Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors

Abstract

The DDR1 and DDR2 receptor tyrosine kinases are activated by extracellular collagen and have been implicated in a number of human diseases including cancer. We performed a fragment-based screen against DDR1 and identified fragments that bound either at the hinge or in the back pocket associated with the DFG-out conformation of the kinase. Modeling based on crystal structures of potent kinase inhibitors facilitated the "back-to-front" design of potent DDR1/2 inhibitors that incorporated one of the DFG-out fragments. Further optimization led to low nanomolar, orally bioavailable inhibitors that were selective for DDR1 and DDR2. The inhibitors were shown to potently inhibit DDR2 activity in cells but in contrast to unselective inhibitors such as dasatinib, they did not inhibit proliferation of mutant DDR2 lung SCC cell lines. KEYWORDS: discoidin domain receptor, fragment-based drug design, back to front kinase design D iscoidin domain receptors, DDR1 and DDR2, are transmembrane receptor tyrosine kinases that are activated by collagen binding to their extracellular domain. 1,2 DDR1 and DDR2 have been associated with extracellular remodeling, cell adhesion, proliferation and migration, and they have been linked to a number of human diseases, including fibrotic disorders, atherosclerosis and cancer. 3−5 There has recently been evidence suggesting that DDR2 inhibitors would be useful for the treatment of lung squamous cell cancer 6,7 although the role of DDR2 may be more complex than first realized. 8−10 Hammerman et al. 6,7 have shown that DDR2 is mutated in approximately 4% of lung squamous cell cancer and have presented data to suggest that these are gain of function mutations. Hammerman et al. 6 have also shown that cell lines harboring these mutations are selectively sensitized through knockdown of DDR2 by RNA interference or by treatment of the multitargeted kinase inhibitor dasatinib. 11 Selective DDR2 inhibitors would therefore be useful to probe the role of DDR2 and may have utility for the treatment of lung cancer. To date, most DDR1/2 inhibitors have been derived from cross-screening of existing kinase inhibitors. 12 Initial compounds often lacked selectivity over homologous enzymes such as Bcr-Abl, but a number of recent papers have described more selective inhibitors which all bind to the DFG-out form of the enzyme. 13−15 Gray and co-workers have identified DDR1/2 inhibitors by screening a library of compounds that had previously been designed by mixing and matching motifs from known Type II kinase inhibitors. 14 The resulting compounds were reported to be selective with IC 50 values versus DDR1 and DDR2 of approximately 100 nM, and experimental binding modes in DDR1 were determined. 14,16 Gao et al. have published a series of potent Type II DDR1 inhibitors that are selective over other kinases, including DDR2. 13 In this Letter we describe a fragment based approach to the discovery of potent and selective DDR1/2 inhibitors. We first obtained a soakable crystal form of DDR1 suitable for high-throughput cry...

Extracellular matrix component signaling in cancer

“…However, the study did not address the contribution of wild-type DDR2 to oncogenesis, and while several more recent studies have confirmed the occurrence of DDR2 mutations in different patient populations [122][123][124], it is far from clear whether the mutations are indeed oncogenic and their roles in lung SCC cell signalling are undefined [125]. Notably, in other studies, some of the 'oncogenic' DDR2 mutants either seemed to play tumour suppressive functions [101], or did not contribute to cell proliferation in lung SCC cell lines [126].…”

“…Inhibitors originally developed to target the activity of BCR-ABL kinase are also potent inhibitors of the DDRs [143,144], but these drugs have a very broad specificity and are active against a number of additional kinases. Orally bioavailable small molecule kinase inhibitors with selectivity over other kinases have been developed for DDR1 and DDR2 [126,[145][146][147]. However, since kinase-independent functions have been discovered for DDR1, in particular its essential role in collective cancer cell migration and invasion [110], DDR-selective kinase inhibitors may not be effective against all DDR-dependent roles in disease progression.…”

Radioiodination and biological distribution of a new s‐triazine derivative for tumor uptake evaluation

“…Based on the previous predicted target, a docking study was performed to confirm the affinity of compound 1 and 2 to the predicted target computationally. The docking study was done using the X‐ray crystal structure of FAK catalytic domain (Protein Data Bank [PDB]: 4K9Y) . The potent FAK inhibitor, TAE226, was also docked using the same procedure to establish a control binding to the enzyme active site.…”

“…The ligands were built by using the builder tool of the MOE program and were subjected to energy minimization (MMFF94x, gradient: 0.05) . The crystal structure of FAK catalytic domain (PDB:4K9Y) was imported from PDB . The downloaded protein was prepared by adding the missing hydrogens and bonds.…”

Synthesis and biological evaluation of novel dasatinib analogues as potent DDR1 and DDR2 kinase inhibitors

“…It shows that the benzene group of dasatinib positions itself deep in the ATP‐binding cleft. Murray et al . reported the X‐ray crystal structures of DDRs with dasatinib (PDB ID: 5BVW).…”