Studies on the interaction between neutral red and bovine hemoglobin by fluorescence spectroscopy and molecular modeling

Characterization of the binding interaction between bovine hemoglobin and riboflavin sodium phosphate: multi-spectroscopic analysis and molecular docking studies

Proteins are essential bimolecular substances that play a crucial role in the maintaining life and are closely associated with its the origin, evolution, and metabolism. Through the use of molecular docking, synchronous fluorescence spectroscopy, ultraviolet-visible absorption, fluorescence, and Fourier transform infrared (FT-IR) spectroscopy, this study sought to clarify the relationship between bovine hemoglobin (BHb) and riboflavin sodium phosphate (RSP) at the normal biological condition. The fluorescence quenching experiment indicated that RSP can cause a static quenching mechanism that quenches BHb's natural fluorescence. Thermodynamic measurements demonstrated that the hydrogen bonding molecular force and hydrophobic contacts caused negative enthalpy and entropy changes during RSP binding to BHb. Using Förster resonance energy transfer, the binding distance between RSP and the BHb tryptophan residues was determined to be 3.11 nm. Fourier transform infrared spectroscopy, synchronous fluorescence, and UV-visible studies revealed that the secondary structure of BHb was considerably altered due to interaction with RSP. The molecular docking simulation revealed that, in addition to hydrophobic interactions, the hydrogen bonds were involved in the interaction of BHb-RSP complex. This study aims to enhance our understanding of the molecular interactions between BHb and RSP, which is significant for elucidating the biochemical pathways involved in metabolic processes.

Investigation of Pyrrole Analogues Inhibition on Main Protease by Spectroscopic Analysis, Molecular Docking, and Enzyme Activity

The main protease (Mpro) is a cysteine enzyme and represents a vital target for antiviral drug screening. In this work, 25 pyrrole derivatives were synthesized and screened by enzyme activity experiments. Results indicate that six pyrrole derivatives can bind to Mpro and have an inhibitory effect on Mpro. The binding mode involves a static quenching process. Among them, 1d exhibits the highest binding affinity. The interactions between pyrrole derivatives and Mpro are investigated by spectra and molecular docking. The interaction between 1d and Mpro is spontaneous and enthalpy-driven. Hydrogen bonding is identified as the primary binding force for 1d. Furthermore, nitro groups are important for the binding between pyrrole analogs and Mpro. This study elucidates the mechanism of interactions and provides direction and valuable insights for developing novel Mpro inhibitors.

Interactions of potato-derived and human recombinant 5-lipoxygenase with sec-O-glucosylhamaudol by multi-spectroscopy and molecular docking

5-lipoxygenase (5-LOX) was a key enzyme involved in many inflammatory diseases. Sec-O-glucosylhamaudol (SOG) was a chromone found in Saposhnikovia divaricata (Turcz.) Schischk (S. divaricate). The potato-derived 5-LOX (p-5-LOX) and human recombinant 5-LOX (h-5-LOX) were selected as model protein due to their simple usability and high stability in this study. Thus, the binding interactions of p-5-LOX and h-5-LOX with SOG were investigated by multi-spectroscopy and molecular docking. As a result, the fluorescence intensities of the two 5-LOX were quenched statically by SOG. However, the binding ability of SOG to h-5-LOX was higher than that of p-5-LOX at the same temperature. The results of multi-spectroscopy revealed that the conformation and micro-environment of the two 5-LOX proteins were changed after binding with SOG. Fluorescence assay and molecular docking indicated that hydrogen bond and electrostatic gravitation were the main forces between the two 5-LOX and SOG. Our results here suggested that SOG may exert anti-inflammatory effect by inhibiting 5-LOX activity.

