Analysing the Effect of Mutation on Protein Function and Discovering Potential Inhibitors of CDK4: Molecular Modelling and Dynamics Studies.

Nagasundaram N,Chiranjib Chakraborty,Luonan Chen,Karthick V,Jiming Liu,George Priya Doss C,Hailong Zhu,Freddie Salsbury

doi:10.1371/journal.pone.0133969

Abstract

The cyclin-dependent kinase 4 (CDK4)-cyclin D1 complex plays a crucial role in the transition from the G1 phase to S phase of the cell cycle. Among the CDKs, CDK4 is one of the genes most frequently affected by somatic genetic variations that are associated with various forms of cancer. Thus, because the abnormal function of the CDK4-cyclin D1 protein complex might play a vital role in causing cancer, CDK4 can be considered a genetically validated therapeutic target. In this study, we used a systematic, integrated computational approach to identify deleterious nsSNPs and predict their effects on protein-protein (CDK4-cyclin D1) and protein-ligand (CDK4-flavopiridol) interactions. This analysis resulted in the identification of possible inhibitors of mutant CDK4 proteins that bind the conformations induced by deleterious nsSNPs. Using computational prediction methods, we identified five nsSNPs as highly deleterious: R24C, Y180H, A205T, R210P, and R246C. From molecular docking and molecular dynamic studies, we observed that these deleterious nsSNPs affected CDK4-cyclin D1 and CDK4-flavopiridol interactions. Furthermore, in a virtual screening approach, the drug 5_7_DIHYDROXY_ 2_ (3_4_5_TRI HYDROXYPHENYL) _4H_CHROMEN_ 4_ONE displayed good binding affinity for proteins with the mutations R24C or R246C, the drug diosmin displayed good binding affinity for the protein with the mutation Y180H, and the drug rutin displayed good binding affinity for proteins with the mutations A205T and R210P. Overall, this computational investigation of the CDK4 gene highlights the link between genetic variation and biological phenomena in human cancer and aids in the discovery of molecularly targeted therapies for personalized treatment.

Highlights

Cyclin-dependent kinases (CDKs) drive cell cycle progression, control transcriptional regulation processes and maintain cell proliferation
Out of 20 nsSNPs submitted to SIFT, 11 nsSNPs were predicted to be deleterious, with SIFT scores
Comparing the predictions made by all three methods, five amino acid variants (R24C, Y180H, A205T, R210P and R246C) of the CDK4protein were identified as highly deleterious, and all five variants were investigated structurally and functionally.For the structural analysis, we modelled the mutant structure with Spdbv software, after which energy minimization was performed for the native and mutant cyclin-dependent kinase 4 (CDK4)-cyclin D1 complexes using a steepest descent force field to check and repair the geometry of the modelled complex

Summary

Introduction

Cyclin-dependent kinases (CDKs) drive cell cycle progression, control transcriptional regulation processes and maintain cell proliferation. The CDK4-cyclin D1-p16 retinoblastoma protein (RB1) pathway (CDK4 pathway) promotes the G1-S cell cycle transition and is commonly dysregulated in most cancers. The CDK4-cyclin D1 complex acts as an essential regulator in the G1-S phase transition of the cell cycle process. Abnormality of the CDK4/cyclin D1 pathway plays a major role in oncogenesis; CDK4 can be genetically tested as a valid molecular therapeutic target. Flavopiridol was the first drug identified as a potent tumour suppressor in several lung and breast cancer cell lines [3]. Various studies have highlighted that flavopiridol has the capability to prevent the proliferation of a broad range of cell lines, leukaemias, lymphomas and human tumours [4, 5]. CDK4 inhibitors are considered the most attractive therapeutic targets because of their ability to control tumour growth with minimal toxicity

Methods

Results

Discussion

Conclusion