Jiawei He

In vitro investigation of the interaction between the hepatitis C virus drug sofosbuvir and human serum albumin through 1H NMR, molecular docking, and spectroscopic analyses

Sofosbuvir (SOF), an oral nucleotide inhibitor of the nonstructural protein 5B RNA of the hepatitis C virus (HCV), was approved for treating chronic HCV infection by the Food and Drug Administration in 2013. Understanding drug–protein interactions is a crucial factor in determining the pharmacokinetics and pharmacodynamics of a drug. In this study, the interaction between SOF and human serum albumin (HSA) was investigated using 1H nuclear magnetic resonance (NMR) spectroscopy, the molecular docking method, fluorescence studies, Fourier transform infrared (FT-IR) spectroscopy, and circular dichroism (CD) spectroscopy. The analysis of saturation transfer difference (STD) and WaterLOGSY data indicated that SOF was bound to HSA, and the STD signals showed that the methyl and aromatic protons of the hydrophobic components of SOF have the most intimate contact with protein. The negative free energies (−7.17 kcal mol−1 and −6.18 kcal mol−1) obtained from molecular docking and fluorescence studies clearly suggested the spontaneity of the interaction of the SOF–HSA complex. STD, WaterLOGSY and fluorescence displacement experiments demonstrated that SOF was preferentially bound to site I of HSA, and this finding was supported by the docking results. In addition, synchronous and three-dimensional (3D) fluorescence, FT-IR, and CD spectrocopy provided complementary information on the micro-environmental and conformational changes of HSA with the addition of SOF. The combination of 1H NMR and conventional methods provided useful information to further elucidate the binding mechanisms of antiviral drugs with HSA.

Insights into the fatty acid ester norethisterone enanthate binding to human albumin: fluorescence, circular dichroism, and docking investigations

Norethisterone enanthate (NET-EN) is a fatty acid ester of norethisterone. The single crystallographic data of NET-EN [a = 6.09236(14) A, b = 12.7347(3) A, c = 30.1234(8) A, α = β = γ = 90°, unit-cell volume V = 2337.11 A3, Z = 4, and space group P212121] were obtained by using acetone as a solvent. The interaction of NET-EN with human serum albumin (HSA) was investigated using different optical techniques and molecular modeling. The fluorescence quenching between NET-EN and HSA was a static quenching process. The fluorescence lifetime measurement provided us with an insight into the occurrence of static quenching. Three commercially available steroid hormone drugs, namely, norethindrone, norethindrone acetate, and ethisterone, were weaker than NET-EN in terms of binding capability with HSA. Displacement experiments demonstrated that similar to progesterone, the binding site of NET-EN was mainly located in site 1 of HSA. A circular dichroism (CD) study showed that NET-EN had a minimal effect on the local conformation of the HSA molecule. This study provided useful information for the better understanding and use of NET-EN.

Binding properties of drospirenone with human serum albumin and lysozyme in vitro.

The interaction of drospirenone (DP) with human serum albumin (HSA)/lysozyme (LYZ) was investigated using different optical techniques and molecular models. Results from the emission and time resolved fluorescence studies revealed that HSA/LYZ emission quenching with DP was initiated by static quenching mechanism. The LYZ-DP system was more easily influenced by temperature than the HSA-DP system. Displacement experiments demonstrated that the DP binding site was mainly located in site 1 of HSA. Based on the docking methods, DP was mainly bound in the active site hinge region where Trp-62 and Trp-63 are located. Conformation study showed that DP had different effects on the local conformation of HSA and LYZ molecules.

Fluorescence spectroscopy and docking study in two flavonoids, isolated tectoridin and its aglycone tectorigenin, interacting with human serum albumin: a comparison study.

Two flavonoids, tectoridin (TD) isolated from rhizomes of Iris tectorum and hydrolyzed aglycone tectorigenin (TG) were prepared and characterized to compare their different interaction ability with human serum albumin (HSA). Based on the results, the affinity of TG-HSA was stronger than that of TD-HAS, and TG combined more closely with HSA than did TD. HSA fluorescence was quenched by TD/TG. The interactions between TD/TG and HSA involved static quenching. The thermodynamic parameters indicated that both binding processes were spontaneous; hydrogen binding and van der Waals force were the main forces between TD and HSA, whereas a hydrophobic interaction was the main binding force between TG and HSA. Synchronous and 3D fluorescence spectra showed that the binding of TD/TG to HSA induced conformational changes. Moreover, a docking study confirmed the experimental results.

