DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico.
CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica.
J Chem Inf Model. 2024 Nov 25;64(22):8495-8509. doi: 10.1021/acs.jcim.4c01560. Epub 2024 Nov 6.
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.
天然产物 (NP) 数据库是计算机辅助药物设计 (CADD) 的重要工具。在过去的十年中，全球范围内一直在努力收集和整理有关在特定地理区域中分离和表征的天然产物 (NP) 的信息。2023 年，发布了 LANaPDB，据我们所知，这是首次尝试收集和标准化拉丁美洲的所有 NP 数据库。在此，我们详细介绍和分析了 LANaPDB 更新版本的内容，其中包括来自哥伦比亚、哥斯达黎加和墨西哥的 619 种新化合物。LANaPDB 的当前版本共有来自七个拉丁美洲国家的十个数据库的 13578 种化合物。对 LANaPDB 进行了 chemoinformatic 特征描述，包括化合物的结构分类、计算六种有药用价值的物理化学性质以及通过使用和比较两种不同指纹（MACCS 键 (166 位) 和 Morgan2 (2048 位)）可视化化学空间。此外，还进行了其他分析，并添加了 LANaPDB 最初版本中未包含的有价值信息，包括结构多样性、分子复杂性、合成可行性、商业可用性以及报道和预测的生物活性。此外，将 LANaPDB 化合物与两个带有生物活性注释的最大公共化学化合物数据库（ChEMBL 和 PubChem）进行交叉引用。
