Insights into the interaction of ulipristal acetate and human serum albumin using multi-spectroscopic methods, molecular docking, and dynamic simulation

Effect of chitooligosaccharide on the binding domain of the SARS-COV-2 receptor

The receptor-binding domain (RBD) is crucial for understanding how severe acute respiratory syndrome coronavirus (SARS-CoV-2) recognizes and infects host cells. Chitooligosaccharide (CS) exhibits diverse antiviral activities, with its derivatives showing remarkable efficacy in blocking SARS-CoV-2 infection. Thus, this study employed spectroscopy, virus-infected cell experiments, and molecular simulation to investigate the molecular interactions between CS and SARS-CoV-2 RBD, as well as their mechanisms. In spectroscopic experiments, all four CS variants with different molecular weights formed interactions with the RBD. These variants increased the resistance of HEK293ACE2 cells to SARS-CoV-2 invasion. Molecular docking revealed that the four CS variants could bind to the RBD through hydrogen bonding or salt-bridge interactions, forming stable complexes. Chitotetraose provided stronger protection to HEK293ACE2 cells compared to other CS variants and displayed higher molecular docking scores. Further investigation into the optimal docking conformation of chitotetraose was conducted through molecular dynamics simulation methods. This study lays a solid theoretical foundation and provides a scientific basis for the development of targeted RBD inhibitors, as well as drug screening and application against novel coronaviruses.

Evidence for paraquat-pepsin interaction: In vitro and silico study

The use of the herbicide paraquat (PQ) has raised concerns about potential environmental consequences due to its toxicity and persistence in the environment. Considering the affinity of dangerous compounds to biological molecules, it is necessary to know their binding properties. This article focuses on the behavior of the pepsin enzyme following its contact with paraquat poison, and the interaction between paraquat and pepsin has been investigated in laboratory conditions and simulated physiological conditions using multispectral techniques. Fluorescence experiments showed that PQ uses a static method to quench pepsin's intrinsic fluorescence. By causing structural damage to pepsin, PQ may be detrimental as it alters its conformational function based on FT-IR spectroscopy. The coupling reaction is a spontaneous process caused by hydrogen bonding and van der Waals forces according to the analysis of the thermodynamic parameters of each system at three different temperatures. The molecular structure of pepsin changes when it binds to PQ. Also, the results showed that PQ is a pepsin inhibitor that changes the function of the enzyme.

Interaction of narcissoside with α-amylase from Bacillus subtilis and Porcine pancreatic by multi-spectral analysis and molecular dynamics simulation

In this work, interaction mechanism of narcissoside with two α-amylase from Bacillus subtilis (BSA) and Porcine pancreatic (PPA) are comparatively studied by multi-spectral analysis, molecular docking and molecular dynamics simulation. The results prove that narcissoside can statically quench fluorescence of BSA/PPA. Two complexes are mainly formed by hydrogen bond and van der Waals force. With the increase of temperature, the two complexes formed by narcissoside and two enzymes become unstable. At the same experimental temperature, the binding force of narcissoside to PPA is higher than that of BSA. The binding of narcissoside to PPA/BSA increases the hydrophobicity of microenvironment. Moreover, the secondary structure of PPA/BSA is mainly changed by decreasing the α-helix. The optimal binding modes of narcissoside with BSA/PPA are predicted by molecular docking, and the stability of the two complexes is evaluated by molecular dynamics simulations.

