Structure-based discovery of the first allosteric inhibitors of cyclin-dependent kinase 2

Rastelli, Giulio; Anighoro, Andrew; Chripková, Martina; Carrassa, Laura; Broggini, Massimo

doi:10.4161/cc.29295

Cited by 47 publications

(56 citation statements)

References 35 publications

(56 reference statements)

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“…In the second step, a solution of 2‐nitrobenzenesulfenyl chloride in MeCN was added at room temperature to a solution of compound 3 in MeCN to provide the final compound in very good yield (80 %) after 1 h as a yellow amorphous solid. The NMR analysis corresponded to commercially available compound BAS00631909, which was previously purchased and tested against CDK2 . However, X‐ray diffraction experiments of a single crystal of the obtained compound showed that the unquestionable structure of 4 differs from that provided by the vendor and that of similar molecules reported in the literature with regard to the position of the chloride and the sulfur atoms, which are reversed (Figure ).…”

Section: Resultsmentioning

confidence: 97%

“…The ANS pocket was immediately proposed as a potential site to accommodate type III allosteric inhibitors, and a series of compounds able to displace ANS from this pocket was identified through a virtual screening of the ASINEX database of commercially available compounds . Interestingly, competition experiments performed in the presence of an ATP‐competitive inhibitor confirmed that the ligands are able to selectively inhibit the CDK2‐mediated phosphorylation of the retinoblastoma protein through an allosteric mechanism.…”

Section: Introductionmentioning

confidence: 99%

“…Except for the crystallographic probe ANS, these compounds are the first type III allosteric ligands of CDK2 reported in the literature. In particular, one of these hits was characterized by a hexahydrocyclopenta[ c ]quinoline scaffold (Figure b) …”

Section: Introductionmentioning

confidence: 99%

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Probing an Allosteric Pocket of CDK2 with Small Molecules

et al. 2016

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The availability of well-characterized allosteric modulators is crucial for investigating the allosteric regulation of protein function. In a recently identified inactive conformation of cyclin-dependent kinase 2 (CDK2), an open allosteric pocket was detected and proposed as a site to accommodate allosteric inhibitors. Previous structure-based approaches allowed the identification of a hit compound expected to bind to this pocket. Herein we report the characterization of this compound by X-ray crystallography, which surprisingly provided a chemical structure different from that previously reported. Therefore, the compound was synthesized and completely characterized. X-ray structures of the synthesized and purchased compounds were found to be superimposable. A reaction mechanism was proposed to explain the formation of the structure indicated by crystallography. Moreover, a stereoselective synthesis was developed to evaluate the biological activity of the pure stereoisomers. Modeling studies were performed to unveil the details of the interaction with CDK2. The activity of the obtained compounds was evaluated with various biological assays. Mutagenesis experiments confirmed binding to the allosteric pocket. Finally, the allosteric ligands were shown to inhibit the growth of lung (A549) and ovarian (SKOV3) cancer cell lines. Therefore, this report presents a thorough chemical and biological characterization of the first small-molecule ligands to be used as probes to study the allosteric modulation of CDK2 activity.

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Section: Resultsmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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Probing an Allosteric Pocket of CDK2 with Small Molecules

et al. 2016

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“…Using the same methodology, Rastelli described in 2014 the first examples of truly Type III allosteric ligands of CDK2. 41 Through virtual screening of commercially available compounds in the allosteric pocket of the CDK2-ANS binary complex, and using a combination of docking (AutoDock) and post docking, the authors identified new core inhibitors. Competition experiments performed in the presence of staurosporine confirmed the allosteric mode of action.…”

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confidence: 99%

Cyclin dependent kinase (CDK) inhibitors as anticancer drugs

Sánchez-Martínez

Gelbert

Lallena

et al. 2015

Bioorganic & Medicinal Chemistry Letters

203

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“…Although 1 ‐Cdk2(WT) showed only minor structural deviations from Cdk2(WT) in the region surrounding the ligand, significant distortion was observed around the αC‐helix (Supporting Information, Figure S11). The αC‐helix is essential for proper formation of the active Cdk2‐cyclin complex and its displacement is implicit in allosteric modulation of various kinases 26, 27…”

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confidence: 99%

High‐Throughput Kinetic Analysis for Target‐Directed Covalent Ligand Discovery

et al. 2018

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Cysteine‐reactive small molecules are used as chemical probes of biological systems and as medicines. Identifying high‐quality covalent ligands requires comprehensive kinetic analysis to distinguish selective binders from pan‐reactive compounds. Quantitative irreversible tethering (qIT), a general method for screening cysteine‐reactive small molecules based upon the maximization of kinetic selectivity, is described. This method was applied prospectively to discover covalent fragments that target the clinically important cell cycle regulator Cdk2. Crystal structures of the inhibitor complexes validate the approach and guide further optimization. The power of this technique is highlighted by the identification of a Cdk2‐selective allosteric (type IV) kinase inhibitor whose novel mode‐of‐action could be exploited therapeutically.

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Structure-based discovery of the first allosteric inhibitors of cyclin-dependent kinase 2

Cited by 47 publications

References 35 publications

Probing an Allosteric Pocket of CDK2 with Small Molecules

Probing an Allosteric Pocket of CDK2 with Small Molecules

Cyclin dependent kinase (CDK) inhibitors as anticancer drugs

High‐Throughput Kinetic Analysis for Target‐Directed Covalent Ligand Discovery

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