Development of potential inhibitors of cell division protein kinase 2 by ligand based drug design

Vildan Enisoǧlu Atalay*, Büşra Savaş

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


Cyclin-dependent kinases (CDKs) are commonly known by their role in cell cycle regulation which affects cancer mechanism. In many cancer types, CDKs show extreme activity or CDK inhibiting proteins are dysfunctional. Specifically, CDK2 plays an indispensable role in cell division especially in the G1/S phase and DNA damage repair. Therefore, it is important to find new potential CDK2 inhibitors. In this study, ligand-based drug design is used to design new potential CDK2 inhibitors. Y8 L ligand is obtained from the X-ray crystal structure of human CDK2 (PDB ID: 2XNB) ( and used as a structure model. By adding hydrophilic and hydrophobic groups to the structure, a training set of 36 molecules is generated. Each molecule examined with Spartan'14 and optimized structures are used for docking to CDK2 structure by AutoDock and AutoDock Vina programs. Ligand-amino acid interactions are analysed with Discovery Studio Visualizer. Van der Waals, Pi-Pi T-shaped, alkyl, pi-alkyl, conventional hydrogen bond and carbon-hydrogen bond interactions are observed. By docking results and viewed interactions, some molecules are identified and discussed as potential CDK2 inhibitors. Additionally, 8 different QSAR descriptors obtained from Spartan'14, Preadmet and ALOGPS 2.1 programs are investigated with multiple linear regulation (MLR) analysis with SPSS program for their impact on affinity value.

Original languageEnglish
Pages (from-to)241-250
Number of pages10
JournalMain Group Chemistry
Issue number3
Publication statusPublished - 2021
Externally publishedYes

Bibliographical note

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  • CDK2
  • docking
  • ligand-based drug design
  • MLR
  • Y8 L ligand


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