Comparative study of the interaction mechanism of astilbin, isoastilbin, and neoastilbin with CYP3A4

The interactions of human CYP3A4 with three selected isomer flavonoids, such as astilbin, isoastilbin and neoastilbin, were clarified using spectral analysis, molecular docking, and molecular dynamics simulation. During binding with the three flavonoids, the intrinsic fluorescence of CYP3A4 was statically quenched in static mode with nonradiative energy conversion. The fluorescence and ultraviolet/visible (UV/vis) data revealed that the three flavonoids had a moderate and stronger binding affinity with CYP3A4 due to the order of the Ka1 and Ka2 values ranging from 104 to 105  L·mol-1 . In addition, astilbin had the highest affinity with CYP3A4, then isoastilbin and neoastilbin, at the three experimental temperatures. Multispectral analysis confirmed that binding of the three flavonoids resulted in clear changes in the secondary structure of CYP3A4. It was found from fluorescence, UV/vis and molecular docking analyses that these three flavonoids strongly bound to CYP3A4 by means of hydrogen bonds and van der Waals forces. The key amino acids around the binding site were also elucidated. Furthermore, the stabilities of the three CYP3A4 complexes were evaluated using molecular dynamics simulation.

Exploring the structural basis of conformational alterations of myoglobin in the presence of spermine through computational modeling, molecular dynamics simulations, and spectroscopy methods

Spermine as polyamines can have interaction with the myoglobin (Mb). The intent of this pondering to evaluate the impact of spermine on Mb properties, for example, the structure and thermal stability. For this analysis, the following approaches are employed. Thermodynamics, molecular dynamics (MD), and docking and the use of other spectroscopic procedures. The results of fluorescence spectroscopy and docking showed that binding spermine to Mb was spontaneous. Spermine quenched the fluorescence of Mb through the static quenching process. The thermal stability of Mb was incremented when the concentration of spermine increased. The CD spectra showed Mb's secondary structure shift with a rise in β-sheet and a decrease in α-helicity Mb's in spermine presence. Molecular docking and MD simulation outcomes demonstrate that electrostatic forces show a critical function in stabilizing of this complex, which is in conforming to spectroscopic results.Communicated by Ramaswamy H. Sarma.

Insight on the microscopic binding mechanism of bisphenol compounds (BPs) with transthyretin (TTR) based on multi-spectroscopic methods and computational simulations

Thyroid hormones are involved in numerous physiological processes as regulators of metabolism, regulating organ growth, and mental state. Bisphenol compounds (BPs) are recognized as chemicals that interfere with endocrine balance. Because BPs have a similar structure to thyroxine, they can compete for binding to thyroid protein and disrupt the normal physiological activity of the thyroid system. In this study, three typical bisphenol compounds were selected to explore the interaction between BPs and TTR by computer simulations and multi-spectroscopic methods. The results revealed that BPs quenched the endogenous fluorescence of TTR via the combination of static quenching and non-radiative energy transfer, and the van der Waals forces and hydrogen bonding played a synergistic role in the binding process of BPs and TTR. Furthermore, the three-dimensional fluorescence spectroscopy, UV-vis spectroscopy, and Fourier transform infrared (FT-IR) spectroscopy, which were employed to determine the conformation of protein, revealed that binding of BPs with TTR could induce conformational changes in TTR. In addition, the binding sites and the residues surrounding the BPs within the TTR were determined through molecular docking and molecular dynamics simulation. Therefore, this work provides new insights into the interaction between BPs and TTR to evaluate the potential toxicity of BPs.

How hydrophilic group affects drug-protein binding modes: Differences in interaction between sirtuins inhibitors Tenovin-1/Tenovin-6 and human serum albumin

Introduction of hydrophilic groups can improve the solubility of leading drugs but inevitably affect their interaction with proteins. This study selected sirtuin inhibitors Tenovin-1 (T1) and Tenovin-6 (T6) as drug models to determine differences in binding mode to human serum albumin (HSA). T1 and T6 quenched the endogenous fluorescence of HSA via static quenching mechanism. Introduction of hydrophilic groups greatly reduced the binding constant, i.e., from 1.302 × 10⁴ L mol^-1 for the HSA-T6 system to 0.128 × 10⁴ L mol^-1 for the HSA-T1 system. HSA-T1 system was mainly driven by electrostatic interactions while that of HSA-T6 system was hydrophobic interaction and both systems were spontaneous reactions. Site marker experiments and molecular docking indicated that both systems mainly bound to the hydrophobic site I of HSA. Molecular dynamics (MD) simulation analysis further revealed that Tyr148, Tyr150 and Arg257 residues played a key role in this recognition process for both systems. In particular, T6 maintained additional several hydrogen bonds with the surrounding residues. T1 had almost no effect on the esterase-like activity of HSA, but T6 inhibited the hydrolysis of p-NPA. Furthermore, differential scanning calorimetry (VP-DSC), circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy confirmed that HSA in the T6 system undergone a more significant conformational transition than that in the T1 system.

