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

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.

Structural dynamics studies on the binding of aflatoxin B1 to chicken egg albumin using spectroscopic techniques and molecular docking.

Aflatoxin B1, a mycotoxin produced by large number of Aspergillus species including Aspergillus flavus and Aspergillus parasiticus, has been described as the most potent carcinogenic mycotoxin. In this study, we have used a multiple spectroscopic and molecular docking approach to investigate the interaction of aflatoxin B1 (AFB1) with chicken egg albumin (CEA). Fluorescence spectroscopy, UV-Vis spectroscopy, and three-dimensional fluorescence spectroscopic techniques were employed to gain insight into the conformational changes in CEA in the presence of AFB1. Fluorescence spectroscopy revealed ligand-induced quenching in the fluorescence emission spectra of CEA upon binding with AFB1. Hyperchromic effect was observed in case of the ground state complex formation between CEA and AFB1 by UV-Vis spectroscopy. To gain further comprehension into the site of binding of AFB1 to CEA, competitive site marker displacement assay was performed using warfarin site marker. The magnitude of ΔG value calculated from fluorescence-based method was negative which confirmed spontaneous process. The results obtained suggest that the binding is enthalpy driven and van der Waals force and hydrogen bonds are stabilizing the AFB1-CEA complex. Three-dimensional fluorescence studies also confirmed the quenching in the fluorescence intensity around tryptophan residues in CEA. Circular dichroism assessment revealed reduction in the alpha helical content of CEA in the presence of AFB1. Molecular docking studies showed hydrophobic interaction, van der Waals forces, and hydrogen bonds as major forces present in interaction between CEA and AFB1. The overall study confirms conformational and structural alteration in the protein due to binding of AFB1.Communicated by Ramaswamy H. Sarma.