Exploiting PubChem and other public databases for virtual screening in 2025: what are the latest trends?
Alberto Marbán‐González, Verónica Ramírez-Cid, Alejandro Cristóbal-Ramírez, José L. Medina‐Franco
Abstract
INTRODUCTION: Cheminformatics has become a cornerstone of modern drug discovery, offering the ability to efficiently manage and analyze large volumes of chemical and biological data. Publicly available databases such as PubChem, ZINC, ChEMBL, DrugBank, ChemDiv, natural product databases, among others, are essential for accessing diverse chemical structures, biological activities, and pharmacological properties. AREAS COVERED: This review provides an overview of recent (2024-2025) trends in mining data from PubChem and other representative public databases for virtual screening. It also discusses the integration of experimental validation and computational tools in drug design and cheminformatics workflows. The article is based on literature retrieved from SciFinder. EXPERT OPINION: Public chemical databases contain thousands to billions of compounds and various computational strategies have necessitated development to navigate this vast chemical space effectively. These include application programming interfaces, similarity searches, physicochemical filtering, and target-based selection. Such filtering strategies have enabled the extraction of focused compound subsets for evaluation through various cheminformatics tools, ultimately supporting informed decision-making in lead discovery and optimization.