The study on the interactions of two 1,2,3-triazoles with several biological macromolecules by multiple spectroscopic methodologies and molecular docking

1-(4-chlorophenyl)-5-phenyl-1H-1,2,3-triazole (CPTC) and 5-(3-chlorophenyl) -1-phenyl-1H-1,2,3-triazole (PCTA) are two new derivatives of 1,2,3-triazole. Their structural and spectral properties were characterized by density functional theory calculations (DFT). The binding properties of CPTC or PCTA with several typical biomacromolecules such as human serum albumin (HSA), bovine hemoglobin (BHb), human immunoglobulin (HIgG) or DNA were investigated by molecular docking and multiple spectroscopic methodologies. The different parameters including binding constants and thermodynamic parameters for CPTC/PCTA-HSA/BHb/HIgG/DNA systems were obtained based on various fluorescence enhancement or quenching mechanisms. The results of binding constants indicated that there were the strong interactions between two triazoles and four biological macromolecules due to the higher order of magnitude between 10³ and 10⁵. The values of thermodynamic parameters revealed that the binding forces for these systems are mainly hydrophobic interactions, electrostatic force, or hydrogen bond, respectively, which are in agreement with the results of molecular docking to a certain extent. Moreover, the information from synchronous, 3D fluorescence and UV-Vis spectroscopies proved that two compounds CPTC and PCTA could affect the microenvironment of amino acids residues of three kinds of proteins. Based on the above experimental results, a comparison of the interaction mechanisms for CPTC/PCTA-proteins/DNA systems have been performed in view of their different molecular structures, which is beneficial for the further research in order to design them as the novel drugs.

Synthesis of new morpholine containing 3-amido-9-ethylcarbazole derivative and studies on its biophysical interactions with calf thymus DNA/HSA

In this work, we presented the synthesis and investigation of binding properties of the new morpholine containing 3-amido-9-ethylcarbazole derivative (CMR) to calf thymus DNA (ctDNA) and human serum albumin (HSA) by fluorescence spectroscopy, UV absorption spectroscopy and molecular docking method. A decrease in Stern-Volmer constants was obtained with increase in temperature; it shows that static quenching mechanism leads to formation of new CMR-DNA/HSA complexes, which have hydrophobic interaction as the predominant role in the binding modes. Also, binding properties of DNA were investigated with competition assays on two probes (EB and H33258) by absorption, ionic strength and iodide ion quenching methods. The results suggested that CMR entered into the minor groove binding on the A-T region of DNA. The spectral data further confirmed by molecular docking which elicited that CMR complexes have similar interaction and conformation trends to each target, DNA and HSA. The experimental and computational results show that CMR has been classified as a promising molecule in drug designing of other carbazole derivatives.Communicated by Ramaswamy H. Sarma.

