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Updated: Jan 17, 2026

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

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Naringenin and its structural analogues inhibit CDK2: a combined MD-MMGBSA and protein-ligand interaction study for

Francis Dhiya1, K S Sindhu2, J Kavitha1

  • 1Sacred Heart College Thevara, Kochi, Kerala 682013 India.

In Silico Pharmacology
|September 22, 2025
PubMed

Insights

Naringenin shows potential as a colon cancer therapy by inhibiting Cyclin-dependent kinase 2 (CDK2). Computational studies confirm its strong binding affinity and stable interaction with CDK2, suggesting it as a promising lead compound for drug development.

Area of Science:

  • Computational chemistry
  • Pharmacology
  • Oncology

Background:

  • Cyclin-dependent kinase 2 (CDK2) is crucial for cell cycle regulation and a target for colon cancer therapies.
  • Naringenin and its derivatives are explored for their potential anticancer properties.

Purpose of the Study:

  • To evaluate the inhibitory potential of Naringenin and related compounds against CDK2 using in silico methods.
  • To identify key molecular interactions and binding characteristics for drug development.

Main Methods:

  • Multi-level in silico approach: molecular docking, Density Functional Theory (DFT), molecular dynamics (MD) simulation, and MMGBSA binding free energy calculations.
  • Analysis of protein-ligand interactions and molecular stability.

Main Results:

  • Naringenin exhibited the highest binding affinity to CDK2 (ΔG_bind = -43.55 kcal/mol), forming stable interactions with key residues.
  • DFT analysis identified the carbonyl group as critical for protein-ligand recognition.
  • MD simulations confirmed Naringenin's structural stability and favorable binding energetics.

Conclusions:

  • Naringenin is a potential lead compound for developing CDK2-targeting colon cancer therapies.
  • Further in vitro and in vivo studies are necessary to validate its anticancer potential and pharmacokinetics.
  • This research provides a computational basis for advancing Naringenin-based scaffolds in preclinical cancer research.
Keywords:
CDK2Colon cancerMMGBSAMolecular dynamicsNaringeninProtein–ligand interaction

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