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: back to front kinase design; discoidin domain receptor; fragment-based drug design.

Figure 1

Crystal structures of compounds bound to DDR1 (PDB Codes: 5bvk, 5bvw, 5bvn and 5bvo). (a) Fragment 1 in DDR1 with pockets annotated. (b) Superimposition of the DDR1–dasatinib cocomplex and the DDR1–fragment 1 cocomplex. (c) Compound 4 superimposed on the crystallographic positioning of fragment 1. The four hydrogen bonding residues are marked. (d) Compound 9 in DDR1.

Figure 2

Schematic of the design process. Molecules are colored according to the binding mode in DDR1: blue = back pocket region, red = linker region, green = selectivity pocket, magenta = hinge binding group.

Figure 3

(a) Knockdown of DDR2 phosphorylation (pY) in HEK293 cells stably transfected with wild type (upper blots) or mutant DDR2 (I638F) (lower blots). Knockdown is reported with specified compounds for collagen I stimulated cells (right) or unstimulated cells (left). (b) Effect of compounds on proliferation of two mutant DDR2 cell lines. More experimental details are provided in the Supporting Information.