Exploring the interaction of tepotinib with calf thymus DNA using molecular dynamics simulation and...

Area of Science:

• Biochemistry
• Molecular Biology
• Pharmacology

Background:

• Understanding biomolecular interactions with DNA is crucial for drug discovery.
• Tepotinib (TPT) is an FDA-approved anti-cancer drug targeting MET tyrosine kinase inhibitors for non-small cell lung cancer.
• Investigating drug-DNA interactions provides insights into drug efficacy and mechanisms.

Purpose of the Study:

• To investigate the binding interaction between Tepotinib (TPT) and cell-free DNA (ctDNA).
• To elucidate the binding mode and thermodynamic properties of the TPT-ctDNA complex.
• To provide insights into the molecular mechanism of TPT's action at the DNA level.

Main Methods:

• Biophysical techniques including absorption spectroscopy and fluorometry.
• Computational methods such as molecular docking and molecular dynamic simulations.
• Displacement assays, KI quenching, and Circular Dichroism (CD) spectroscopy.

Main Results:

• Spectroscopic analysis revealed a hypochromic effect and a binding constant (Ka) of 9.91 × 10^4 M⁻¹ for the TPT-ctDNA complex.
• Fluorometric studies indicated a static quenching mechanism for fluorescence enhancement, suggesting ground-state complex formation.
• Binding assays and spectroscopy confirmed TPT preferentially binds to the minor groove of ctDNA, validated by computational simulations.

Conclusions:

• Tepotinib (TPT) interacts with cell-free DNA (ctDNA) through binding to its minor groove.
• The interaction is characterized by a static quenching process and a specific binding affinity.
• These findings enhance our understanding of TPT's molecular interactions and potential DNA-related mechanisms in cancer therapy.