Computational analysis of bevacizumab binding with protein receptors for its potential anticancer activity

• Published in: Journal of biomolecular structure & dynamics pp. 1 - 21
• Main Authors: Alsakhen, Nada, Radwan, Enas S, Zafer, Imran, Abed Alfattah, Husam, Shamkh, Israa M, Rehman, Md Tabish, Shahwan, Moayad, Khan, Khalid Ali, Ahmed, Shimaa A
• Format: Journal Article
• Language: English
• Published: England 28.01.2024
• Subjects: bevacizumab; Breast cancer; molecular docking; molecular dynamic simulation
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2024.2307445

Breast cancer poses a significant global challenge, prompting researchers to explore novel approaches for potential treatments. In this study, we investigated the binding free energy (Δ ) of bevacizumab, an anti-cancer therapy targeting angiogenesis through the inhibition of vascular endothelial growth factor (VEGF), with various proto-oncogenes including CDK4, EGFR, frizzled, IGFR, OmoMYC, and KIT. Our in-silico investigation revealed that hydrogen bonding is pivotal in inducing conformational changes within the DNA structure, impeding its replication and preventing cell death. Molecular docking results revealed the presence of crucial hydrogen bonds and supported the formation of stable bevacizumab complexes. The molecular docking scores for the tested complexes were CDK4 (Score = -7.2 kcal/mol), EGFR (Score = -8.5 kcal/mol), frizzled (Score = -6.9 kcal/mol), IGFR (Score = -7.8 kcal/mol), KIT (Score = -6.5 kcal/mol), and MYC (Score = -8.3 kcal/mol). The binding mode demonstrated vital hydrogen bonds correlated with the observed energy gap. Notably, the calculated binding free energies of the tested compounds are as follows: CDK4 (Δ  = 24275.195 ± 6411.293 kJ/mol), EGFR (Δ  = 363273.625 ± 8731.466 kJ/mol), frizzled (Δ  = 181751.990 ± 28438.515 kJ/mol), IGFR (Δ  = 162414.725 ± 10728.367 kJ/mol), KIT (Δ  = 40162.585 ± 4331.017 kJ/mol), and MYC (Δ  = 434783.463 ± 53989.676 kJ/mol). Furthermore, through extensive 100 ns MD simulations, we observed the formation of a stable bevacizumab complex structure. The simulations confirmed the stability of the bevacizumab complex with the proto-oncogenes. The results of this study highlight the potential of bevacizumab complex as a promising candidate for anticancer treatment. The identification of hydrogen bonding, along with the calculated binding free energies and molecular docking scores, provides valuable insights into the molecular interactions and stability of the bevacizumab complexes. These findings and the extensive MD simulations open new avenues for future research and development of bevacizumab as a targeted therapy for breast cancer and other related malignancies.Communicated by Ramaswamy H. Sarma.