Probing the interaction of doxycycline to trypsin and bovine hemoglobin by using multi-spectral techniques and molecular docking

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.

Inhibition of albendazole and 2-(2-aminophenyl)-1H-benzimidazole against tyrosinase: mechanism, structure-activity relationship, and anti-browning effect

BACKGROUND

Tyrosinase is the key enzyme involved in enzymatic browning of plant-derived foods. Inhibition of tyrosinase activity contributes to the control of food browning. Due to safety regulations or other issues, most identified tyrosinase inhibitors are not suitable for practical use. Therefore, it is necessary to search for novel tyrosinase inhibitors. In this study, the anti-tyrosinase activity and mechanism of albendazole and 2-(2-aminophenyl)-1H-benzimidazole (2-2-A-1HB) were investigated through ultraviolet-visible absorption spectroscopy, fluorescence spectra, molecular docking, and molecular dynamic (MD) simulation. The anti-browning effect of albendazole on fresh-cut apples was then elucidated.

RESULTS

Albendazole and 2-2-A-1HB were both efficient tyrosinase inhibitors with IC₅₀ of 51 ± 1.5 and 128 ± 1.3 μmol L^-1 , respectively. Albendazole suppressed tyrosinase non-competitively and formed tyrosinase-albendazole complex statically. Hydrogen bond and hydrophobic interaction were major driving forces in stabilizing the tyrosinase-albendazole complex. While 2-2-A-1HB inhibited the enzyme competitively and quenched its intrinsic fluorescence through a static mechanism, it generated strong binding affinity with tyrosinase through hydrophobic interaction. MD simulations further validated that albendazole/2-2-A-1HB could form stable complexes with tyrosinase and loosened its basic framework structure, leading to a change in secondary structure and conformation. In addition, albendazole could delay the browning of fresh-cut apples by inhibiting the activity of polyphenol oxidase, peroxidase and phenylalanine ammonia-lyase, and reducing the oxidation of phenolic compounds.

CONCLUSION

This research might provide a deep view of tyrosinase inhibition by benzimidazole derivatives and a theoretical basis for developing albendazole as a potential fresh-keeping agent. © 2023 Society of Chemical Industry.

Investigation on conformational variation and enzymatic activity of trypsin affected by Ti3C2 QDs via spectroscopic technique and molecular modeling

In this paper, Ti₃C₂ quantum dots (Ti₃C₂ QDs) were synthesized by simply treating Ti₃C₂ MXene powder with acid and base via hydrothermal method. Ti₃C₂ QDs exhibited superior fluorescence property and were used for the fluorescent imaging of living HeLa cells successfully. In order to evaluate the influence of Ti₃C₂ QDs on protease with specific biological functions, binding interaction of Ti₃C₂ QDs with trypsin was studied comprehensively and deeply through spectroscopic strategies and molecular modeling technique. The intrinsic fluorescence of trypsin was spontaneously quenched by Ti₃C₂ QDs through static quenching mode under van der Waals interaction force, and Ti₃C₂ QDs bound with the inactive residue domain of trypsin firmly with stoichiometric ratio of 1:1. Ti₃C₂ QDs induced the microenvironmental variation of the amino acid residues in trypsin, reducing the thermal stability of trypsin significantly. Gel electrophoresis experiments and microscopic imaging experiments demonstrated that Ti₃C₂ QDs inhibited the enzymatic activity of trypsin on the digestion of human serum albumin and HeLa cells obviously. These results revealed not only the deep interaction mechanism between Ti₃C₂ QDs and protease but also the influence of Ti₃C₂ QDs on the enzymatic activity of trypsin, paving the way for the safe biological application of Ti₃C₂ QDs in the diagnosis and the therapy of protease-related diseases.

