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In silico Identification of Natural Compounds as Potential TrkA Inhibitors for Anticancer Drug Development
Mujtaba Fadhil1, Dhurgham Al-Fahad2, Faizul Azam3
1Department of Biology, Faculty of Science, University of Mohaghegh Ardabili, Ardabil, Iran.
Background:
Tropomyosin receptor tyrosine kinase A (TrkA) is essential for cancer cell migration and for stabilizing focal adhesions required for attachment to the extracellular matrix. However, resistance to inhibitors targeting the ATP-binding pocket of the TrkA kinase domain complicates treatment. These inhibitors block ATP binding, which is required for TrkA activation, thereby disrupting downstream signaling pathways involved in cell proliferation and survival in cancers characterized by TrkA overexpression or mutation.
Objectives:
This study aimed to identify natural compounds as potential TrkA inhibitors for anticancer drug development. The identified compounds exhibited higher binding affinity and greater stability than the control compounds.
Methods:
Virtual screening, molecular dynamics simulations, MM-GBSA free energy calculations, and principal component analysis were performed using the Schrödinger Desmond software to screen a comprehensive library from the NPACT and PhytoHub databases for potential novel TrkA inhibitors.
Results:
Two promising inhibitors derived from natural compounds, PHUB000399 and NPACT01417, were identified. Toxicity assessments indicated that both compounds had lower toxicity levels (class 5) than Entrectinib, the reference inhibitor (class 4); the molecular weights of PHUB000399, NPACT01417, and Entrectinib were 275.25, 316.35, and 560.64 g/mol, respectively. Docking studies showed that PHUB000399 and NPACT01417 had superior binding affinities, with grid scores of -13.239 and -13.103, respectively, compared with the co-crystal ligand (-12.567) and Entrectinib (-10.996). Molecular dynamics simulations indicated that the TrkA-PHUB000399 and TrkA-NPACT01417 complexes were more stable than the TrkA-Entrectinib complex. The calculated binding free energies for TrkA-PHUB000399 and TrkA-NPACT01417 were -87.74 and -86.09 kcal/mol, respectively, exceeding those of the co-crystal ligand (-84.14 kcal/mol) and Entrectinib (-73.03 kcal/mol).
Conclusions:
These findings suggest that NPACT01417 and PHUB000399 are promising candidates for targeting cancer cell migration, with binding affinities comparable to those of established inhibitors. This study provides valuable insights for the development of effective anticancer therapies.
Insights
Natural compounds PHUB000399 and NPACT01417 show promise as Tropomyosin receptor tyrosine kinase A (TrkA) inhibitors. These compounds exhibit superior binding affinity and stability, offering potential for novel anticancer drug development targeting cancer cell migration.
Area of Science:
- Oncology
- Pharmacology
- Computational Chemistry
Background:
- Tropomyosin receptor tyrosine kinase A (TrkA) is crucial for cancer cell migration and focal adhesion stability.
- Resistance to conventional TrkA inhibitors targeting the ATP-binding pocket poses a significant challenge in cancer therapy.
- Targeting TrkA signaling is vital for treating cancers with TrkA overexpression or mutation.
Purpose of the Study:
- To identify novel natural compounds as potential inhibitors of Tropomyosin receptor tyrosine kinase A (TrkA) for anticancer drug development.
- To evaluate the binding affinity and stability of identified natural compounds against TrkA.
Main Methods:
- Virtual screening of comprehensive natural compound libraries (NPACT and PhytoHub) using Schrödinger Desmond software.
- Molecular dynamics simulations and MM-GBSA free energy calculations to assess complex stability and binding affinity.
- Principal component analysis for in-depth simulation analysis.
Main Results:
- Two potent natural compounds, PHUB000399 and NPACT01417, were identified as TrkA inhibitors.
- PHUB000399 and NPACT01417 demonstrated superior binding affinities (grid scores: -13.239 and -13.103) compared to Entrectinib (-10.996).
- Molecular dynamics simulations confirmed enhanced stability for TrkA-PHUB000399 and TrkA-NPACT01417 complexes, with binding free energies of -87.74 and -86.09 kcal/mol, respectively.
Conclusions:
- NPACT01417 and PHUB000399 are promising candidates for developing novel anticancer therapies targeting TrkA.
- These natural compounds exhibit favorable binding characteristics and stability, comparable to established inhibitors.
- The findings provide a foundation for further investigation into TrkA-targeted cancer treatments.
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