Multi-spectroscopic studies on the interaction between traditional Chinese herb, helicid with pepsin.

Study on the binding properties of helicid by pepsin systematically using multi-spectroscopic techniques and molecular docking method, and these interactions comprise biological recognition at molecular level and backbone of biological significance in medicine concerned with the uses, effects, and modes of action of drugs. We investigated the mechanism of interaction between helicid and pepsin by using various spectroscopic techniques viz., fluorescence spectra, UV-Vis absorption spectra, circular dichroism (CD), 3D spectra, synchronous fluorescence spectra and molecular docking methods. The quenching mechanism associated with the helicid-pepsin interaction was determined by performing fluorescence measurements at different temperatures. From the experimental results show that helicid quenched the fluorescence intensity of pepsin via a combination of static and dynamic quenching process. The binding constants (Ka) at three temperatures (288, 298, and 308 K) were 7.940 × 107, 2.082 × 105 and 3.199 × 105 L mol-1, respectively, and the number of binding sites (n) were 1.44, 1.14, and 1.18, respectively. The n value is close to unity, which means that there is only one independent class of binding site on pepsin for helicid. Thermodynamic parameters at 298 K were calculated as follows: ΔHo (- 83.85 kJ mol-1), ΔGo (- 33.279 kJ mol-1), and ΔSo (- 169.72 J K-1 mol-1). Based on thermodynamic analysis, the interaction of helicid with pepsin is driven by enthalpy, and Van der Waals' forces and hydrogen bonds are the main forces between helicid and pepsin. A molecular docking study further confirmed the binding mode obtained by the experimental studies. The conformational changes in the structure of pepsin was confirmed by 3D fluorescence spectra and circular dichroism.

In vitro studies on the interaction between human serum albumin and fosfomycin disodium salt, an antibiotic drug by multi-spectroscopic and molecular docking methods.

The interaction between the human serum albumin (HSA) and drug, fosfomycin disodium salt (FOS) has been studied by different spectroscopic techniques. The experimental results showed a static quenching mechanism in the interaction of FOS with HSA. The number of binding sites, n and observed binding constant K a were measured by fluorescence quenching method. The thermodynamic parameters ΔG°, ΔH° and ΔS° were calculated according to van't Hoff equation. The calculated distance r between FOS and the protein is evaluated according to the theory of Förster energy transfer. A change in the secondary structure of the protein was evident from the circular dichroism measurements, synchronous fluorescence and three-dimensional fluorescence spectra.

Ionic Pairing and Selective Solvation of Butylmethylimidazolium Chloride Ion Pairs in DMSO-Water Mixtures: A Comprehensive Examination via Molecular Dynamics Simulations and Potentials of Mean Force Analysis.

Ionic liquids (ILs) with dimethyl sulfoxide (DMSO) and water act as a promising solvent medium for the dissolution of cellulose in an efficient manner. To develop a proper solvent system, it is really important to understand the thermodynamics of the molecular solutions consisting of ILs, DMSO, and water. The ion-pairing propensity of the ILs in the presence of DMSO and water plays a crucial role in governing the property of the solvent mixtures. Employing all-atom molecular dynamics simulations, we estimate the potentials of mean force between BMIM+ and Cl- ions in DMSO-water mixtures. Analysis reveals a significant increase in the thermodynamic stability of both contact ion pair (CIP) and solvent-assisted ion pair (SAIP) states with a rising DMSO mole fraction. Thermodynamic assessments highlight the entropic stabilization of CIP states and SAIP states in pure water, in DMSO-water mixtures, and in pure DMSO. The structural analysis reveals that in comparison to the DMSO local density, the local water density is relatively very high around ion pairs, more specifically in the solvation shell of a chloride ion. Preferential binding coefficients also consistently indicate exclusion of DMSO from the ion pair in DMSO-water mixtures. To enhance our understanding regarding the solvent molecules kinetics around the ion pairs, the survival probabilities of DMSO and water are computed. The calculations reveal that the water molecules prefer a prolonged stay in the solvation shell of Cl- ions.

Trypsin inhibition by Ligupurpuroside B as studied using spectroscopic, CD, and molecular docking techniques.

It is well known that Ligupurpuroside B is a water-soluble polyphenolic compound and used to brew bitter tea with antioxidant activities. It acted as a stimulant to the central nervous system and a diuretic (increase the excretion of urine), was used to treat painful throat and high blood pressure, and also exerted weight-loss function. In this regard, a detailed investigation on the mechanism of interaction between Ligupurpuroside B and trypsin could be of great interest to know the pharmacokinetic behavior of Ligupurpuroside B and for the design of new analogues with effective pharmacological properties. Ligupurpuroside B successfully quenched the intrinsic fluorescence of trypsin via static quenching mechanism. The binding constants (Ka) at three temperatures (288, 298, and 308 K) were 1.7841 × 104, 1.6251 × 104 and 1.5483 × 104 L mol-1, respectively. Binding constants revealed the stronger binding interaction between Ligupurpuroside B and trypsin. The number of binding sites approximated to one, indicating a single class of binding for Ligupurpuroside B in trypsin. The enzyme activity result suggested that Ligupurpuroside B can inhibit trypsin activity. Thermodynamic results revealed that both hydrogen bonds and hydrophobic interactions play main roles in stabilization of Ligupurpuroside B-trypsin complex. Circular dichroism (CD) results showed that the conformation of trypsin changed after bound to ligupurpuroside B. Molecular docking indicated that Ligupurpuroside B can enter the hydrophobic cavity of trypsin and was located near Trp215 and Tyr228 of trypsin. Communicated by Ramaswamy H. Sarma.

