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

Area of Science:

• Biochemistry and Molecular Biology
• Medicinal Chemistry
• Cancer Research

Background:

• NIMA-related kinase 2 (Nek2) is a cell cycle-dependent kinase overexpressed in human cancers.
• Nek2 overexpression correlates with tumor growth; its suppression can induce apoptosis.
• Targeting Nek2 with small molecule inhibitors presents a potential cancer therapeutic strategy.

Purpose of the Study:

• To understand the structural requirements for selective Nek2 inhibition.
• To synthesize and evaluate novel purine derivatives as potential Nek2 inhibitors.
• To identify compounds with selectivity for Nek2 over CDK2.

Main Methods:

• Synthesis of a library of 6-cyclohexylmethoxy-2-arylaminopurines.
• Incorporation of carboxamide, sulfonamide, and urea substituents on the 2-arylamino ring.
• Synthesis of compounds with an (E)-dialkylaminovinyl substituent at the C-6 position.
• Enzyme inhibition assays to determine IC50 values for Nek2 and CDK2.
• Structural biology studies to rationalize structure-activity relationships.

Main Results:

• A compound, 3-((6-(cyclohexylmethoxy)-9H-purin-2-yl)amino)-N,N-dimethylbenzamide, showed >10-fold selectivity for Nek2 (IC50=0.62 µM) over CDK2 (IC50=7.0 µM).
• Compounds with an (E)-dialkylaminovinyl substituent at C-6 exhibited selectivity for Nek2, with one compound showing IC50=0.27 µM for Nek2 and 2.70 µM for CDK2.
• The synthesized carboxamide 11 was identified as the first reported inhibitor of Nek2 in the DFG-in conformation.

Conclusions:

• Judicious modification of purine scaffolds can yield selective Nek2 inhibitors.
• The identified compounds, particularly those with (E)-dialkylaminovinyl groups, represent promising leads for Nek2-targeted cancer therapy.
• The discovery of a Nek2 inhibitor in the DFG-in conformation provides new insights into kinase inhibition mechanisms.