Benzimidazole Inhibitors Induce a DFG-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (Nek2) without Binding to the Back Pocket and Reveal a Nonlinear Structure−Activity Relationship

Solanki, Savade; Innocenti, Paolo; Mas-Droux, Corine; Boxall, Kathy; Barillari, Caterina; Montfort, R.L.M. van; Aherne, G. Wynne; Bayliss, Richard; Hoelder, Swen

doi:10.1021/jm1011726

Cited by 45 publications

(69 citation statements)

References 38 publications

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“…By contrast, inhibitors able to induce and stabilize the DFG-out conformation are considered superior, as they render the active site architecture incompatible with substrate binding, resulting in enhanced potency and target selectivity. The clinical success of imatinib (Gleevec) as an inhibitor of Abl kinase (12) is attributed in large part to this distinct mode of action (13) and has spurred the design of DFG-out inhibitors for other kinases, including MAP (14), JNK2(15), Nek2 (16), and Eph receptor tyrosine kinase (17). However, all known Aurora kinase inhibitors, such as the aforementioned chemical probe VX680, are DFG-in inhibitors.…”

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confidence: 99%

A Novel Mechanism by Which Small Molecule Inhibitors Induce the DFG Flip in Aurora A

et al. 2012

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Most protein kinases share a DFG (Asp-Phe-Gly) motif in the ATP site which can assume two distinct conformations, the active DFG-in and the inactive DFG-out states. Small molecule inhibitors able to induce the DFG-out state have received considerable attention in kinase drug discovery. Using a typical DFG-in inhibitor scaffold of Aurora A, a kinase involved in the regulation of cell division, we found that halogen and nitrile substituents directed at the N-terminally flanking residue Ala273 induced global conformational changes in the enzyme, leading to DFG-out inhibitors that are among the most potent Aurora A inhibitors reported to date. The data suggest an unprecedented mechanism of action, in which induced-dipole forces along the Ala273 side chain alter the charge distribution of the DFG backbone, allowing the DFG to unwind. As the ADFG sequence and three-dimensional structure is highly conserved, DFG-out inhibitors of other kinases may be designed by specifically targeting the flanking alanine residue with electric dipoles.

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confidence: 99%

A Novel Mechanism by Which Small Molecule Inhibitors Induce the DFG Flip in Aurora A

et al. 2012

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“…Structures of Nek2 in apo form, bound to ATP analogues and in the presence of two other series of chemical inhibitors show Tyr 70 (equivalent to Tyr 97 in Nek7) adopting the same position found in active kinase structures [28][29][30]. In contrast, the aminopyridine/aminopyrazine compounds induce Tyr 70 in Nek2 to jut down into the ATP-binding pocket in a manner similar to Tyr 97 in Nek7.…”

Section: Exploiting Kinase Conformation In Drug Discoverymentioning

confidence: 80%

The structural mechanisms that underpin mitotic kinase activation

Dodson

Haq

Yeoh

et al. 2013

Biochemical Society Transactions

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In eukaryotic cells, the peak of protein phosphorylation occurs during mitosis, switching the activities of a significant proportion of proteins and orchestrating a wholesale reorganization of cell shape and internal architecture. Most mitotic protein phosphorylation events are catalysed by a small subset of serine/threonine protein kinases. These include members of the Cdk (cyclin-dependent kinase), Plk (Polo-like kinase), Aurora, Nek (NimA-related kinase) and Bub families, as well as Haspin, Greatwall and Mps1/TTK. There has been steady progress in resolving the structural mechanisms that regulate the catalytic activities of these mitotic kinases. From structural and biochemical perspectives, kinase activation appears not as a binary process (from inactive to active), but as a series of states that exhibit varying degrees of activity. In its lowest activity state, a mitotic kinase may exhibit diverse autoinhibited or inactive conformations. Kinase activation proceeds via phosphorylation and/or association with a binding partner. These remodel the structure into an active conformation that is common to almost all protein kinases. However, all mitotic kinases of known structure have divergent features, many of which are key to understanding their specific regulatory mechanisms. Finally, mitotic kinases are an important class of drug target, and their structural characterization has facilitated the rational design of chemical inhibitors.

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“…Reminiscent of the CDK/SRC--like inactive conformation, the αC--helix is positioned outwards and the activation loop forms an α--helix (αT) that stabilizes the outward position of the αC--helix. Nek2 is found in a DFG--out conformation in the presence of two other series of inhibitors, the hybrid series of potent Nek2 inhibitors and the benzimidazoles upon which the hybrid compounds were based ( Figure 4B) [44,46]. With the exception of the activation loop and the residues that interact with the inhibitors, these two inhibitor--bound conformations of Nek2 are similar and the R--spine is disrupted due to displacement of three out of four side chains (Leu59, Phe160 and His139).…”

Section: Targeting Autoinhibitory Mechanisms In Nek2mentioning

confidence: 99%

The Ys and wherefores of protein kinase autoinhibition

Bayliss

Haq

Yeoh

2015

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

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Protein phosphorylation is a key reaction in the regulation of cellular events and is catalyzed by over 500 protein kinases in humans. The activities of protein kinases are strictly controlled through a diverse set of mechanisms. Structural studies have shown that the conformation adopted by kinases in their active state are highly similar, whereas inactive kinases can adopt a variety of conformations. Many kinases are maintained in a catalytically inactive state through autoinhibition. This involves a conformation of the kinase active site that is unable to support catalysis and requires activation through a signal such as binding of a regulatory protein. In this review, we briefly summarize some of the well--established autoinhibitory mechanisms and then focus on a relatively unexplored mode of autoinhibition that was first discovered in the Nek family of kinases and is also relevant to IRE1. This involves a tyrosine side--chain that blocks the active site and which must undergo a conformational change to enable kinase activity. We have termed this the Tyr--down autoinhibitory mechanism. We summarise the evidence for this mechanism and describe its role in kinase inhibitor design. Finally, we survey the kinome to identify other kinases with the potential to be governed by an autoinhibitory Tyr--down mechanism.

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Benzimidazole Inhibitors Induce a DFG-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (Nek2) without Binding to the Back Pocket and Reveal a Nonlinear Structure−Activity Relationship

Cited by 45 publications

References 38 publications

A Novel Mechanism by Which Small Molecule Inhibitors Induce the DFG Flip in Aurora A

A Novel Mechanism by Which Small Molecule Inhibitors Induce the DFG Flip in Aurora A

The structural mechanisms that underpin mitotic kinase activation

The Ys and wherefores of protein kinase autoinhibition

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