Studies of DNA-binding properties of lafutidine as adjuvant anticancer agent to calf thymus DNA using multi-spectroscopic approaches, NMR relaxation data, molecular docking and dynamical simulation

The interactions between lafutidine (LAF) and calf thymus DNA (ctDNA) have been investigated both experimentally and theoretically. UV-vis absorption studies confirmed that LAF binds to ctDNA through non-covalent interactions. Fluorescence quenching and time-resolved fluorescence spectroscopy studies showed that the binding of LAF with ctDNA occurred through static quenching mechanism, resulting in the formation of a LAF-ctDNA complex. The binding constants (K) of the complex were found to be around 103M-1 via NMR relaxation rates and fluorescence data, and the calculated thermodynamic parameters indicated that hydrogen bonds and van der Waals forces played major roles in the binding of LAF to ctDNA. The changes in CD spectra indicated that LAF induced a slight perturbation on the base stacking and helicity of B-DNA. A comparative study of the LAF-ctDNA complex with respect to potassium iodide quenching experiments and competition displacement assays with ethidium bromide, acridine orange, and Hoechst 33258 probes suggested that LAF interacted with ctDNA by minor groove mode. Molecular docking analysis further supported the minor groove binding. Molecular dynamics simulation indicated that LAF depart from the C-G region of DNA, but it can steadily bind with the middle part of DNA composed by A-T base pairs.

Comparative analysis the binding affinity of mycophenolic sodium and meprednisone with human serum albumin: Insight by NMR relaxation data and docking simulation.

Mycophenolic sodium is an immunosuppressive agent that is always combined administration with corticosteroid in clinical practice. Considering the distribution and side-effect of the drug may change when co-administrated drug exist, this paper comparatively analyzed the binding ability of mycophenolic sodium and meprednisone toward human serum albumin by nuclear magnetic resonance relaxation data and docking simulation. The nuclear magnetic resonance approach was based on the analysis of proton selective and non-selective relaxation rate enhancement of the ligand in the absence and presence of macromolecules. The contribution of the bound ligand fraction to the observed relaxation rate in relation to protein concentration allowed the calculation of the affinity index. This approach allowed the comparison of the binding affinity of mycophenolic sodium and meprednisone. Molecular modeling was operated to simulate the binding model of ligand and albumin through Autodock 4.2.5. Competitive binding of mycophenolic sodium and meprednisone was further conducted through fluorescence spectroscopy.

Domain-specific interactions between MLN8237 and human serum albumin estimated by STD and WaterLOGSY NMR, ITC, spectroscopic, and docking techniques

Alisertib (MLN8237) is an orally administered inhibitor of Aurora A kinase. This small-molecule inhibitor is under clinical or pre-clinical phase for the treatment of advanced malignancies. The present study provides a detailed characterization of the interaction of MLN8237 with a drug transport protein called human serum albumin (HSA). STD and WaterLOGSY nuclear magnetic resonance (NMR)-binding studies were conducted first to confirm the binding of MLN8237 to HSA. In the ligand orientation assay, the binding sites of MLN8237 were validated through two site-specific spy molecules (warfarin sodium and ibuprofen, which are two known site-selective probes) by using STD and WaterLOGSY NMR competition techniques. These competition experiments demonstrate that both spy molecules do not compete with MLN8237 for the specific binding site. The AutoDock-based blind docking study recognizes the hydrophobic subdomain IB of the protein as the probable binding site for MLN8237. Thermodynamic investigations by isothermal titration calorimetry (ITC) reveal that the non-covalent interaction between MLN8237 and HSA (binding constant was approximately 105 M−1) is driven mainly by favorable entropy and unfavorable enthalpy. In addition, synchronous fluorescence, circular dichroism (CD), and 3D fluorescence spectroscopy suggest that MLN8237 may induce conformational changes in HSA.

