Kinase fragments galore: a free virtual collection

Kinases hold a special place in fragment-based drug discovery. Vemurafenib, the first approved FBDD-derived drug, targets a kinase, as do more than a third of fragment-derived drugs to enter the clinic. These efforts have produced a wealth of knowledge, and in a new paper in J. Chem Inf. Mod. Andrea Volkamer and collaborators at Universitätsmedizin Berlin and Bayer have extracted thousands of virtual fragments and made them freely available in a database called KinFragLib.

 

The researchers started with a prior database called KLIFS, which compiles thousands of crystal structures of kinases bound to small molecules. Kinase inhibitor binding modes are classified into several  types, and to keep things simple the focus here was on Type I and Type I¹/₂. Both bind to the active, DFG-in form of the kinase, the only difference being that Type I¹/₂ binders extend into a back pocket. A total of 2801 crystal structures were selected for analysis.

 

Next, the ligands were computationally fragmented using a methodology called BRICS (Breaking of Retrosynthetically Interesting Chemical Substructures). Molecules such as ATP and other substrate analogs were discarded to keep the focus on drug-like compounds, and some particularly large, complex molecules such as staurosporine could not be fragmented. The researchers were particularly interested in molecules that bind to the so-called hinge region, where the adenine moiety of ATP binds, so the few ligands that did not bind here were also removed. This reduced the total number of structures to 2553, which yielded 7486 fragments.

 

The kinase active site was divided into six sub-sites: the adenine pocket, solvent-exposed pocket, front pocket, gate area, and two back pockets. Each of the fragments was then assigned to one sub-pocket. More than 80% of the original (unfragmented) ligands bound to two or three sub-pockets, while another 13% bound to four sub-pockets. Just 5% of the original ligands bound only to the adenine sub-site, but these 127 ligands – with an average of 15 non-hydrogen atoms – could be quite interesting as crystallographically validated fragments.

 

Various analyses of the fragments binding in each of the sub-pockets reveal trends. Those binding in the adenine sub-pocket tend towards more hydrogen bond donors and acceptors than those in other pockets, as expected. The shapeliness of fragments binding in the various sub-pockets is not quantitatively analyzed, though the interested reader could run these calculations. The 50 most common fragments for each sub-pocket are presented as figures in the supporting information.

 

Aside from extracting interesting cheminformatic trends, what else can you do with these fragments? The researchers took a subset of 624 rule-of-three compliant fragments and recombined them to generate 6,720,637 distinct molecules. The vast majority of these appear to be novel, and among the 218 that had previously been reported in ChEMBL, more than 20% were potent (IC₅₀ ≤ 500 nM) kinase inhibitors.

 

With the inexorable increase in docking speeds, this virtual collection of fragments will be useful for building even larger libraries and using them to find ligands for new kinases. And, as the researchers point out, the collection could be useful for fragment growing or merging to new experimentally identified fragments. This is a resource that should be broadly useful for the community.