Interactions of tetracyclines with milk allergenic protein (casein): a molecular and biological approach

Tetracycline (TC), oxytetracycline (OTC), and chlortetracycline (CTC) interactions with the allergenic milk protein casein (CAS) were here evaluated simulating food conditions. The antibiotics assessed interact with CAS through static quenching and form non-fluorescent complexes. At 30 °C, the binding constant (K_b) varied from 0.05 to 1.23 × 10⁶ M^-1. Tetracycline interacts with CAS preferably through electrostatic forces, while oxytetracycline and chlortetracycline interactions occur by hydrogen bonds and van der Waals forces. The interaction process is spontaneous, and the magnitude of interaction based on K_b values, followed the order: TC < CTC < OTC. The distances between the donor (protein) and the receptors (TC, OTC, and CTC) were determined by Förster resonance energy transfer (FRET) and varied from 3.67 to 4.08 nm. Under natural feeding conditions, the citrate decreased the affinity between TC and CAS; a similar effect was observed for OTC in the presence of Ca(II), Fe(III) and lactose. Synchronized and three-dimensional (3D) fluorescence studies indicated alterations in the original protein conformation due to the interaction process, which may influence allergenic processes. In addition, complexation with CAS modulated the antimicrobial activity of CTC against S. aureus, demonstrated that the interaction process possibly alters the biological properties of antibiotics and the own protein, in the food conditions.Communicated by Ramaswamy H. Sarma.

An ultrasensitive fluorescent aptasensor for detection of cancer marker proteins based on graphene oxide-ssDNA

A novel biosensing platform was developed by integrating a new ssDNA aptamer and graphene oxide (GO) for highly sensitive and selective detection of liver cancer biomarkers (alpha-fetoprotein, AFP). The key concept of this biosensing platform is that the fluorescence of dye-modified ssDNA can be effectively quenched by GO after forming the hybrid structure of graphene oxide-ssDNA (GO-ssDNA). The AFP can selectively react with GO-ssDNA and lead to the decomposition of GO-ssDNA, which results in the recovery of fluorescence, and an increase in fluorescence intensity with the increasing concentration of AFP in the range of 0 to 300 pg mL-1. The linear range was obtained from 1 to 150 pg mL-1 and the detection limit was 0.909 pg mL-1. Moreover, this biosensing platform can be applied to serum and cell imaging for the detection of AFP. The results show that the proposed biosensor has great potential application in AFP-related clinical diagnosis and research.

Characterization of interaction between scoparone and bovine serum albumin: spectroscopic and molecular docking methods

Scoparone is a major biological active substance derived from the traditional Chinese herbal medicine called Artemisia capillaris. It has been confirmed that scoparone has anti-inflammatory, anti-tumor, hepatoprotective and antioxidant effects. However, the binding interaction of scoparone with bovine serum albumin (BSA) still remains unknown. Therefore, the present study was conducted to clarify the binding interaction of scoparone with BSA under simulated physiological conditions (pH = 7.4) by utilizing spectroscopic and molecular docking methods. The formation of the scoparone–BSA complex was identified by UV-vis absorption spectroscopy experiment results. The fluorescence experiment results revealed that the quenching mechanism was static quenching and the binding procedure was spontaneous mainly driven by hydrophobic interaction. At 310 K, the number of binding sites was approximately equal to 1 and the binding constant was 6.79 × 10⁵ mol L⁻¹. The binding distance (4.81 nm) between scoparone and BSA was determined by Förster's non-radiative energy transfer theory. Molecular docking and site marker competitive experiment results verified that scoparone was more likely to be located in site I of BSA. In addition, the results of synchronous fluorescence spectroscopy and circular dichroism spectroscopy experiments proved that scoparone slightly changed the conformation of BSA by binding interaction with BSA. These findings would be useful for understanding the pharmacokinetics of scoparone in vivo, including scoparone transport, distribution, metabolism and excretion.

The interaction of scoparone with bovine serum albumin (BSA) was studied by utilizing spectroscopic and molecular docking methodologies.

Comparative study of the binding of 3 flavonoids to the fat mass and obesity-associated protein by spectroscopy and molecular modeling

This study aims to investigate the interaction between 3 flavonoids (quercetin, apigenin, and naringenin) and fat mass and obesity-associated protein by fluorescence, ultraviolet-visible absorption spectroscopy, and molecular modeling. Results indicate that the intrinsic fluorescence of fat mass and obesity-associated protein can be quenched by the 3 flavonoids through a static quenching procedure. Thermodynamic analysis and molecular modeling results suggest that hydrophobic interaction and hydrogen bond forces play the major roles in the binding process. Moreover, results also show that the rank order of quenching constant and binding constant is quercetin > apigenin > naringenin.

