Assessment on the binding characteristics of residual marbofloxacin in animal-derived food to bovine/human serum albumin by spectroscopy and molecular modelling

Comparative Study of Binding Behaviors of Cyanidin, Cyanidin-3-Galactoside, Peonidin with Tyrosinase

Cyanidin, peonidin and cyanidin-3-galactoside are the common anthocyanins with a variety of biological activities. Tyrosinase is a speed-limiting enzyme associated with melanin production. The inhibition of tyrosinase activity can prevent melanin disease while contributing to whitening. The interaction behaviors of the three anthocyanins against tyrosinase have been discussed in this paper. Cyanidin has strongest inhibitory effect on tyrosinase, and then peonidin, cyanidin-3-galactoside. Furthermore, the inhibition of tyrosinase by the three anthocyanins is mixed modes. The three anthocyanins can induce the static fluorescence quenching of tyrosinase. Cyanidin exhibits strongest binding affinity on tyrosinase, and then peonidin, cyanidin-3-galactoside based on Ka values obtain by fluorescence analysis. The binding of all anthocyanin to tyrosinase induce its conformation changes. According to molecular docking and fluorescence studies, they bind to tyrosinase by hydrogen bond and van der Waals force. In addition, the optimal modes of the three anthocyanins with tyrosinase are predicated by molecular docking. This work emphasizes that cyanidin, peonidin and cyanidin-3-galactoside may be potential drugs for the treatment of diseases caused by melanin.

Probing binding mode between sodium acid pyrophosphate and albumin: multi-spectroscopic and molecular docking analysis

Sodium acid pyrophosphate (SAPP) food additive is widely used as a preservative, bulking agent, chelating agent, emulsifier and pH regulator. It is also used as an improver of color and water retention capacity in the processing of various types of seafood, canned food, cooked meat and flour products. For the first time, we evaluated the SAPP interaction with bovine serum albumin (BSA) using spectroscopic methods including UV-Vis absorption, fluorescence spectroscopy, and surface plasmon resonance, and docking analysis to understand the mechanisms of complex formation and binding. The fluorescence intensity of BSA reduces when titrated with various concentrations of SAPP by forming a complex with BSA via a static quenching mechanism. The binding constant between BSA and SAPP decreased from 123,300 to 15,800 (M-1) with rising temperature, which indicates a decrement in complex formation owing to the interaction of SAPP with BSA. A negative ΔG° value means that SAPP binds spontaneously to BSA at all temperatures, and both ΔH° and ΔS° negative values indicate that hydrogen bonds (H-bonding) and van der Waals forces are the primary forces involved in the binding processes. The UV-Vis spectrum of BSA reduced upon increasing SAPP concentrations due to forming a new ground state complex between SAPP and BSA. Molecular docking study shows that residues Arg256, Ser259, Ser286, Ile 289 and Ala 290 play an important role in SAPP binding process to site I (subdomain IIA) of BSA through H-bonding and van der Waals forces, which is supported by the thermodynamic study.Communicated by Ramaswamy H. Sarma.

Interactions studies of CYP2D6 with quercetin and hyperoside by spectral analysis and molecular dynamics simulations

Some ingredients from herbal medicine can significantly affect the activity of CYP2D6, thus leading to serious interactions between herbs and drugs. Quercetin and hyperoside are active ingredients widely found in vegetables, fruits, and herbal medicines. Quercetin and hyperoside have many biological activities. In this work, the characteristic bindings of CYP2D6 with quercetin/hyperoside are revealed by multi-spectroscopy analysis, molecular docking, and molecular dynamics simulations. The fluorescence of CYP2D6 is statically quenched by quercetin and hyperoside. The binding constant (Ka ) values of CYP2D6-quercetin/hyperoside range from 104  L mol-1 , which indicates that these two flavonoids bind moderately to CYP2D6. Meanwhile, quercetin has a stronger quenching ability to CYP2D6 than that of hyperoside. The secondary structure of CYP2D6 is obviously changed by binding with quercetin/hyperoside. The docking results reveal that the quercetin/hyperoside enters the active site of CYP2D6 near heme and binds to CYP2D6 by hydrogen bonds and van der Waals forces. The molecular dynamics simulation results indicate that the binding of quercetin/hyperoside can stabilize the two complexes, enhance the flexibility of CYP2D6 backbone atoms, and make a more unfolded and looser structure of CYP2D6.

