Pyrrolo[3,2-b]quinoxaline Derivatives as Types I_1/2 and II Eph Tyrosine Kinase Inhibitors: Structure-Based Design, Synthesis, and in Vivo Validation

Abstract

The X-ray crystal structures of the catalytic domain of the EphA3 tyrosine kinase in complex with two type I inhibitors previously discovered in silico (compounds A and B) were used to design type I1/2 and II inhibitors. Chemical synthesis of about 25 derivatives culminated in the discovery of compounds 11d (type I1/2), 7b, and 7g (both of type II), which have low-nanomolar affinity for Eph kinases in vitro and a good selectivity profile on a panel of 453 human kinases (395 nonmutant). Surface plasmon resonance measurements show a very slow unbinding rate (1/115 min) for inhibitor 7m. Slow dissociation is consistent with a type II binding mode in which the hydrophobic moiety (trifluoromethyl-benzene) of the inhibitor is deeply buried in a cavity originating from the displacement of the Phe side chain of the so-called DFG motif as observed in the crystal structure of compound 7m. The inhibitor 11d displayed good in vivo efficacy in a human breast cancer xenograft.

Three stories on Eph kinase inhibitors: From in silico discovery to in vivo validation

“…In the next sections, we review the optimization campaigns started from Xan-A1, [55][56] Pyr-A1 50 and Qui-A1 hits, 57 with emphasis on their in depth in vitro and in vivo characterization, together with previously unpublished angiogenesis and fluorescence based assays.…”

Quinoxaline‐Based Scaffolds Targeting Tyrosine Kinases and Their Potential Anticancer Activity

“…This structural information was used to design type I 1/2 and II derivatives by taking advantage of the existing knowledge on privileged chemical motif: For designing type I 1/2 hydroxyl group should be located in meta position of the phenyl ring. For designing type II hydrophobic moieties should be connected to the phenyl ring by amide or urea linkers. It is possible to “elongate” a type I 1/2 into a type II inhibitor by introducing an amide or urea linked to a bulky hydrophobic group. These type II linkers are involved in the same hydrogen bonds as the type I 1/2 bearing a hydroxyl group in the same position, whereas the hydrophobic moiety occupies the pocket resulting from the displacement of the Phe side chain of the DFG motif. The similar selectivity profiles of types I 1/2 and II inhibitors show that the moiety in contact with the gatekeeper's side chain and hinge region is crucial for determining specificity (Fig. ). …”

“…Unzue et al in 2014 synthesized about 25 pyrrolo[3,2‐ b ]quinoxaline derivatives, three of which (compounds 47 – 49 ) having low IC 50 values for Eph kinases in vitro and a good selectivity profile on a panel of 453 human kinases.

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“…The amino substituent at position 2 of the pyrrole ring is involved in a hydrogen bond with the side chain hydroxyl of the Thr693 gatekeeper and the backbone carbonyl of Glu694. Furthermore, the amide substituent at position 3 of the pyrrole ring is optimally oriented for two hydrogen bonds with the backbone polar groups of Met696 providing a total of three hydrogen bonds with the backbone of the hinge region .…”

Supramolecular structure, in vivo biological activities and molecular-docking-based potential cardiotoxic exploration of aconine hydrochloride monohydrate as a novel salt form

“…The X-ray crystal structure of CAMK2G was downloaded from the RCSB Protein Data Bank (PDB) (PDB entry 2v7o, Rellos et al, 2010). The 3D structure of the CAMK2Gcationic aconine complex was derived by automatic docking Unzue et al, 2014). The 3D coordinate of the ATP-binding pocket was defined as À26.773, À7.994, À34.54, À21.179, À19.406 and À2.289 for x min , x max , y min , y max , z min and z max , respectively.…”