“…In the examined range of temperatures, the obtained K b values were in the order of 10 3 M −1 , demonstrating that PLB has a moderate affinity for CT-DNA binding. Furthermore, the K b values appear to be in the same range as groove binders 7 , 10 , 50 , 52 , 54 and lower than those of classic intercalators, as the DNA-EB complex ( K b = 1.4 × 10 6 M −1 ) 55 , 56 , confirming that the binding between PLB and CT-DNA is via a minor groove mechanism. Figure 6 Plot of A 0 /( A − A 0 ) versus 1/ C PLB at different temperature settings ( C DNA = 8.25 × 10 −5 M), where r is the correlation coefficient.…”
Section: Resultsmentioning
confidence: 81%
“…The positive ΔS 0 value is commonly because of the hydrophobic interaction. Furthermore, the negative value of ΔH 0 is not an indicator of electrostatic interactions because ΔH 0 is close to zero in the case of electrostatic interactions, implying that the negative ΔH 0 value is likely due to hydrogen bonding interactions 7 , 50 , 58 – 60 . As a result, hydrophobic interactions and hydrogen bonding may be the primary binding forces for the PLB-CT-DNA interaction, as validated by molecular docking studies.…”
Section: Resultsmentioning
confidence: 99%
“…Rg is considered a measure of DNA compactness; accordingly, Rg measurements can provide information about changes in DNA structure and thus its structural stability 7 , 41 , 68 . Figure 11 demonstrates that during the MD simulation, the Rg values for free DNA and the DNA-PLB complex were nearly comparable with a difference of less than 1 Angstrom, indicating that when PLB attached to DNA did not induce any conformational changes, which was consistent with the results of the FT-IR spectroscopy.…”
Studying the binding interaction between biological macromolecules and small molecules has formed the core of different research aspects. The interaction of palbociclib with calf thymus DNA at simulated physiological conditions (pH 7.4) was studied using different approaches, including spectrophotometry, spectrofluorimetry, FT-IR spectroscopy, viscosity measurements, ionic strength measurements, thermodynamic, molecular dynamic simulation, and docking studies. The obtained findings showed an apparent binding interaction between palbociclib and calf thymus DNA. Groove binding mode was confirmed from the findings of competitive binding studies with ethidium bromide or rhodamine B, UV–Vis spectrophotometry, and viscosity assessment. The binding constant (Kb) at 298 K calculated from the Benesi–Hildebrand equation was found to be 6.42 × 103 M−1. The enthalpy and entropy changes (∆H0 and ∆S0) were − 33.09 kJ mol−1 and 61.78 J mol−1 K−1, respectively, showing that hydrophobic and hydrogen bonds constitute the primary binding forces. As indicated by the molecular docking results, palbociclib fits into the AT-rich region of the B-DNA minor groove with four base pairs long binding site. The dynamic performance and stability of the formed complex were also evaluated using molecular dynamic simulation studies. The in vitro study of the intermolecular binding interaction of palbociclib with calf thymus DNA could guide future clinical and pharmacological studies for the rational drug scheming with enhanced or more selective activity and greater efficacy.
