Drug-Like, Shape Profiling and Diversity Assessment of the Molport in-Stock Compound Database
Andrea Altieri, Normunds Kinne, Andrievs Auzins, Ratis Brodezonoks, Martin Razuks-Ebels, Artis Erglis, Ieva Kluga, Janis Oslejs, Kristine Skulme, Kristaps Boss, Inga Salmina, Uldis Ledainis, Ieva Kovalenko, Roland Capars, Elza Dzene, Helena Daiga Litvina, Enia Tina Susta, Dita Duka, Inese Sulca, Kristine Rauska-Zeltina, Kirils Bidzans, Diana Zelencova-GopejenkoAbstract
Publicly accessible compound repositories are essential for virtual screening and hit identification, but their continuous growth brings inconsistent structure representations, reactive groups, and a computational burden from standardizing millions of entries. Many repositories also contain outdated or out-of-stock compounds that are no longer procurable, weakening the practical value of screening results. We present a 20-year effort to build and maintain an open-access compound repository: the Molport in-stock catalog, now a collection of 6.1 M purchasable compounds sourced exclusively from validated suppliers. We describe the cheminformatics workflow applied to this catalog, which harmonizes structures from openly accessible, heterogeneous sources into a standardized format, maintains dynamic currency by including only compounds confirmed in stock and removing outdated or unavailable molecules, and profiles physicochemical properties, druglikeness, three-dimensional (3D) shape, and structural diversity to produce chemically meaningful, medicinally relevant subsets. The result is an organized, up-to-date view of purchasable chemical space that supports faster and more reliable identification of experimentally accessible hit candidates for downstream screening campaigns.