predicted biological activity. In addition, the LANaPDB compounds were cross-referenced to two of the largest public chemical compound databases annotated with biological activity: ChEMBL and PubChem.
Authors
- William J. Zamora (ORCID: https://orcid.org/0000-0003-4029-4528)
- Hoover Valencia-Sánchez (ORCID: https://orcid.org/0000-0001-9193-2089)
- Adriano D. Andricopulo (ORCID: https://orcid.org/0000-0002-0457-818X)
- Daniel A. Acuña Jiménez (ORCID: https://orcid.org/0009-0007-3038-4374)
- Marvin J. Núñez (ORCID: https://orcid.org/0000-0002-0411-6962)
- Haruna Luz Barazorda-Ccahuana (ORCID: https://orcid.org/0000-0001-8791-0506)
- Dionisio A. Olmedo (ORCID: https://orcid.org/0000-0002-4681-1365)
- Oscar Marino Mosquera Martínez (ORCID: https://orcid.org/0000-0003-2998-0842)
- Alejandro Gómez‐García (ORCID: https://orcid.org/0000-0003-4444-8221)
- H. Hernández (ORCID: https://orcid.org/0000-0001-7242-0192)
- Miguel Á. Chávez‐Fumagalli (ORCID: https://orcid.org/0000-0002-8394-4802)
- Pablo N. Solís (ORCID: https://orcid.org/0000-0002-9214-0339)
- Marília Valli (ORCID: https://orcid.org/0000-0003-1106-183X)
- José L. Medina‐Franco (ORCID: https://orcid.org/0000-0003-4940-1107)
- Vanderlan da Silva Bolzani (ORCID: https://orcid.org/0000-0003-0615-8776)
- Johny R. Rodríguez-Pérez (ORCID: https://orcid.org/0000-0002-5216-220X)
Institutions
- Universidad de Panamá (PA)
- Universidade de Ribeirão Preto (BR)
- Universidade Federal de São Carlos (BR)
- Universidade de São Paulo (BR)
- Technological University of Pereira (CO)
- Universidad de Costa Rica (CR)
- Catholic University of Santa María (PE)
- Universidad Nacional Abierta y a Distancia (CO)
- University of El Salvador (SV)
- Universidade Estadual Paulista (Unesp) (BR)
- Universidad Nacional Autónoma de México (MX)
Publication Details
- Journal
- Journal of Chemical Information and Modeling
- Published
- 2024-11-06
- DOI
- https://doi.org/10.1021/acs.jcim.4c01560
- Citations
- 8
- Primary Topic
- Computational Drug Discovery Methods
- Type
- article
- Field-Weighted Citation Impact
- 2.89
Funders
- Universidad Tecnológica de Panamá
- Deutscher Akademischer Austauschdienst
- Deutsche Forschungsgemeinschaft
- Fundação de Amparo à Pesquisa do Estado de São Paulo
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
- Consejo Nacional de Ciencia y Tecnología
- Conselho Nacional de Desenvolvimento Científico e Tecnológico
- Universidad de Costa Rica
- Universidad Tecnológica de Pereira
- Vicerrectoría de Investigación, Universidad de Costa Rica
- Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México