Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors

Abstract

Analyses of compounds in clinical development have shown that ligand efficient-molecules with privileged physical properties and low dose are less likely to fail in the various stages of clinical testing, have fewer postapproval withdrawals, and are less likely to receive black box safety warnings. However, detailed side-by-side examination of molecular interactions and properties within single drug classes are lacking. As a class, VEGF receptor tyrosine kinase inhibitors (VEGFR TKIs) have changed the landscape of how cancer is treated, particularly in clear cell renal cell carcinoma, which is molecularly linked to the VEGF signaling axis. Despite the clear role of the molecular target, member molecules of this validated drug class exhibit distinct clinical efficacy and safety profiles in comparable renal cell carcinoma clinical studies. The first head-to-head randomized phase III comparative study between active VEGFR TKIs has confirmed significant differences in clinical performance [Rini BI, et al. (2011) Lancet 378:193-1939]. To elucidate how fundamental drug potency-efficiency is achieved and impacts differentiation within the VEGFR TKI class, we determined potencies, time dependence, selectivities, and X-ray structures of the drug-kinase complexes using a VEGFR2 TK construct inclusive of the important juxtamembrane domain. Collectively, the studies elucidate unique drug-kinase interactions that are dependent on distinct juxtamembrane domain conformations, resulting in significant potency and ligand efficiency differences. The identified structural trends are consistent with in vitro measurements, which translate well to clinical performance, underscoring a principle that may be broadly applicable to prospective drug design for optimal in vivo performance.

Fig. 1.

Crystal structures reveal a JM_in and JM_out in VEGFR2. (A) JM_in position in the unactivated VEGFR2 axitinib complex and apoenzyme cKit. Coloring: VEGFR KD (purple), VEGFR JM (red), and cKit (green). The red dashed lines indicate a segment of the VEGFR JM domain that could not be unambiguously modeled from the electron density. (B) JM_out position (cyan) in the VEGFR2 sorafenib complex. For comparison, the position of the JM in the VEGFR2 axitinib complex is also shown (red).

Fig. 2.

A superposition of the autoinhibitory JM_in (blue) in its axitinib complex position onto the (A) tivozanib and (B) sorafenib complexes illustrates how the larger inhibitor substituents clash with this position of I804. A van der Waals representation shows a favorable hydrophobic interaction between (C) axitinib and I804 of the JM.

Fig. 3.

Model of autoinhibitory to active conformation transitions for JM and DFG. The perspective in this graphic is from below with respect to Figs. 1 and 2 and rotated ∼160° from the top. Surface coloring: DFG (yellow), JM (red), ATP (cyan), and axitinib and tivozanib (gray). The ATP binding position was modeled from PDB ID code 1IR3. The DFG and JM positions are fixed in the vertical comparisons, where A and D are taken from the axitinib complex and B and E are taken from the tivozanib complex. (C) The activated VEGFR2 kinase domain including DFG was reported previously (PDB ID code 1VR2), and the JM is modeled from the tivozanib complex. The conformations from left to right correspond to TKI binding (D) type IV and (E) type II, type II, and type IV.

Fig. 4.

Graph of data generated from both constructs plotted on the y axis vs. cellular data. Coloring by binding mode: type II (red), type IVa (blue), and type IVb (green). Shape and shade by construct: plus-JM is darker and designated with +; minus-JM is lighter and designated with −. The minus-JM K_i values differ to the plus-JM for type IV TKIs and not for the two type II TKIs with the largest RDP groups. The type II exception is tivozanib. The minus-JM results fall above the 1:1 line vs. pVEGFR2 cell IC₅₀, a rare circumstance for kinase inhibitors that bind the ATP site.

Fig. 5.

(A) Kinome selectivity tree of Food and Drug Administration-approved VEGFR TK drugs in RCC. Circle sizes are inversely proportional to fold selectivity ratios calculated as (K_i for kinase)/(plus-JM K_i). (B) x axis broken after 0.1 and 0.8 and contracted. Coloring indicates channel occupancy: yes (blue) and no (red). The KPI measure of selectivity correlates with LipE for channel binders.

Fig. 6.

The five TKI/plus-JM complexes are vertically aligned to depict the similarities of ATP site occupancy and differences in the interactions with the channel and RDP. The translucent skins are protein surfaces generated for each complex and colored by atom type. (A–E) The TKIs are ordered from top to bottom by the greatest fill of the channel and RDP for (A) sorafenib to the least for (E) sunitinib. Black dashed lines represent hydrogen bonds.

Fig. 7.

A shows the PFS results from cytokine refractory RCC trials (PFS1) plotted against plus-JM LipE. B shows PFS results from mostly first-line RCC studies (PFS2) plotted against plus-JM LipE.