Spectroscopy and Molecular Modeling Study on the Interaction Between Mycophenolate Mofetil and Pepsin

Investigating the impact of common migration substances found in milk packaging on proteases: A multispectral and molecular docking approach

The effects of common migration substances in milk packaging on digestive protease were studied. We choose the common migrants found in eight types of multi-layer composite milk packaging. Enzyme activity experiments revealed that pepsin activity decreased by approximately 18 % at 500 μg/mL of stearic acid and stearamide treatment, while trypsin activity decreased by approximately 18 % only by stearic acid treatment (500 μg/mL). Subsequently, fluorescence spectroscopy, circular dichroism spectroscopy, and molecular docking technology were employed to investigate the inhibition mechanism of protease activity by migrating substances in three systems: stearic acid-trypsin, stearic acid-pepsin, and stearamide-pepsin. Results showed that the inhibitory effect of stearic acid on trypsin is a reversible mixed inhibition, whereas the inhibitory effects of stearic acid and stearamide on pepsin are non-competitive. In all three systems, ΔH < 0, ΔS < 0, and ΔG < 0, indicating the binding process between the migrant and the protease is a spontaneous exothermic process primarily driven by hydrogen bonding and van der Waals forces. In addition, their binding constants are all around 104 L/moL, indicating that there are moderate binding affinities exist between migrants and proteases. The binding process results in the quenching of the protease's endogenous fluorescence and induces alterations in the enzyme's secondary structure. Synchronized fluorescence spectroscopy showed that stearic acid enhanced the hydrophobicity near the Tyr residue of trypsin. The molecular docking results indicated that the binding affinity of stearic acid-trypsin, stearic acid-pepsin, and stearamide-pepsin was -22.51 kJ/mol, -12.35 kJ/mol, -19.28 kJ/mol respectively, which consistent with the trend in the enzyme activity results. This study can provide references for the selection of milk packaging materials and the use of processing additives, ensuring food health and safety.

Binding interactions of Vildagliptin with pepsin: A multi-spectroscopic and in-silico approach and a comparative account with metformin

Vildagliptin (VDG) and Metformin (Met) belong to a class of dipeptidylpeptidase-4 (DPP-4) inhibitor and biguanide, respectively and used for the management of diabetes mellitus type II (DMTII). Both the drugs are orally available which leads to various side effects due to its oral ingestion. Occurrence of these side effects might be due to some interactions with pepsin at a molecular level. Therefore, in order to investigate these interactions, multi-spectroscopic and in-silico techniques have been extensively studied to identify the binding characteristics of VDG with pepsin. Fluorescence data suggested that the quenching is due to dynamic and static mechanism and static was dominant one. However, fluorescence and UV-Vis spectroscopic measurement analysis suggested that VDG tends to associate with pepsin, via ground-state complex formation. Fluorescence study revealed the binding-constant value which was found to be 0.559 × 103 M-1 at 298.15 K that is non-covalent in nature. VDG-pepsin complex shows exothermic and spontaneous binding as confirmed by the calculated values of ΔH, ΔS, and ΔG, are majorly caused by van der Waals forces and H-bonding interactions. CD spectra of pepsin in presence of VDG confirmed post binding conformational change. Enzyme-activity assay showed that activity of pepsin was decreased by upto 28 %. FRET analysis suggested that energy transfer efficiency is negligible for VDG-pepsin interaction. In-silico analysis reveals that H-bonding and electrostatic negative forces are the significant driving forces involved in the interaction of VDG and pepsin.

Perception of the interaction behavior between pepsin and the antimicrobial drug secnidazole with combined experimental spectroscopy and computer-aided techniques

Drug-pepsin interaction possibly affects pepsin activity, leads to undesirable shift of its functionality, and likely induces adverse effects in the gastrointestinal tract. The present study aims at exploring the interaction of pepsin with the antiprotozoal/antibacterial drug secnidazole adopting a combination of experimental spectroscopy and computational techniques. For this purpose, different spectroscopic methods including fluorescence, synchronous fluorescence, UV-Visible absorption, and infrared spectroscopy were adopted and coordinated with in silico analysis via molecular docking. The employed synchronized approaches evidenced that; pepsin interacted with secnidazole via static mechanism at stomach pH inferring some consequent conformational changes in the structure of pepsin. Thermodynamic study of drug-pepsin interaction demonstrated that the interaction is spontaneous via van der Waals and hydrogen bonding interaction and the orientation of ligand within pepsin cavity was illustrated by molecular docking. The synchronous fluorescence study proved that tyrosine amino acid residues were involved in the interaction more than tryptophan amino acid residues. Eventually, the combined experimental and molecular docking approaches suggest that secnidazole interacts with pepsin and alter its structure, that finding correlates to gastrointestinal side effects related to secnidazole oral administration.

