Aminopyrazine Inhibitors Binding to an Unusual Inactive Conformation of the Mitotic Kinase Nek2: SAR and Structural Characterization

Whelligan, Daniel K.; Solanki, Savade; Taylor, Dawn; Thomson, Douglas W.; Cheung, Kwai-Ming J.; Boxall, Kathy; Mas-Droux, Corine; Barillari, Caterina; Burns, Samantha; Grummitt, Charles G.; Collins, Ian; Montfort, R.L.M. van; Aherne, G. Wynne; Bayliss, Richard; Hoelder, Swen

doi:10.1021/jm1008727

Cited by 65 publications

(79 citation statements)

References 43 publications

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“…C) Crystal structure of Nek2 bound to ADP (PDB ID: 2W5A) [47]. D) Crystal structure of Nek2 in a Tyr--down conformation bound to an aminopyrazine inhibitor (PDB ID: 2XKF) [48]. The side chain -OH group of Tyr70 forms a H--bond with the main chain at the DFG--motif (black dashed line).…”

Section: Discussionmentioning

confidence: 99%

“…Tyr70 is also clearly in the up position in the ADP--bound structure ( Figure 4C). The conformation of Tyr70 is altered when Nek2 is bound to inhibitors based on aminopyrazine or aminopyridine scaffolds ( Figure 4D) [33,48]. In 7 of these structures, Tyr70 is observed in a down conformation (PDB IDs: 2WQO, 2XK3, 2XK6, 2XK8, 2XKD, 2XKE, 2XKF), and in 3 structures there is evidence of both Tyr--up and Tyr--down conformations (PDB IDs: 2XK4, 2XK7, 2XKC).…”

Section: Targeting Autoinhibitory Mechanisms In Nek2mentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

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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“…The Tyr-down inactive conformation observed in unphosphorylated Nek7 is exploited in inhibitors of the related kinase Nek2 based on aminopyridine and aminopyrazine scaffolds [24,27]. 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].…”

Section: Exploiting Kinase Conformation In Drug Discoverymentioning

confidence: 98%

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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“…Examples include the aminopyrazine ATP-competitive inhibitor 1 (Nek2IC 50 = 0.23 μM) [15] and a benzimidazole-based series with > 200-fold selectivity for Nek2 over Plk1 ( e.g . 2 :Nek2 IC 50 = 0.36 μM) [16].…”

Section: Introductionmentioning

confidence: 99%

Structure-guided design of purine-based probes for selective Nek2 inhibition

et al. 2016

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Nek2 (NIMA-related kinase 2) is a cell cycle-dependent serine/threonine protein kinase that regulates centrosome separation at the onset of mitosis. Overexpression of Nek2 is common in human cancers and suppression can restrict tumor cell growth and promote apoptosis. Nek2 inhibition with small molecules, therefore, offers the prospect of a new therapy for cancer. To achieve this goal, a better understanding of the requirements for selective-inhibition of Nek2 is required. 6-Alkoxypurines were identified as ATP-competitive inhibitors of Nek2 and CDK2. Comparison with CDK2-inhibitor structures indicated that judicious modification of the 6-alkoxy and 2-arylamino substituents could achieve discrimination between Nek2 and CDK2. In this study, a library of 6-cyclohexylmethoxy-2-arylaminopurines bearing carboxamide, sulfonamide and urea substituents on the 2-arylamino ring was synthesized. Few of these compounds were selective for Nek2 over CDK2, with the best result being obtained for 3-((6-(cyclohexylmethoxy)-9H-purin-2-yl)amino)-N,N-dimethylbenzamide (CDK2 IC50 = 7.0 μM; Nek2 IC50 = 0.62 μM) with >10-fold selectivity. Deletion of the 6-substituent abrogated activity against both Nek2 and CDK2. Nine compounds containing an (E)-dialkylaminovinyl substituent at C-6, all showed selectivity for Nek2, e.g. (E)-6-(2-(azepan-1-yl)vinyl)-N-phenyl-9H-purin-2-amine (CDK2 IC50 = 2.70 μM; Nek2 IC50 = 0.27 μM). Structural biology of selected compounds enabled a partial rationalization of the observed structure activity relationships and mechanism of Nek2 activation. This showed that carboxamide 11 is the first reported inhibitor of Nek2 in the DFG-in conformation.

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Aminopyrazine Inhibitors Binding to an Unusual Inactive Conformation of the Mitotic Kinase Nek2: SAR and Structural Characterization

Cited by 65 publications

References 43 publications

The Ys and wherefores of protein kinase autoinhibition

The Ys and wherefores of protein kinase autoinhibition

The structural mechanisms that underpin mitotic kinase activation

Structure-guided design of purine-based probes for selective Nek2 inhibition

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