Alejandro Gómez-García

The aim of this research is to introduce the first curated natural product database from Colombia, Natural Products DataBase EjeCol (NPDBEjeCol), that has been made publicly available at www.npdbejecol.com. The compound library, compiled from the peer-reviewed literature, is composed of natural products derived from plants in the coffee region of Colombia. After extensive data standardization and curation, molecular descriptors of pharmaceutical relevance and molecular fingerprints of different designs were calculated in order to evaluate the structural diversity and explore their chemical space of compounds in NPDBEjeCol in comparison with natural products reference libraries. The current version of NPDBEjeCol contains 236 molecules, for which detailed information is available. This includes the compound name, linear notation, references to the peer-reviewed literature, CAS number, synonym names, and constitutional descriptors. Analysis of the drug-like properties suggest that NPDBEjeCol natural products are on average, compliant with the empirical Lipinski’s rule. Visualizations of the chemical space based on fingerprints uncovered one to three clusters of compounds and fragments. Among the phytochemical groups present in the database, terpenes are the most prominent, particularly those derived from monoterpenes and sesquiterpenes. NPDBEjeCol is the first Colombian natural products database of its kind in the country that can be publicly accessed through a web portal, facilitating open query, navigation, and visualization of the identified molecules.

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.

Los productos naturales son la mayor fuente de moléculas bioactivas. A lo largo del mundo han sido publicadas bases de datos de productos naturales aislados y caracterizados en determinadas regiones geográficas. Una aplicación práctica de estas bases de datos es el diseño de fármacos asistido por computadora (DIFAC). El objetivo de este artículo es mostrar de manera general la significancia de las bases de datos moleculares de productos naturales enfocándose en el DIFAC. A partir de una revisión bibliográfica exhaustiva, se exponen ejemplos de bases de datos moleculares publicadas alrededor del mundo y se muestra el estado del arte actual en el desarrollo de este rubro en Latinoamérica.

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.

The analysis of chemical data sets represents a significant challenge for researchers due to the large quantity and dispersion of the data. In order to facilitate accessible recovery, it is necessary to organize the data into databases. The aim of this research is to compile and analyze information on natural products derived from plants in the Coffee region of Colombia through the online Natural Products DataBase EjeCol (NPDBEjeCol). It is the first database of its kind for the country. The workflow for the creation of the database began with the compilation of reported molecules of natural products derived from plants studied and present to the Coffee region of Colombia. This was achieved through a systematic literature review and dataset compilation conducted using the specified bibliometric equations, with a focus on articles published up to December 2023 and collecting information from research groups at Colombian universities. Once the set of molecules had been curated, molecular descriptors and fingerprints were calculated in order to evaluate the structural diversity and explore their chemical space in comparison with natural products reference libraries. The NPDBEjeCol database contains 236 molecules, for which detailed information is available. This includes the compound name, SMILES notation, references (journal name, DOI number, and year of publication), CAS number, synonym names, and constitutional descriptors. The database places an emphasis on small molecules with an average molecular weight of 234.77 g/mol and features a high structural diversity. The calculated physicochemical properties are in accordance with Lipinski's Rule of Five. Visualizations using PCA and t-SNE demonstrate the existence of distinct clusters of compounds and fragments, thereby highlighting the structural diversity. The compound database is publicly accessible via the web portal www.npdbejecol.com. The objective of the website is to facilitate open consultation, navigation, management, and visualization of the molecules identified through research on natural products derived from plants in the coffee region of Colombia.

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 an 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.

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.

Searching, retrieving, and analyzing chemical information is one of the main tasks faced by students and professionals in chemistry-related scientific disciplines. Currently, freely available modules developed in programming languages, such as Python, allow efficient data management and facilitate obtaining information and knowledge from the data. This manuscript describes an electronic handbook generated on the GitBook platform to introduce the Python programming language and the Analysis, computational representation, and visualization of chemical data. This manual explores the most common molecular representations of low molecular weight organic compounds and their applications in various contexts. It also illustrates the acquisition of chemical information from large public molecular databases such as ChEMBL and PubChem and the Analysis and visualization of chemical information using concepts such as chemical space. The GitBook is freely available and is expected to foster open science and facilitate learning for chemistry students at the undergraduate and graduate levels and professionals interested in chemical data analysis and visualization.

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.