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Inhibition of Cdk Activity02:34

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The orderly progression of the cell cycle depends on the activation of Cdk protein by binding to its cyclin partner. However, the cell cycle must be restricted when undergoing abnormal changes. Most cancers correlate to the deregulated cell cycle, and since Cdks are a central component of the cell cycle, Cdk inhibitors are extensively studied to develop anticancer agents. For instance, cyclin D associates with several Cdks, such as Cdk 4/6, to form an active complex. The cyclin D-Cdk4/6 complex...
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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Related Experiment Video

Updated: Aug 9, 2025

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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Palbociclib (PD 0332991) Interaction with Kinases. Theoretical and Comparative Molecular Docking Study.

Juan M Aceves-Hernández1, María Inés Nicolás Vázquez1, José Luis Garza Rivera1

  • 1Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli, Estado de México, 54740, México.

Chemistry & Biodiversity
|February 17, 2023
PubMed
Summary

Palbociclib

Keywords:
kinases CDK4/CPD6molecular dockingpalbociclibpoly target agentquantum chemistry

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Drug discovery

Background:

  • Palbociclib (PD 0332991) is a targeted therapy.
  • Understanding its interactions with kinases is crucial for expanding its therapeutic applications.

Purpose of the Study:

  • To computationally investigate the molecular interactions of Palbociclib with CDK4 and CDK6 kinases.
  • To explore the potential of Palbociclib in treating other cancer types.

Main Methods:

  • Density Functional Theory (DFT) for optimizing Palbociclib's geometry and electronic properties.
  • Molecular docking simulations to analyze Palbociclib-kinase complexes.
  • Analysis of HOMO-LUMO energy gaps to predict reactivity and hydrogen bonding.

Main Results:

  • Optimized geometry and electrostatic potential map of Palbociclib were determined.
  • Molecular docking revealed hydrogen bonding interactions with CDK4 and CDK6 kinases.
  • Palbociclib's promiscuity suggests potential efficacy against other cancers, including resistant types.

Conclusions:

  • Computational analysis supports Palbociclib's mechanism of action.
  • Findings indicate Palbociclib's potential utility beyond myeloid leukemia, particularly in CDK4/CDK6-related cancers.
  • This study provides insights for developing novel cancer therapies.