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CustomKinFragLib: Filtering the Kinase-Focused Fragmentation Library
Paula Linh Kramer1, Katharina Buchthal1, Dominique Sydow2
1Data Driven Drug Design, Center for Bioinformatics, Saarland University, Campus, 66123 Saarbrücken, Germany.
ACS Omega
|March 23, 2026
Summary
CustomKinFragLib streamlines fragment-based drug discovery for kinase inhibitors by reducing large libraries into smaller, synthesis-friendly sets. This approach enhances the efficiency of identifying potential drug candidates for diseases like cancer.
Area of Science:
- Medicinal Chemistry
- Computational Drug Discovery
- Biochemistry
Background:
- Protein kinases are critical regulators of cellular processes.
- Dysregulation of kinases is implicated in diseases such as cancer and autoimmune disorders.
- Kinases are vital drug targets, making kinase inhibitor development a key area of research.
Purpose of the Study:
- To address the computational challenges in fragment-based drug discovery (FBDD) for kinase inhibitors.
- To introduce CustomKinFragLib, a pipeline for curating and reducing fragment libraries.
- To generate a smaller, more tractable, and synthesis-friendly fragment set for kinase inhibitor design.
Main Methods:
- Developed CustomKinFragLib, a user-oriented pipeline building on the KinFragLib framework.
- Implemented a systematic post hoc reduction and filtering strategy for fragment sets.
- Integrated literature-derived drug-relevant filters, including synthetic accessibility and drug-likeness properties.
Main Results:
- Reduced the KinFragLib library from 9131 to 837 fragments.
- Retained diverse fragments with drug-like properties and high synthetic tractability.
- Generated a practical fragment set suitable for downstream kinase inhibitor design workflows.
Conclusions:
- CustomKinFragLib offers a practical and customizable solution for generating focused fragment libraries for kinase inhibitor discovery.
- The pipeline enhances the efficiency of FBDD by providing curated, synthesis-friendly fragment sets.
- This approach facilitates the design of novel kinase inhibitors for therapeutic applications.
