Binding and thermodynamic study of thalidomide with calf thymus DNA: Spectroscopic and computational approaches.

The thalidomide-DNA interactions have been investigated in detail by numerous biophysical techniques such as UV-vis, dye displacement assay, viscosity, cyclic voltammetry, circular dichroism, molecular docking, molecular dynamic simulation, FT-IR and 1H NMR spectroscopy. CD spectroscopy, thermal denaturation and viscosity measurement explained that thalidomide is groove binder. Molecular docking analysis highlighted that thalidomide binds trough minor groove of calf thymus DNA which also confirmed from dye displacement experiment. To our knowledge, this is the first instance thalidomide was shown to binds with calf thymus DNA. Molecular dynamic simulation indicated that the thalidomide-DNA system was stabilized by electrostatic attraction as the main interaction and mode of binding is minor groove. Our study provides a better understanding to the DNA-thalidomide binding affinity and it mechanism. Overall, all these in formations can be used for further understanding the pharmacological effects of thalidomide.

Pyrazoline analogs as potential anticancer agents and their apoptosis, molecular docking, MD simulation, DNA binding and antioxidant studies.

N-formyl pyrazoline derivatives (3a-3l) were designed and synthesized via Michael addition reaction through cyclization of chalcones with hydrazine hydrate in presence of formic acid. The structural elucidation of N-formyl pyrazoline derivatives was carried out by various spectroscopic techniques such as 1H, 13C NMR, FT-IR, UV-visible spectroscopy, mass spectrometry and elemental analysis. Anticancer activity of the pyrazoline derivatives (3a-3l) was evaluated against human lung cancer (A549), fibrosarcoma cell lines (HT1080) and human primary normal lung cells (HFL-1) by MTT assay. The results of anticancer activity showed that potent analogs 3b and 3d exhibited promising activity against A549 (IC50 = 12.47 ± 1.08 and 14.46 ± 2.76 µM) and HT1080 (IC50 = 11.40 ± 0.66 and 23.74 ± 13.30 µM) but low toxic against the HFL-1 (IC50 = 116.47 ± 43.38 and 152.36 ± 22.18 µM). The anticancer activity of potent derivatives (3b and 3d) against A549 cancer cell line was further confirmed by flow cytometry based approach. DNA binding interactions of the pyrazoline derivatives 3b and 3d have been carried out with calf thymus DNA (Ct-DNA) using absorption, fluorescence and viscosity measurements, circular dichroism and cyclic voltammetry. Antioxidant potential of N-formyl pyrazoline derivatives (3a-3l) has been also estimated through DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical and H2O2. Results revealed that all the compounds exhibited significant antioxidant activity. In silico molecular modelling and ADMET properties of pyrazoline derivatives were also studied using PyRx software against topoisomerase II receptor with PDB ID: 1ZXM to explore their best hits. MD simulation of 3b and 3d was also carried out with topoisomerase II for structure-function correlation in a protein. HuTopoII inhibitory activity of the analogs (3a-3l) was examined by relaxation assay at varying concentrations 100-1000 µM.

Characterization of interactions between cromolyn sodium and bovine serum albumin by spectroscopic, calorimetric and computational methods.

Cromolyn sodium (CS), an anti-inflammatory drug is used in the treatment of allergic disorders. Bovine serum albumin (BSA) a blood plasma protein is used as a model protein for studying protein folding and ligand binding mechanism as it is the main transporter protein which decides the disposition and pharmacodynamics of numerous drugs. In this study, interaction of CS with BSA was investigated using isothermal titration calorimetry, UV-vis, fluorescence, circular dichroism (CD) spectroscopy and molecular docking techniques. Steady state fluorescence data revealed that BSA-CS complex formation occurred through static mode of quenching. Negative values of Gibbs free energy change and enthalpy change showed that BSA-CS complexation was spontaneously favorable and enthalpy driven. CS preferentially interacted at Sudlow's site I (sub-domain IIA) of BSA and the finding was further substantiated by molecular docking study. The binding of CS induced changes in secondary motif of BSA resulting decrease of α-helical content as evident from CD. We explored detailed thermodynamic and structural parameters of interaction of CS to BSA that will be helpful for understanding the more precise binding mechanism of the drug at molecular level.Communicated by Ramaswamy H. Sarma.

Unraveling the thermodynamics, binding mechanism and conformational changes of HSA with chromolyn sodium: Multispecroscopy, isothermal titration calorimetry and molecular docking studies.

Cromolyn sodium is an anti-allergic drug effective for treatment in asthma and allergic rhinitis. In this project, interaction of chromolyn sodium (CS) with human serum albumin (HSA) has been investigated by various techniques such as UV-vis, fluorescence, circular dichorism (CD), fourier transform infrared (FT-IR) spectroscopy, isothermal titration calorimetric (ITC) and molecular docking. The fluorescence quenching results revealed that there was static quenching mechanism in the interactions of CS with HSA. The binding constant (Kb), enthalpy change (ΔH°), entropy change (ΔS°) and Gibbs free energy change (ΔG°) were calculated. The negative values of TΔS° and ΔH° obtained from fluorescence spectroscopy and isothermal titration calorimetry, indicate that hydrogen bonding and van der Waal's forces played major role in the binding process and the reaction is exothermic in nature. The binding constant (Kb) was found to be in the order of 104M-1 which depicts a good binding affinity of CS towards HSA. The conformational changes in the HSA due to interaction of CS were investigated from CD and FT-IR spectroscopy. The binding site of CS in HSA was sub-domain IIA as evident from site probing experiment and molecular docking studies.