Analysis of binding properties and interaction of thiabendazole and its metabolite with human serum albumin via multiple spectroscopic methods

Thiabendazole (TBZ), which is oxidized into 5-hydroxythiabendazole (5-OH-TBZ) in vivo, is a commonly used food preservative. Interactions of TBZ and 5-OH-TBZ with human serum albumin (HSA) were comprehensively studied via multiple spectroscopic methods and molecular docking. This study focussed on the mechanistic and structural information on binding of TBZ and 5-OH-TBZ to HSA to evaluate the impact of the food additive on HSA. 1H NMR spectra of the two ligands showed the binding exists. ITC and fluorescence spectroscopy results revealed that TBZ was a stronger ligand, with a binding constant of 105l/mol and formed a more stable complex with HSA than did 5-OH-TBZ via electrostatic interaction. Spectroscopic results (UV-vis, FT-IR, and CD) showed that TBZ and 5-OH-TBZ caused conformational changes in HSA, in which α-helix and β-turn transformed into β-sheet, causing HSA structure to loosen. Docking programs showed that both TBZ and 5-OH-TBZ bound to HSA via IB.

Characterization of the interaction between acotiamide hydrochloride and human serum albumin: 1H STD NMR spectroscopy, electrochemical measurement, and docking investigations

The interaction between acotiamide hydrochloride (Z-338) and human serum albumin (HSA) was investigated by multiple spectroscopic analyses, electrochemical approaches, and computer-aided molecular docking studies. 1H nuclear magnetic resonance (NMR) spectroscopy and saturation transfer difference (STD) data indicated that Z-338 weakly interacted with HSA. STD signals showed that the benzene and five-membered rings of Z-338 were responsible for the binding efficiency. Fluorescence lifetime measurements implied that Z-338 quenched the intrinsic fluorescence of HSA with a new complex formation via static mode. Key parameters regarding this interaction were calculated from differential pulse voltammetry and fluorescence spectroscopy. Results obtained from the two methods above ascertained the static mechanism and revealed that hydrogen bonding combined with van der Waals forces played a major role in HSA–Z-338 binding. Although the displacement of probes from both sites I and II was observed from competitive STD-NMR experiments, molecular docking results suggested that Z-338 was preferentially bound to site II of HSA. This finding was supported by the esterase-like activity result. A decrease in the esterase-like activity of HSA after Z-338 binding showed that the Arg-410 and Tyr-411 of subdomain IIIA were directly involved in the binding process, which corroborated the accuracy of docking studies. Furthermore, circular dichroism spectra, Fourier transform infrared spectroscopy, and 3D fluorescence demonstrated that Z-338 slightly disturbed the microenvironment of amino residues and affected the secondary structure of HSA. Overall, this study provides valuable information to further understand the use of Z-338.

Interaction of lafutidine in binding to human serum albumin in gastric ulcer therapy: STD-NMR, WaterLOGSY-NMR, NMR relaxation times, Tr-NOESY, molecule docking, and spectroscopic studies

In this study, lafutidine (LAF) was used as a model compound to investigate the binding mechanism between antiulcer drugs and human serum albumin (HSA) through various techniques, including STD-NMR, WaterLOGSY-NMR, (1)H NMR relaxation times, tr-NOESY, molecule docking calculation, FT-IR spectroscopy, and CD spectroscopy. The analyses of STD-NMR, which derived relative STD (%) intensities, and WaterLOGSY-NMR, determined that LAF bound to HSA. In particular, the pyridyl group of LAF was in close contact with HSA binding pocket, whereas furyl group had a secondary binding. Competitive STD-NMR and WaterLOGSY-NMR experiments, with warifarin and ibuprofen as site-selective probes, indicated that LAF preferentially bound to site II in the hydrophobic subdomains IIIA of HSA. The bound conformation of LAF at the HSA binding site was further elucidated by transferred NOE effect (tr-NOESY) experiment. Relaxation experiments provided quantitative information about the relationship between the affinity and structure of LAF. The molecule docking simulations conducted with AutoDock and the restraints derived from STD results led to three-dimensional models that were consistent with the NMR spectroscopic data. The presence of hydrophobic forces and hydrogen interactions was also determined. Additionally, FT-IR and CD spectroscopies showed that LAF induced secondary structure changes of HSA.