The characterization of 1-(4-bromophenyl)-5-phenyl-1H-1,2,3-triazole on acute toxicity, antimicrobial activities, photophysical property, and binding to two globular proteins

1-(4-Bromophenyl)-5-phenyl-1H-1,2,3-triazole (BPT) was a newly synthesized compound. The acute toxicities of BPT to mice by intragastric administration have been determined and the result indicates that the intragastric administration of BPT did not produce any significant toxic effect on Kunming strain mice. It is also evaluated for the antimicrobial activity of BPT against three kinds of plant mycoplasma, Fusarium Wilt (race 4), Colletotrichum gloeosporioides Penz. and Xanthomonas oryzae by different method in vitro. The compound exhibited distinct inhibitory activities against Fusarium Wilt (race 4) and Colletotrichum gloeosporioides Penz. by mycelium growth rate test and the values of EC₅₀ were 29.34 and 12.53μg/mL respectively. And BPT had also the most potent inhibitory activities against Xanthomonas oryzae when compared with that of control drugs by the agar well diffusion method. In addition, the structural and photophysical properties of BPT including ionization energy, electron affinities, and theoretical spectrum was studied by quantum-chemical methods. Then the interaction of BPT with two kinds of globular proteins, human immunoglobulin (HIg) and bovine hemoglobin (BHg) was investigated by using UV-vis absorption spectra, synchronous fluorescence, 3D fluorescence spectra, and fluorescence titration in combination with molecular modeling. UV-vis absorption, 3D and synchronous fluorescence measurements show that BPT has influence on the microenvironment surrounding HIg or BHg in aqueous solution and the fluorescence experiments show that BPT quenches the fluorescence intensity of HIg or BHg through a static mechanism. The binding parameters including the binding constants, the number of binding site and average binding distance between BPT and HIg or BHg at different temperatures were calculated. The thermodynamic parameters suggest that the hydrophobic interaction is the predominant intermolecular forces in stabilizing the BPT-HIg or BPT-BHg complex. Molecular docking was performed to reveal that the BPT moiety binds to the hydrophobic cavity of HIg or BHg and they are in good agreement with the spectroscopic measurements.

Spectroscopic studies and molecular docking on the interaction of organotin antitumor compound bis[2,4-difluoro-N-(hydroxy-⟨κ⟩O)benzamidato-⟨κ⟩O]diphenyltin(IV) with human cytochrome P450 3A4 protease

A novel organotin DFDPT was synthesized and characterized by elemental analysis, IR, (1)H, (13)C, (119)Sn, NMR techniques,etc. In order to investigate profoundly the relationship between DFDPT with human CYP3A4 proteaset and anticancer molecular mechanism of DFDPT, the intercalative mode of binding of DFDPT with CYP3A4 under physiological conditions were comprehensively evaluated using steady state, synchronous, three-dimensional fluorescence spectroscopy,circular dichroism and molecular docking. Fluorescence emission data showed that CYP3A4 fluorescence affected by DFDPT was a static quenching procedure, which implied that DFDPT-CYP3A4 complex had been formed. Apparent binding constants Kb of CYP3A4 with compound at 298 and 310K were 2.51×10(7) and 3.09×10(5), respectively. The binding sites number n was 1.64 and 1.22, respectively. The thermodynamic parameters ΔH and ΔS of the DFDPT-CYP3A4 complex were negative, which indicated that their interaction was driven mainly by hydrogen bonding and van der Waals force. The binding of DFDPT-CYP3A4 was spontaneous process in which ΔG was negative. The synchronous results showed DFDPT induced conformational changes of CYP3A4 protein. Three-dimensional fluorescence and circular dichroism spectra results also revealed conformation of CYP3A4 protein had been possible changed in the presence of DFDPT. Molecular docking was used to study the interaction orientation between DFDPT and CYP3A4 protease. The results indicated that DFDPT interacted with a panel of amino acids in the active sites of CYP3A4 protein mainly through formation of hydrogen bond. Furthermore, the predicted binding mode of DFDPT into CYP3A4 appeared to adopt an orientation with interactions among Arg105, Ser119 and Thr309.