Investigation on the interaction between myricetin and dihydromyricetin with trypsin, α-chymotrypsin, lysozyme by spectroscopy and molecular docking methods

The interaction between myricetin and dihydromyricetin with trypsin, α-chymotrypsin and lysozyme was investigated using multispectral and molecular docking methods. The results of fluorescence quenching revealed that myricetin and dihydromyricetin could quench the intrinsic fluorescence of three different proteinases through a static quenching procedure. The binding constant and number of binding sites at different temperatures were measured. The thermodynamic parameters obtained at different temperatures showed van der Waals' interactions and hydrogen bonds played the main roles in the interaction of myricetin with trypsin and lysozyme, hydrophobic force was dominant both in myricetin with α-chymotrypsin interaction and dihydromyricetin with trypsin and lysozyme interaction, as for the electrostatic forces, it was the mainly driving force in dihydromyricetin binding to α-chymotrypsin. There was non-radiative energy transfer between three proteinases and myricetin or dihydromyricetin with high probability. The microenvironment of trypsin, α-chymotrypsin and lysozyme is changed. The docking studies revealed that myricetin and dihydromyricetin entered the hydrophobic cavity of three proteinases and formed hydrogen bond. The binding affinity of myricetin or dihydromyricetin is difference with the trypsin, α-chymotrypsin and lysozyme due to the different molecular structure.

Insights on the interaction mechanism of exemestane to three digestive enzymes by multi-spectroscopy and molecular docking

Exemestane is an irreversible steroidal aromatase inhibitor, typically used to treat breast cancer. As an anti-tumor drug, exemestane has more obvious side effects on the gastrointestinal tract. The purpose of this work is to investigate the combination of exemestane with three important digestive enzymes including pepsin (Pep), trypsin (Try) and α-Chymotrypsin (α-ChT) so as to analyze the mechanism of the gastrointestinal adverse effects causing by exemestane binding. Enzyme activity experiment showed that the enzyme activity of Pep was decreased in the presence of exemestane. Fluorescence spectra revealed that exemestane formed stable complexes with digestive enzymes, and the quenching mechanism of drug-digestive enzymes interaction were all static quenching. The binding constants of Pep, Try and α-ChT at 298 K were 2.34 × 10⁵, 1.45 × 10⁵, and 2.05 × 10⁵ M^-1, respectively. Synchronous fluorescence and 3D fluorescence spectroscopy showed that the conformation of exemestane was slightly changed after combining with digestive enzymes, and non-radiative energy transfer occurred. Circular dichroism results indicated that exemestane could change the secondary structure of digestive enzymes via increase the α-helix content and decrease in the β-sheet content. Thermodynamic parameters (ΔH⁰, ΔS⁰, and ΔG⁰) revealed that exemestane interacted with α-ChT through electrostatic force, and the binding force with Pep and Try was van der Waals interactions and hydrogen, which was basically consistent with the molecular docking results.

Lactoferrin-ginsenoside Rg3 complex ingredients: Study of interaction mechanism and preparation of oil-in-water emulsion

Revealing the interaction mechanism between bovine lactoferrin (LF) and 20(S)-ginsenoside Rg3 (Rg3), thereby introducing Rg3 to LF and even into stable emulsions will contribute significantly to food valorization and food industry. Adding Rg3 to LF caused slight absorbance increment and static fluorescence quench of LF, implying the successful combination. Synchronous fluorescence, three-dimensional fluorescence and circular dichroism spectroscopy indicated the conformation changing of LF after binding with Rg3. Thermodynamic analysis showed that the binding happened spontaneously to form a LF-Rg3 complex with a molar ratio of 1:1, which was mainly driven by hydrogen bonding and van der Waals force. Molecular docking simulation provided extensive information about the optimized binding sites and the involved interactions. Finally, we prepared stable LF-Rg3 oil-in-water emulsion, showing great potential in foods and beverages. This work prepares all-natural functional ingredients, and also diversifies the effective food molecule-based delivery systems for LF and Rg3.

