FRAGMENTISE: A user‐friendly, cross‐platform tool to create and analyze comprehensive small‐molecule fragment databases

• Published in: Journal of computational chemistry 2023-10, Vol.44 (26), p.2096-2102
• Main Authors: Zarnecka, Joanna M., Kaminska, Katarzyna H.
• Format: Article
• Language: English
• Subjects: Annotations; building blocks; fragment‐based drug design; Libraries; molecular fragments; Pharmaceuticals; small molecules; Windows (computer programs)
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.27183

The ongoing COVID‐19 pandemic, and constant demand for new therapies in unmet clinical needs, necessitates strategies to identify drug candidates for rapid clinical deployment. Over the years, fragment‐based drug design (FBDD) has emerged as a mainstream lead discovery strategy in academia, biotechnology start‐ups, and large pharma. Chemical building block libraries are the fundamental component of virtually any FBDD campaign. Current trends focus on smaller and smarter libraries that offer synthetically amenable starting points for rational lead generation. Therefore, there remains an ever‐increasing need for new methods to generate fragment libraries to seed early‐stage drug discovery programs. Here, we present FRAGMENTISE—a new user‐friendly, cross‐platform tool for user‐tunable retrosynthetic small‐molecule fragmentation. FRAGMENTISE allows for visualization, similarity search, annotation, and in‐depth analysis of the fragment databases in the medicinal chemistry context. FRAGMENTISE is available as standalone software for Linux, Windows, and macOS users, with a graphical interface or command‐line version. Chemical fragment libraries are the fundamental component of virtually any fragment‐based drug design campaign. Therefore, there remains an ever‐increasing need for new methods to generate “tailor‐made” fragment libraries to seed early‐stage drug discovery programs. To this end and to support researchers in various scientific environments we have built FRAGMENTISE—an easy‐to‐use, platform‐independent tool to generate and analyze comprehensive fragment databases. FRAGMENTISE is available as standalone software with a graphical interface or command‐line version that do not require lengthy tuning or setup procedures.