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KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination

submitted on 23.07.2020, 09:00 and posted on 24.07.2020, 09:18 by Dominique Sydow, Paula Schmiel, Jérémie Mortier, Andrea Volkamer
Protein kinases play a crucial role in many cell signaling processes, making them one of the most important families of drug targets. In this context, fragment-based drug design strategies have been successfully applied to develop novel kinase inhibitors, usually following a knowledge-driven approach to optimize a focused set of fragments to a potent kinase inhibitor.
Alternatively, KinFragLib is a new method that allows to explore and extend the chemical space of kinase inhibitors using data-driven fragmentation and recombination, built on available structural kinome data from the KLIFS database for over 2,500 kinase DFG-in complexes. The computational fragmentation method splits the co-crystallized non-covalent kinase inhibitors into fragments with respect to their 3D proximity to six predefined functionally relevant subpocket centers. The resulting fragment library consists of six subpocket pools with over 7,000 fragments, available at
KinFragLib offers two main applications: (i) In-depth analyses of the chemical space of known kinase inhibitors, subpocket characteristics and connections, as well as (ii) subpocket-informed recombination of fragments to generate potential novel inhibitors. The latter showed that recombining only a subset of 624 representative fragments generated a combinatorial library of 6.7 million molecules, containing, besides some known kinase inhibitors, more than 99% novel chemical matter compared to ChEMBL and 63% molecules compliant with Lipinski's rule of five.


Deutsche Forschungsgemeinschaft (VO 2353/1-1)

Bundesministerium für Bildung und Forschung (031A262C)


Email Address of Submitting Author


Charité - Universitätsmedizin Berlin



ORCID For Submitting Author


Declaration of Conflict of Interest


Version Notes

Version v1.0.0