Interaction study of astilbin, isoastilbin and neoastilbin toward CYP2D6 by multi-spectroscopy and molecular docking

Astilbin, isoastilbin and neoastilbin are the three flavonoid isomers prevalent in Rhizoma Smilax glabra. The interactions between human cytochrome P450 2D6 (CYP2D6) and the three isomers were investigated by multiple spectroscopic coupled with molecular docking. As a result, the fluorescence intensity of CYP2D6 was quenched statically by the three isomers. Meanwhile, astilbin had the strongest binding ability to CYP2D6, followed by isoastilbin and neoastilbin under the identical temperature. Synchronous fluorescence, three-dimensional fluorescence, ultraviolet-visible spectroscopy, circular dichroism and Fourier-transform infrared spectra confirmed that the conformation and micro-environment of CYP2D6 protein were changed after binding with the three isomers. As suggested from molecular docking, the three isomers had strong binding affinity to CYP2D6 via the bonding of hydrogen and van der Waals forces, and the results were in agreement with the fluorescence results. The findings here suggested that astilbin, isoastilbin and neoastilbin may cause the herb-drug interactions for their inhibition of CYP2D6 activity.

Assessment of binding interaction dihydromyricetin and myricetin with bovine lactoferrin and effects on antioxidant activity

The binding interactions of bovine lactoferrin (BLF) with two flavonoids dihydromyricetin (DMY) and myricetin (MY) were investigated by the multi-spectroscopic, microscale thermophoresis (MST) techniques, molecular docking, and then their antioxidant activities were studied by detection of free radical scavenging activity against DPPH. Results of UV-vis and fluorescence spectroscopies showed that DMY/MY and BLF formed the ground state complex through the static quenching mechanism. Moreover, MY with more planar stereochemical structure had higher affinity for BLF than DMY with twisted stereochemical structure, according to the binding constant (K_b), free energy change (ΔG°), dissociation constant (K_d) and donor-acceptor distance (r). Thermodynamic parameters revealed that hydrogen bond and van der Waals force were major forces in the formation of BLF-DMY complex, while hydrophobic interactions played major roles in the formation of BLF-DMY complex. The circular dichroism (CD) study indicated that MY induced more conformational change in BLF than DMY. Furthermore, molecular modeling provided insights into the difference of binding interactions between BLF and two flavonoids. Finally, the radical scavenging activity assays indicated the presence of BLF delayed the decrease in antioxidant capacities of two flavonoids. These results were helpful to understand the binding mechanism and biological effects of non-covalent BLF-flavonoid interaction.

Comparative studies on the interaction of nine flavonoids with trypsin

In this study, the interaction between nine classic flavonoids (including baicalin, quercetin, myricetin, rutin, puerarin, daidzein, liquiritin and isoliquiritin) and trypsin was investigated by fluorescence spectroscopy and molecular modeling methods. The results reveal that all flavonoids can interact with trypsin to form flavonoid-trypsin complexes. The binding parameters obtained from the data at different temperatures indicate that all flavonoids can spontaneously bind with trypsin with one binding site. The binding constants of trypsin with nine classic flavonoids are in the following order as: baicalin > myricetin > rutin > isoliquiritin > hesperidin > puerarin > quercetin > daidzein > liquiritin. The interaction forces between flavonoids and trypsin may be electrostatic forces (except for rutin/puerarin/daidzein), hydrophobic interactions as well as van der Waals forces. Synchronous fluorescence spectroscopy shows that the interaction between flavonoids and trypsin changes the hydrophobicity of the microenvironment of tryptophan (Trp) residues. All flavonoids close to tyrosine (Tyr) residues but have no effect on the microenvironment around Tyr residues except for hesperidin and liquiritin. Molecular modeling displays that all flavonoids bind directly into trypsin cavity site and lead to a decrease in enzyme activity.