Protein corona of metal-organic framework nanoparticals: Study on the adsorption behavior of protein and cell interaction

Nanoscale metal-organic frameworks (NMOFs) have attracted considerable attention for controlled drug delivery. However, the interaction between nanoparticles and the biological macromolecules of physiological system must be valued because the formed protein corona will endow NMOFs with new biorecognition properties. In this study, we carried out detailed protein adsorption studies in vitro and cell uptake tests of HeLa cells for nanospherical Uio66 and nanooctahedral Uio67. Uio67 with higher binding constants to human serum albumin needed to combine more protein molecules to achieve colloidal stability state than that needed by Uio66, and this phenomenon led Uio67 to aggregate under the same incubation condition due to the formation of a single-layer protein. Uio67 also induced an evident conformation change in protein to stabilize the combination. In particular, the cell uptake efficiencies of the two systems showed a significant thickness dependence on the protein corona. When samples incubated in 10% fetal bovine serum (FBS), the intracellular rate was the highest for both systems, but the rate was not proportional to the FBS concentration. Results of this work are important to the development of the considerable potential NMOFs-based medicals and also provide additional insight into protein corona.

Differences between the binding modes of enantiomers S/R-nicotine to acetylcholinesterase

Nicotine causes neurotoxic effects because it quickly penetrates the blood–brain barrier after entering the human body. Acetylcholinesterase (AChE) is a key enzyme in the central and peripheral nervous system associated with neurotoxicity. In this study, a spectroscopic method and computer simulation were applied to explore the mode of interaction between AChE and enantiomers of nicotine (S/R-nicotine). Fluorescence spectroscopy showed that the quenching mechanism of endogenous fluorescence of AChE by S/R-nicotine was static, as confirmed by the time-resolved steady-state fluorescence. The binding strength of both nicotine to AChE was weak (S-AChE: K_a = 80.06 L mol⁻¹, R-AChE: K_a = 173.75 L mol⁻¹). The main driving forces of S-AChE system interaction process were van der Waals force and hydrogen bonding, whereas that of R-AChE system was electrostatic force. Computer simulations showed that there were other important forces involved. S/R-Nicotine had a major binding site on AChE, and molecular docking showed that they bound mainly to the cavities enclosed by the active sites (ES, PAS, OH, AACS, and AP) in the protein. UV-vis spectroscopy and 3D spectroscopy indicated that nicotine significantly affected the microenvironment of Trp amino acids in AChE. The CD spectra indicated that S-nicotine increased the α-helical structure of AChE, but the overall conformation did not change significantly. By contrast, R-nicotine significantly changed the secondary structure of AChE. 5,5′-Dithiobis-2-nitrobenzoic acid (DTNB) method indicated that S and R nicotine produced different degrees of inhibition on the catalytic activity of AChE. Both experimental methods and computer simulations showed that R-nicotine had a significantly higher effect on AChE than S-nicotine. This research comprehensively and systematically analyzed the mode of interaction between nicotine and AChE for neurotoxicity assessment.

Study on the binding modes of AChE to S/R-nicotine.

Exploring the binding pattern between pepsin and deferasirox using detailed experimental and computer simulation methods

Steady-state fluorescence spectroscopy indicated that a ground state complex was formed between deferasirox (DFX) and pepsin. The binding parameters and thermodynamic parameters of pepsin-DFX complex formation suggested the presence of only one high affinity binding site in the binding process of DFX and pepsin and that the binding process was hydrogen bond dominated. According to the MD simulation optimal pepsin-DFX binding model analysis, the binding force between DFX and pepsin was mainly hydrogen bonding, and the hydrophobic interaction was supplemented. Synchronous fluorescence spectroscopy and 3D fluorescence spectroscopy indicated that the binding of DFX to pepsin had minor effect on the protein structure and function. Circular dichroism spectra showed that DFX had no significant effect on the main secondary structure of pepsin. MD analysis also showed that DFX did not affect the looseness of pepsin and the overall secondary structure, but it affected the amino acid residue sequence Leu48-Ala49-Cys50-Ser51-Asp52. Pepsin enzyme activity test showed that the addition of DFX had a slight enhancement effect on the activity of pepsin. Combined with the MD results, DFX bound to pepsin and was closer to the pepsin active site Asp-215, which may affect the electrical environment of Asp-215 residues and enhance the activity of pepsin.