Exploring the Interaction Between the Newly Designed Antitumor Zn(II) Complex and CT-DNA/BSA: Spectroscopic Methods, DFT Computational Analysis, and Docking Simulation

A new zinc(II) complex formulated as [Zn(pipr-ac)2], where pipr-ac stands for piperidineacetate, was synthesized and structurally identified with the help of experimental and DFT methods. Frontier molecular orbital (FMO) analysis demonstrated that the new complex has higher biological activity compared to the free ligand. Molecular electrostatic potential (MEP) showed the nitrogen atoms and oxygen of carbonyl groups are the active sites of Zn(II) compound. Also, natural bond orbital (NBO) analysis confirmed the charge transfer from the ligating atoms to the metal ion and formation of four coordinated Zn(II) complex. MTT assay illustrated a noticeable cytotoxic activity of the new zinc(II) complex compared to cisplatin on K562 cell line. The CT-DNA and serum albumin (SA) binding of the Zn(II) complex were explored individually. In this regard, UV-Vis spectroscopy and florescence titration revealed the occurrences of fluorescence quenching of CT-DNA/SA by metal compound via static mechanism and creation of hydrogen bonds and van der Waals interactions between them. The binding was further confirmed by viscosity measurement and gel electrophoresis assay for CT-DNA and circular dichroism spectroscopy for SA. Moreover, molecular docking simulation demonstrated that the new compound binds mainly through hydrogen bonds to the groove of DNA and hydrogen bonds and van der Waals interactions to site I of SA.

Interactions between hydroxylated polycyclic aromatic hydrocarbons and serum albumins: Multispectral and molecular docking analyses

Hydroxylated polycyclic aromatic hydrocarbons (OH-PAHs) can bind to serum albumin and influence their distribution and elimination in organisms. Herein, multispectral analysis and molecular docking methods were used to investigate the binding mechanism of two OH-PAHs, 1-hydroxyphenanthrene (1-OHPhe) and 9-hydroxyphenanthrene (9-OHPhe), with two homologous serum albumins, human serum albumin (HSA) and bovine serum albumin (BSA). The quenching constants of HSA with 1-OHPhe and 9-OHPhe were much larger than those for BSA. Energy transfer from the tryptophan (Trp) residues in HSA to 1-OHPhe and 9-OHPhe was more probable than from Trp in BSA. The interactions of 1-OHPhe and 9-OHPhe with Trp in HSA and BSA altered the microenvironment of Trp. Molecular docking results revealed that the binding modes and binding forces of 1-OHPhe and 9-OHPhe with HSA and BSA were different. The two OH-PAHs were used as fluorescent probes to analyze the microenvironmental hydrophobicities of HSA and BSA, which were distinctly different. The structural difference between HSA and BSA induced significant variations in their binding behavior with 1-OHPhe and 9-OHPhe. Moreover, HSA was more susceptible to 1-OHPhe and 9-OHPhe than BSA. This work suggests that the differences between the two serum albumins should be considered in related studies.

Interaction mechanism of pelargonidin against tyrosinase by multi-spectroscopy and molecular docking

The interaction mechanism of pelargonidin (PG) with tyrosinase was investigated by multi-spectroscopy and molecular docking. As a result, PG had strong inhibitory activity on tyrosinase with the IC₅₀ value of 41.94×10^-6 mol·L^-1 . The inhibition type of PG against tyrosinase was determined as a mixed mode. Meanwhile, the fluorescence of tyrosinase was quenched statically by PG, and accompanied by non-radiative energy transfer. The three-dimensional (3-D) fluorescence, ultraviolet-visible spectroscopy (UV-Vis) and circular dichroism spectroscopies (CD) indicated that PG decreased the hydrophobicity of the micro-environment around tryptophan (Trp) and tyrosine (Tyr), which resulted in the conformational change of tyrosinase. In addition, fluorescence and molecular docking analysis indicated that PG bound to tyrosinase via hydrogen bonds (H-bonds) and van der Waals force (vdW force). We herein recommended that PG might be a potential candidate drug for the treatment of melanin-related diseases.

Interaction study of engeletin toward cytochrome P450 3A4 and 2D6 by multi-spectroscopy and molecular docking

The inhibitory effects of engeletin on the activities of human cytochrome P450 3A4 and 2D6 (CYP3A4 and CYP2D6) were investigated by enzyme kinetics, multi-spectroscopy and molecular docking. Engeletin was found to strongly inhibit CYP3A4 and CYP2D6, with the IC₅₀ of 1.32 μM and 2.87 μM, respectively. The inhibition modes of engeletin against CYP3A4 and CYP2D6 were a competitive type and a mixed type, respectively. The fluorescence of the two CYPs was quenched statically by engeletin, which was bound to CYP3A4 stronger than to CYP2D6 at the same temperature. Circular dichroism spectroscopy, three-dimensional fluorescence, ultraviolet-visible spectroscopy and synchronous fluorescence confirmed that the conformation and micro-environment of the two CYPs protein were changed after binding with engeletin. Molecular docking, ultraviolet-visible spectroscopy and the fluorescence data revealed that engeletin had strong binding affinity to the two CYPs through hydrogen and van der Waals forces. The findings here suggested that engeletin may cause the herb-drug interactions for its inhibition of CYP3A4 and CYP2D6 activities.