Biophysical study of phloretin with human serum albumin in liposomes using spectroscopic methods

The ability of drugs to diffuse through the lipid bilayer of cell membranes is important for their metabolism, distribution, and efficacy. In this study, the interaction between phloretin and human serum albumin (HSA) in an L-egg lecithin phosphatidylcholine (PC) liposome suspension was investigated by fluorescence and absorbance spectroscopy. The spectroscopic and fluorescence quenching experiments show that phloretin molecules penetrated into the lumen of the liposome. The partition coefficient of phloretin in the PC liposome suspensions was calculated from fluorescence quenching measurements. The results show that phloretin efficiently quenches the intrinsic fluorescence of HSA through a combination of dynamic and static quenching. The values of Gibbs free energy, and the enthalpy and entropic change in the binding process of phloretin with HSA in the PC liposome suspensions were negative, suggesting that the binding process of phloretin and HSA was spontaneous. Hydrogen bonding and van der Waals force interactions play an important role in the interaction between the two molecules. In addition, binding of phloretin to HSA in liposome suspensions was investigated by synchronous fluorescence spectroscopy.

Interaction mechanism of aloe-emodin with trypsin: molecular structure-affinity relationship and effect on biological activities

The molecular mechanism of interaction between aloe-emodin (AE) and trypsin was investigated, exhibiting remarkable outcomes. To detect the interaction mechanism, the binding of AE with trypsin was examined by a multi-spectroscopy and molecular docking method. Results showed that the binding of AE and trypsin would lead to static quenching and their binding forces were van der Waals forces and hydrogen bonding. The results of simultaneous and three-dimensional fluorescence spectroscopy showed that the combination of AE and trypsin caused changes in the microenvironment around the trypsin fluorophore, which might change the spatial structure of trypsin. FT-IR spectroscopy showed that the contents of α-helix and β-turn in trypsin were decreased and the contents of β-sheet, random coil and antiparallel β-sheet were increased. Moreover, all these experimental results were verified and reasonably explained by molecular docking results. We also investigated the enzyme activity of trypsin and the antioxidant activity of AE. The results showed that both the enzyme activity of trypsin and the antioxidant activity of AE were decreased after interaction between AE and trypsin. The findings outlined in this study should elucidate the molecular mechanisms of interaction between AE and trypsin and contribute to making full use of AE in the food industry.

Targeting the heme protein hemoglobin by (−)-epigallocatechin gallate and the study of polyphenol–protein association using multi-spectroscopic and computational methods

(−)-Epigallocatechin gallate binds to BHb and exhibits anti-glycating as well as antioxidant behaviors towards glycation and photo-oxidation of BHb.

Probing the interaction between levamlodipine and hemoglobin based on spectroscopic and molecular docking methods

In recent years, levamlodipine (LAML) has been widely used as a common drug for the treatment of hypertension. However, no reports exist that focus on the binding process of LAML with the transport proteins present in blood circulation. Here, several spectroscopy techniques, molecular docking and a molecular dynamics simulation were employed to comprehensively analyze the mechanism underlying the interaction between bovine hemoglobin (BHb) and LAML, as well as the effect of other drugs on the BHb-LAML system. The results indicated that a stable BHb-LAML complex was formed and that the binding site for LAML was located at β-37 tryptophan in the central cavity of BHb. Van der Waals force and hydrogen bonds played major roles in this binding process, and the number of binding sites (n) in the binary system was approximately equal to 1. Multiple spectroscopy experiments (FT-IR and three-dimensional fluorescence spectrometry) and a dynamics simulation revealed that LAML could induce a conformational in BHb and that the microenvironment of Trp/Tyr changed. Interestingly, the values of the binding constant between LAML and BHb significantly increased due to the effect of rofecoxib, propranolol and enalapril. Meanwhile, these drugs did not produce synergistic or negative synergistic effects on the LAML binding with BHb. These results provide new insight into the transport mechanisms for LAML in the human body.