Dissection of binding of trypsin to its natural inhibitor Gensenoside-Rg1 using spectroscopic methods and molecular modeling.

The interaction of trypsin with Gensenoside-Rg1 (G-Rg1) was studied using fluorescence, ultraviolet-visible (UV-vis), and circular dichroism (CD) spectroscopies along with enzyme activity assay and molecular docking. The enzyme activity assays showed that G-Rg1 inhibited the activity of trypsin effectively. The fluorescence experiments indicated that a complex of G-Rg1-trypsin was formed and that the fluorescence of trypsin was quenched by G-Rg1 via a mixed-quenching mechanism (both static and dynamic quenching). The thermodynamic analysis suggested that hydrophobic interaction and hydrogen bond were the major forces between G-Rg1 and trypsin. According to the theory of Förster's non-radiation energy transfer, the binding distance between trypsin and G-Rg1 was calculated to be 2.01 nm, which implies that energy transfer occurred within the complex. The experimental results obtained from UV-vis absorption spectra, synchronous fluorescence spectra, and CD spectra indicated that G-Rg1 was mainly located on tryptophan moiety and that the interaction between G-Rg1 and trypsin led to conformational changes of trypsin with some α-helix and unordered coil structures being transformed into ß-sheet structures. In addition, docking results supported the above experimental findings and suggested the possible binding location of G-Rg1 on trypsin along with the possible hydrogen bonds and hydrophobic interactions between G-Rg1 and trypsin. The experimental results from this study should be useful to minimize the antinutritional effects and make full use of Genseng extracts in the food industry and also be helpful to the design of the drugs for the diseases related to overexpression of trypsin. Communicated by Ramaswamy H. Sarma.

Binding mechanism of lipase to Ligupurpuroside B extracted from Ku-Ding tea as studied by multi-spectroscopic and molecular docking methods.

The interaction of lipase with Ligupurpuroside B was studied by multiple spectroscopic techniques, enzyme activity and molecular modeling under simulative physiological condition. According to Stern-Volmer equation, fluorescence of lipase was quenched by Ligupurpuroside B via a static quenching mechanism because of formation of Ligupurpuroside B-lipase complex. Binding constants, number of binding sites & thermodynamic parameters were evaluated. The values of ΔGo (-25.085 kJ mol-1), ΔHo (-12.14 kJ mol-1) and ΔSo (+43.45 J mol-1 K-1) at 298 K indicated that Ligupurpuroside B-lipase interaction is spontaneous and hydrophobic interaction is the main force stabilizing the Ligupurpuroside B-lipase complex. The enzyme activity assay showed that Ligupurpuroside B inhibited lipase activity efficiently. Synchronous fluorescence spectra (SFS) suggested that Ligupurpuroside B is closer to Trp residues than to Tyr residues. All above experimental results were confirmed by molecular docking studies, which further indicated the binding site of Ligupurpuroside B on the surface of lipase, and the amino acid residues of lipase interacting with Ligupurpuroside B. Our present research work gives valuable information on the design of drugs with lipase as a carrier and should be useful for food industries.

Multi-spectroscopic investigation of the binding interaction of fosfomycin with bovine serum albumin.

The interaction between fosfomycin (FOS) and bovine serum albumin (BSA) has been investigated effectively by multi-spectroscopic techniques under physiological pH 7.4. FOS quenched the intrinsic fluorescence of BSA via static quenching. The number of binding sites n and observed binding constant KA were measured by the fluorescence quenching method. The thermodynamic parameters ΔG0, ΔH0 and ΔS0 were calculated at different temperatures according to the van't Hoff equation. The site of binding of FOS in the protein was proposed to be Sudlow's site I based on displacement experiments using site markers viz. warfarin, ibuprofen and digitoxin. The distance r between the donor (BSA) and acceptor (FOS) molecules was obtained according to the Förster theory. The effect of FOS on the conformation of BSA was analyzed using synchronous fluorescence spectra (SFS), circular dichroism (CD) and 3D fluorescence spectra. A molecular modeling study further confirmed the binding mode obtained by the experimental studies.

Multi-spectral characterization & effect of metal ions on the binding of bovine serum albumin upon interaction with a lincosamide antibiotic drug, clindamycin phosphate.

The interaction of clindamycin phosphate (CP) with bovine serum albumin (BSA) is studied by using fluorescence spectra, UV-visible absorption, synchronous fluorescence spectra (SFS), CD, 3D fluorescence spectra and lifetime measurements under simulated physiological conditions. CP effectively quenched intrinsic fluorescence of BSA. The binding constants KA values are 2.540×10(5), 4.960×10(5), 7.207×10(5) L mol(-1), the number of binding sites n and corresponding thermodynamic parameters ΔG(o), ΔH(o) and ΔS(o) between CP and BSA were calculated at different temperatures. The interaction between CP and BSA occurs through dynamic quenching and the effect of CP on the conformation of BSA was also analyzed using SFS. The average binding distance r between the donor (BSA) and acceptor (CP) was determined based on Förster's theory. The results of fluorescence spectra, UV-vis absorption spectra and SFS show that the secondary structure of the protein has been changed in the presence of CP.