“…In the examined range of temperatures, the obtained K b values were in the order of 10 3 M −1 , demonstrating that PLB has a moderate affinity for CT-DNA binding. Furthermore, the K b values appear to be in the same range as groove binders 7 , 10 , 50 , 52 , 54 and lower than those of classic intercalators, as the DNA-EB complex ( K b = 1.4 × 10 6 M −1 ) 55 , 56 , confirming that the binding between PLB and CT-DNA is via a minor groove mechanism. Figure 6 Plot of A 0 /( A − A 0 ) versus 1/ C PLB at different temperature settings ( C DNA = 8.25 × 10 −5 M), where r is the correlation coefficient.…”
Section: Resultsmentioning
confidence: 81%
“…The positive ΔS 0 value is commonly because of the hydrophobic interaction. Furthermore, the negative value of ΔH 0 is not an indicator of electrostatic interactions because ΔH 0 is close to zero in the case of electrostatic interactions, implying that the negative ΔH 0 value is likely due to hydrogen bonding interactions 7 , 50 , 58 – 60 . As a result, hydrophobic interactions and hydrogen bonding may be the primary binding forces for the PLB-CT-DNA interaction, as validated by molecular docking studies.…”
Section: Resultsmentioning
confidence: 99%
“…Rg is considered a measure of DNA compactness; accordingly, Rg measurements can provide information about changes in DNA structure and thus its structural stability 7 , 41 , 68 . Figure 11 demonstrates that during the MD simulation, the Rg values for free DNA and the DNA-PLB complex were nearly comparable with a difference of less than 1 Angstrom, indicating that when PLB attached to DNA did not induce any conformational changes, which was consistent with the results of the FT-IR spectroscopy.…”
Studying the binding interaction between biological macromolecules and small molecules has formed the core of different research aspects. The interaction of palbociclib with calf thymus DNA at simulated physiological conditions (pH 7.4) was studied using different approaches, including spectrophotometry, spectrofluorimetry, FT-IR spectroscopy, viscosity measurements, ionic strength measurements, thermodynamic, molecular dynamic simulation, and docking studies. The obtained findings showed an apparent binding interaction between palbociclib and calf thymus DNA. Groove binding mode was confirmed from the findings of competitive binding studies with ethidium bromide or rhodamine B, UV–Vis spectrophotometry, and viscosity assessment. The binding constant (Kb) at 298 K calculated from the Benesi–Hildebrand equation was found to be 6.42 × 103 M−1. The enthalpy and entropy changes (∆H0 and ∆S0) were − 33.09 kJ mol−1 and 61.78 J mol−1 K−1, respectively, showing that hydrophobic and hydrogen bonds constitute the primary binding forces. As indicated by the molecular docking results, palbociclib fits into the AT-rich region of the B-DNA minor groove with four base pairs long binding site. The dynamic performance and stability of the formed complex were also evaluated using molecular dynamic simulation studies. The in vitro study of the intermolecular binding interaction of palbociclib with calf thymus DNA could guide future clinical and pharmacological studies for the rational drug scheming with enhanced or more selective activity and greater efficacy.
“…The severity of the decrease in the fluorescence intensity of the EB‐DNA system is related to the degree of mixing of the small molecule into the DNA. Therefore, with the addition of the small molecule to the EtBr‐DNA complex, any appreciable change in the fluorescence intensity of the complex would be predicted to be intercalation of the DNA binding mode of the small molecule [32] …”
Ofloxacin (OFL), a quinolone antibiotic, shows a bactericidal effect by inhibiting the DNA gyrase enzyme in bacteria. In addition to its use in various infections has a wide range of benefits from urinary system disorders to pneumonia and bronchitis. DNA is the main molecular target for many small molecules of therapeutic importance. In this article, the interaction between OFL and fsDNA (fish sperm DNA) is reported using a combination of biophysical (spectroscopic and electrochemical) and in silico techniques (molecular docking and molecular dynamics). The interaction and complex formation were studied using UV-visible and steady-state fluorescence spectroscopy. Ethidium bromide (EtBr), Rhodamine B (RB) competitive displacement, potassium iodide quenching, and ionic strength assays confirmed the binding mode between OFL and DNA via minor groove binding. Thermodynamic parameters at various temperatures supported the enthalpically driven, exothermic, and spontaneous reaction between OFL and fsDNA. It was found that hydrogen bond interaction and van der Waals forces play a dominant role in forming the complex form. DNA melting experiments corroborated these findings. In-silico molecular docking and molecular dynamics simulation studies revealed the interaction mode, major stabilizing forces, and the nucleotide sequences OFL binds and dock into the GC-rich region of the DNA minor groove, confirming the in vitro experiment results.
“…The concentration of ss-DNA (1.81 × 10 -4 mol L −1 ) was determined spectrophotometrically, using known molar absorption coefficient value ε 260 = 6600 M −1 cm −1 at 25 °C. 75,76 The stock solutions were stored at 4 °C and used within 4 days. The stock solution of the complexes 1-3 (5 × 10 -4 mol L −1 ) and 4 (2.5 × 10 -4 mol L −1 ) were prepared after dissolving the necessary amount of solvent and dilution was made with the help of a buffer solution.…”
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