Interaction of a digestive protease, Candida rugosa lipase, with three surfactants investigated by spectroscopy, molecular docking and enzyme activity assay

The extensive use of surfactants in food, laundry products and agriculture has caused concern about their biosafety. However, few studies have been done on their potential effect on the lipase which has always been used with surfactants in food and laundry industry. Herein, we investigated the interaction of three surfactants (sodium dodecyl sulfate (SDS), sodium dodecyl benzene sulfonate (SDBS), sodium lauryl sulfonate (SLS)) with Candida rugosa lipase (CRL), which is a popular biocatalyst used regularly with surfactants. The effect of the three surfactants on the conformation and activity of CRL was evaluated by using multiple spectral methods, enzyme activity assay and molecular docking modeling. The results demonstrated that CRL interacted with SDS, SDBS and SLS primarily through hydrophobic forces, H-bonding and electrostatic forces, respectively. The binding constants (K_A) of SDBS with CRL varied with temperature: 1.99×10³mol/L at 298K and 4.13×10³mol/L at 318K. SDS and SDBS affected the secondary structure and skeleton of CRL, which changed the polarity of CRL and enhanced its activity. SLS also changed the secondary structure and activity of CRL moderately, but had little effect on its polarity and chromophore microenvironment. Accordingly, all three surfactants exhibited effect to CRL on the molecular level calling for more attention to pay on their biosafety. The work demonstrates that SDS, SDBS and SLS could cause negative effects to CRL from different angles and therefore are not bio-friendly detergents.

A photosensitizer loaded hemoglobin–polymer conjugate as a nanocarrier for enhanced photodynamic therapy

A hemoglobin–polymer conjugate (HbTcMs) with oxygen supply was applied to generate more singlet oxygen for enhanced photodynamic therapy.

Combined spectroscopy methods and molecular simulations for the binding properties of trametinib to human serum albumin

Trametinib is a novel anticancer drug for treating metastatic cutaneous melanoma. The present study probed into the binding of trametinib to human serum albumin (HSA) through spectroscopy methods and molecular simulations. Trametinib could quench the fluorescence of HSA through static quenching which could be probed via fluorescence spectroscopy and time-resolved fluorescence. Thermodynamic parameters and docking results indicated that hydrogen bonds and van der Waals forces play crucial roles in this binding process, which exerts almost no effect on the HSA conformation under synchronous fluorescence, three-dimensional fluorescence, circular dichroism spectra, and molecular dynamics simulations. Site marker displacement experiments and molecular docking reveal that trametinib primarily binds to Sudlow site I of HSA. In addition, the trametinib–HSA interaction was hardly influenced by varying amino acid (glutamine, alanine, glycine, and valine) concentrations. This study can provide useful information for the pharmacokinetic properties of trametinib.

Probing the binding properties of trametinib to human serum albumin.

Investigating the site selective binding of busulfan to human serum albumin: Biophysical and molecular docking approaches

We have studied the binding of busulfan (BN) to human serum albumin (HSA) at physiological pH 7.4 by using fluorescence, UV-vis and circular dichroism (CD) spectroscopic tools, as well as dynamic light scattering (DLS) measurements and molecular simulation approaches. HSA fluorescence quenching experiments showed that BN reduces the HSA native fluorescence intensity through the static mechanism. In addition, a single binding site on the HSA is occupied by BN with a binding constant at 298K of 1.84×10³M^-1. The enthalpy change (ΔH) and entropy change (ΔS) of BN-HSA interaction were calculated as -1.40kcalmol^-1 and +10.14calmol^-1K^-1 respectively, which suggest the possible interaction mode as hydrophobic and hydrogen bonding. Moreover, the secondary structure alteration of HSA following its complexation with BN was studied and showed that α-helical content of HSA gets increased on interacting with BN. Ligand binding site to HSA was further investigated by site-specific markers in fluorescence measurements as well molecular modeling approach which indicated that BN bind to the nearby sudlow site II of HSA through hydrophobic as well as hydrogen bonding interaction. The present study will be helpful for understanding the binding mechanism of BN to human serum albumin.