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Updated: Jul 9, 2025
Biotinylated Cell-penetrating Peptides to Study Intracellular Protein-protein Interactions
Published on: December 20, 2017
Exploring the interaction of tepotinib with calf thymus DNA using molecular dynamics simulation and
Mohd Amir1, Mohd Aamir Qureshi1, Ashma Khan2
1Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
Abstract:
In recent times, there has been a surge in the discovery of drugs that directly interact with DNA, influencing gene expression. As a result, understanding how biomolecules interact with DNA has become a major area of research. One such drug is Tepotinib (TPT), an FDA-approved anti-cancer medication known as a MET tyrosine kinase inhibitor, used in chemotherapy for metastatic non-small cell lung cancer (NSCLC) with MET exon 14 skipping alterations. In our study, we adopted both biophysical and in-silico methods to investigate the binding relationship of TPT and ctDNA. The absorption spectra of ctDNA exhibited a hypochromic effect when titrated with TPT and the binding constant of TPT-ctDNA complex was calculated, Ka = 9.91 × 104 M-1. By computing bimolecular enhancement constant (KB) and thermodynamic enhancement constant (KD) in fluorometric investigations, it was found that the fluorescence enhancement is a result of a static process involving the ctDNA-TPT complex formation in the ground state, as opposed to a dynamic process. The displacement assay results further supported this finding, showing that TPT exhibits a binding preference for minor groove of ct-DNA and was also demonstrated by KI quenching and CD spectroscopy. The molecular docking and molecular dynamic simulations validated TPT's groove binding nature and binding pattern with ctDNA, respectively. Thus, the results of our present investigation offer valuable insights into the interaction between TPT and ctDNA. It is evident that TPT, as an anti-cancer medication, binds to the minor groove of ctDNA.
Insights
Tepotinib (TPT), an anti-cancer drug, binds to the minor groove of cell-free DNA (ctDNA). Biophysical and computational methods confirm this interaction, offering insights into TPT
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.
