Daniel A. Acuña Jiménez

Natural products are outstanding resources of bioactive compounds with potential applications not only in drug discovery but also in the cosmetic industry and natural pesticides. Costa Rica is among the most biologically diverse countries in terms of the number of known species per unit of area, even above conventionally considered megadiverse countries. In this work, we introduce the Natural Products Repository of Costa Rica (NAPRORE-CR): the first dedicated database that compiles structural representations and predicted properties of natural products found and/or characterized in Costa Rica. The first version of this collection comprises 1161 compounds, annotated with structural classifications, calculated structural and physicochemical properties (MW, HBD, HBA, RB, AlogP, and TPSA), and complex descriptors (SA score, QED, nSPS). The diversity and chemical space coverage of compounds in NAPRORE-CR were compared to drugs, pesticides, and cosmetics. Through the analysis and visualization of chemical space coverage and diversity, it was found that NAPRORE-CR has a property profile compatible with applications in all three fields, and that its compounds are structurally similar to those of approved drugs and natural pesticides. Cross-referencing NAPRORE-CR with PubChem and ChEMBL, combined with activity predictions, facilitated the identification of both known applications of the included compounds and potential new areas of study. In favour of open science and FAIR principles for data sharing, NAPRORE-CR is freely available at https://doi.org/10.5281/zenodo.7858061.

The consideration of the ionic partition coefficient in estimating pH-dependent lipophilicity profiles for small molecules has been previously emphasized through classification Machine Learning protocols. In alignment with the principles of Findable, Accessible, Interoperable, and Reusable (FAIR) data to enhance data management and sharing, we introduce LiProS: a FAIR workflow accessible via Google Colab. LiProS assists researchers in efficiently determining the appropriate pH-dependent lipophilicity profile based on the SMILES code of their molecules of interest. LiProS demonstrated its applicability in discerning the most suitable lipophilicity formalism based on small structural variations in potential cases of structure-based drug design.

Natural product (NP) databases are crucial tools in computer-aided drug design (CADD). Over the last 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, to our knowledge, it 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, visualization of the chemical space, determination of the structural diversity, molecular complexity, synthetic feasibility, commercial availability, predicted and reported 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. The Latin American natural product collection LANaPDB is publicly available and can be downloaded at https://github.com/alexgoga21/LANaPDB-version-2/tree/main.

Compound databases of natural products play a crucial role in drug discovery and development projects and have implications in other areas, such as food chemical research, ecology and metabolomics. Recently, we put together the first version of the Latin American Natural Product database (LANaPDB) as a collective effort of researchers from six countries to ensemble a public and representative library of natural products in a geographical region with a large biodiversity. The present work aims to conduct a comparative and extensive profiling of the natural product-likeness of a recently updated version of LANaPDB and the individual ten compound databases that form part of LANaPDB. The natural product-likeness profile of the Latin American compound databases is contrasted with the profile of other major natural product databases in the public domain and a set of small-molecule drugs approved for clinical use. As part of the extensive characterization, we employed several chemoinformatics metrics of natural product likeness. The results of this study will capture the attention of the global community engaged in natural product databases, not only in Latin America but across the world.

The number of databases of natural products (NPs) has increased substantially. Latin America is extraordinarily rich in biodiversity, enabling the identification of novel NPs, which has encouraged both the development of databases and the implementation of those that are being created or are under development. In a collective effort from several Latin American countries, herein we introduce the first version of the Latin American Natural Products Database (LANaPDB), a public compound collection that gathers the chemical information of NPs contained in diverse databases from this geographical region. The current version of LANaPDB unifies the information from six countries and contains 12,959 chemical structures. The structural classification showed that the most abundant compounds are the terpenoids (63.2%), phenylpropanoids (18%) and alkaloids (11.8%). From the analysis of the distribution of properties of pharmaceutical interest, it was observed that many LANaPDB compounds satisfy some drug-like rules of thumb for physicochemical properties. The concept of the chemical multiverse was employed to generate multiple chemical spaces from two different fingerprints and two dimensionality reduction techniques. Comparing LANaPDB with FDA-approved drugs and the major open-access repository of NPs, COCONUT, it was concluded that the chemical space covered by LANaPDB completely overlaps with COCONUT and, in some regions, with FDA-approved drugs. LANaPDB will be updated, adding more compounds from each database, plus the addition of databases from other Latin American countries.

The number of databases of natural products (NPs) have increased substantially. Latin America is extraordinarily rich in biodiversity enabling the identification of novel NPs, which has encouraged both the development of databases and the implementation of those that are being created or are under development. In a collective effort from several Latin American countries, herein we introduce the first version of Latin American Natural Products Database (LANaPDB), a public compound collection that gathers the chemical information of NPs contained in diverse databases from this geographical region. The current version of LANaPD unifies the information from six countries and contains 12,959 chemical structures. The structural classification showed that the most abundant compounds are the terpenoids 63.2%, phenylpropanoids 18% and the alkaloids 11.8%. From the analysis of the distribution of properties of pharmaceutical interest, it was observed that many LaNaPDB compounds satisfy some drug-like rules of thumb for physicochemical properties. The concept of the chemical multiverse was employed to generate multiple chemical spaces from two different fingerprints and two dimensionality reduction techniques. Comparing LaNaPDB with FDA-approved drugs and the major open-access repository of NPs, COCONUT it was concluded that the chemical space covered by LaNaPDB completely overlaps with COCONUT and in some regions with FDA-approved drugs. LANaPD will be updated adding more compounds from each database plus the addition of databases from other Latin American countries. The database is freely available at https://github.com/alexgoga21/LaNaPDB.