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The abstract Cancer cells evade cell death and proliferate uncontrollably, primarily due to dysregulated apoptosis. The B-cell lymphoma (Bcl-2) family proteins, essential regulators of apoptosis, are often overexpressed in cancer, disrupting the balance between cell survival and death. This study presents an in-silico analysis of the bioactive interactions between the Bcl-2 protein and thirteen potential anticancer compounds derived from Lentinula edodes. Binding affinities and interaction modes were predicted to identify compounds with the highest therapeutic potential. Notably, Nandrolone, Cyclohexane Carboxylic Acid, and Cordilin demonstrated superior binding affinity with Bcl-2. Using Google Colab’s computational resources, protein structural analyses and molecular dynamics (MD) simulations were conducted, including energy minimization to evaluate Bcl-2-compound complexes’ stability and dynamics. MD simulations assessed Root Mean Square Deviation (RMSD) and Radius of Gyration (Rg) within 0–5 nm and 2–3 nm, respectively, to understand complex stability. Further analyses, including Root Mean Square Fluctuations (RMSF), Solvent-Accessible Surface Area (SASA), Principal Component Analysis (PCA), hydrogen bond assessment, Dynamic Cross-Correlation Matrix (DCCM), and Free Energy Landscape (FEL) analysis, provided detailed insights into the structural and dynamic properties of the Bcl-2-compound interactions. This comprehensive computational framework supports drug discovery efforts, offering promising candidates for effective cancer treatment.

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Molecular Dynamic Simulation of BCL-2 Upon Binding with Anticancer Compounds

  • 会议论文

  • 发表日期：

    2026年

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  • Puniethaa Prabhu,
  • S. Balamurugan,
  • G. Javeed Akthar,
  • M. Ashna,
  • K. Sanjay Kumar,
  • T. Monesh,
  • J. M. Kaaviyaa

摘要

The abstract Cancer cells evade cell death and proliferate uncontrollably, primarily due to dysregulated apoptosis. The B-cell lymphoma (Bcl-2) family proteins, essential regulators of apoptosis, are often overexpressed in cancer, disrupting the balance between cell survival and death. This study presents an in-silico analysis of the bioactive interactions between the Bcl-2 protein and thirteen potential anticancer compounds derived from Lentinula edodes. Binding affinities and interaction modes were predicted to identify compounds with the highest therapeutic potential. Notably, Nandrolone, Cyclohexane Carboxylic Acid, and Cordilin demonstrated superior binding affinity with Bcl-2. Using Google Colab’s computational resources, protein structural analyses and molecular dynamics (MD) simulations were conducted, including energy minimization to evaluate Bcl-2-compound complexes’ stability and dynamics. MD simulations assessed Root Mean Square Deviation (RMSD) and Radius of Gyration (Rg) within 0–5 nm and 2–3 nm, respectively, to understand complex stability. Further analyses, including Root Mean Square Fluctuations (RMSF), Solvent-Accessible Surface Area (SASA), Principal Component Analysis (PCA), hydrogen bond assessment, Dynamic Cross-Correlation Matrix (DCCM), and Free Energy Landscape (FEL) analysis, provided detailed insights into the structural and dynamic properties of the Bcl-2-compound interactions. This comprehensive computational framework supports drug discovery efforts, offering promising candidates for effective cancer treatment.