Discovery of Type II Inhibitors of TGFβ-Activated Kinase 1 (TAK1) and Mitogen-Activated Protein Kinase Kinase Kinase Kinase 2 (MAP4K2)

Abstract

We developed a pharmacophore model for type II inhibitors that was used to guide the construction of a library of kinase inhibitors. Kinome-wide selectivity profiling of the library resulted in the identification of a series of 4-substituted 1H-pyrrolo[2,3-b]pyridines that exhibited potent inhibitory activity against two mitogen-activated protein kinases (MAPKs), TAK1 (MAP3K7) and MAP4K2, as well as pharmacologically well interrogated kinases such as p38α (MAPK14) and ABL. Further investigation of the structure–activity relationship (SAR) resulted in the identification of potent dual TAK1 and MAP4K2 inhibitors such as 1 (NG25) and 2 as well as MAP4K2 selective inhibitors such as 16 and 17. Some of these inhibitors possess good pharmacokinetic properties that will enable their use in pharmacological studies in vivo. A 2.4 Å cocrystal structure of TAK1 in complex with 1 confirms that the activation loop of TAK1 assumes the DFG-out conformation characteristic of type II inhibitors.

Pathophysiological significance and therapeutic targeting of germinal center kinase in diffuse large B-cell lymphoma

“…We further demonstrate that GCK may be targetable by a previously described small molecule inhibitor HG6-64-1, 10 which induces marked DLBCL cell cytotoxicity in vitro, in vivo, and in primary DLBCL tumors. Of note, marked activity was also observed in double-hit DLBCL cell lines (OCILY-19, SUDHL-6, and VAL), a subtype of DLBCL with very poor response to current therapies, representing a subgroup with unmet medical need for novel therapeutic approaches.…”

“…10 In DLBCL cell lines, the 50% effective concentration (EC 50 ) of HG6-64-1 ranged from 1.83 to 257 nM, with the exception of the low GCK-expressing cell line G452, which had an EC 50 of 1.19 mM (Figure 4A-B). The molecular mechanism that leads to a relatively wide range of sensitivities to HG6-64-1 within DLBCL cell lines is not known, but may relate to variable dependence on this particular pathway.…”

“…HG6-64-1 was synthesized in our laboratory as reported. 10 Unless otherwise stated, all experiments in DLBCL cells were performed at a concentration of 400 nM. Doxorubicin was from Sigma-Aldrich.…”

Development of a Method for Converting a TAK1 Type I Inhibitor into a Type II or c-Helix-Out Inhibitor by Structure-Based Drug Design (SBDD)

“…Additionally, we had obtained a type II TAK1 binder, biaryl urea compound 2 (TAK1 K d =12 nM) with multi-kinase inhibitory activity (Journal of Biomolecular Screening, submmited); therefore, we tried to gain the co-crystal of 2 with TAK1 in the DFG-out conformation and reveal binding mode of 2 in TAK1. (Recently researchers from two different groups have revealed X-ray structures in which a ligand binds to TAK1 in the DFG-out conformation, 25,26) but this information was not available at the beginning of this study.) Fortunately, we obtained this co-crystal and were able to utilize this X-ray structure information ( Fig.…”

7-Azaindole: A Versatile Scaffold for Developing Kinase Inhibitors

“…In contrast, there is open space facing the solvent-exposed space when compounds bind with the "flipped" binding mode, and this would bring a significant preference for binding orientation of 2-substituted azaindoles. Compounds 12-16 also bind to kinases with the "flipped" orientation [24][25][26][27][28] ; these compounds are type II kinase inhibitors, which can interact with a deep allosteric pocket created by conformational change in the activation loop that adopts the inactive-DFG-out conformation. Almost all 7-azaindoles with "normal" binding modes are type I kinase inhibitors except one ligand (PDB code, 3ETA), suggesting that there might be some relation between binding orientation of azaindole and type of kinase inhibitors.…”