Process and mechanism between water-extracted organic matter and trace metallic ions in sediments of Yangtze River estuary

In order to better understand the bioavailability, toxicity, migration and transformation behaviors of trace metals in river estuary, this study deeply investigated the interactions between organic matters in sediments and trace metals. The results suggested that both protein-like molecules and marine humic acids could react with trace metals (Cu²⁺ and Cd²⁺). These two fluorescent substances fixed trace metals through carboxyl group, hydroxyl group, and phenol hydroxyl group, and protein-like molecules were more sensitive than marine humic acids. Moreover, Cu²⁺ possessed stronger binding ability and more active sites with both protein-like molecules and marine humic acids. Hence, Cd²⁺ exhibited higher environmental risks due to the higher migration and transformation. The thermodynamic results revealed that the reaction between WEOM and trace metals was spontaneous and exothermic, and low temperature was favorable for immobilization of Cu²⁺ or Cd²⁺.This study could help to understand environmental behaviors and impact of trace metals on the sediments of Yangtze River estuary.

Polysaccharides from mulberry (Morus alba L.) leaf prevents obesity by inhibiting pancreatic lipase in high-fat diet induced mice

Pancreatic lipase (PL) is a key enzyme related to the prevention and treatment of obesity. The aim of the study was to evaluate the inhibitory effects of mulberry leaf polysaccharides (MLP) on PL and possible interaction mechanism, inhibition on lipid accumulation in vitro and in vivo. The results revealed that MLP had obvious inhibitory effects on PL (P < 0.05). The interaction of MLP-PL complexes was in a spontaneous way driven by enthalpy, and hydrogen bonds were the main factors in the binding. MLP could significantly inhibit the development of lipid accumulation in HepG2 cells (P < 0.05). Furthermore, consumption of high-fat diet containing MLP showed protective effects on liver and adipose tissue damages in mice, and inhibited the lipid absorption in digestive tract. MLP also significantly reduced the increased expression level of pancreatic digestive enzymes (P < 0.05). The study indicated that the anti-obesity effect of MLP might be caused by inhibition of lipid absorption via reducing PL activity.

Insight into the role of extracellular polymeric substances in denitrifying biofilms under nitrobenzene exposure

Denitrifying biofilm promises to be very useful for remediation of nitro-aromatic compounds (NACs) and nitrates in wastewater. Little is known about the role of extracellular polymeric substances (EPS) in nitrobenzene (NB, a typical NAC) remediation, despite the indispensability of EPS for biofilm formation. Herein, the significance of the mechanistic role of EPS in the response of denitrifying biofilms to various levels of NB was investigated. The removal of NB was predominantly controlled via absorption, with little biodegradation during the short-term exposure. Specifically, NB was adsorbed by EPS, as shown by a total adsorption of 40.06% at the initial step, which declined to around 10.52% in the equilibrium stage, while sorption via cells gradually increased from 59.93% to 89.47% over the same period. The results suggested that EPS might act as an important reservoir for NB, which endows inner cells with increased adsorption ability. The presence of EPS might also alleviate the negative impacts of NB toxicity on inner cells, thus protecting microorganisms. This was indicated by the difference in denitrification performance and cell integrity between intact and EPS-free biofilms. High-throughput sequencing data demonstrated that EPS could maintain the stability of microbial communities under NB stress. The fluorescence quenching analysis further indicated that EPS formed stable complexes with NB mainly through hydrophobic interactions with protein-like fractions (tryptophan and tyrosine). Moreover, Fourier transform infrared spectroscopy identified that the hydroxyl, amino, carboxyl, and phosphate groups of EPS were the candidate functional groups binding with NB. Protein secondary structures were also significantly affected, resulting in a loose structure and enhanced hydrophobic performance for EPS. These results provide insights into the role of EPS in alleviating NB-caused cellular stress and the underlying binding mechanisms between NB and EPS.

Using FDA-approved drugs as off-label fluorescent dyes for optical biopsies: from in silico design toex vivoproof-of-concept

Optical biopsies bring the microscope to the patient rather than the tissue to the microscope, and may complement or replace the tissue-harvesting component of the traditional biopsy process with its associated risks. In general, optical biopsies are limited by the lack of endogenous tissue contrast and the small number of clinically approvedin vivodyes. This study tests multiple FDA-approved drugs that have structural similarity to research dyes as off-labelin situfluorescent alternatives to standardex vivohematoxylin & eosin tissue stain. Numerous drug-dye combinations shown here may facilitate relatively safe and fastin situor possiblyin vivostaining of tissue, enabling real-time optical biopsies and other advanced microscopy technologies, which have implications for the speed and performance of tissue- and cellular-level diagnostics.

Multi-spectral techniques and molecular docking to investigation of the interaction between ferulic acid and pepsin

In this work, the interaction between ferulic acid (FA) and pepsin was explored by UV-visible absorption spectroscopy, fluorescence spectroscopy, synchronous fluorescence, circular dichroism (CD) spectroscopy, Fourier transform infrared spectroscopy (FT-IR) and molecular docking. The results of fluorescence revealed that FA had a strong ability to quench the intrinsic fluorescence of pepsin through a static quenching procedure. The binding constant and the number of binding sites were determined. Thermodynamic dates and docking information suggest that FA combine with pepsin is mainly driven via electrostatic force. It also requires synergistic drive of hydrophobic and hydrogen bonding. The consequences from UV-Vis, synchronous, CD and FT-IR spectra measurements manifested that the secondary structure of pepsin was changed and the microenvironments of certain amino acid residues was modulated by the binding of FA. FA induced conformational changes in pepsin. The β-sheet, α-Helix, and Random fractions of pepsin increased and the β-turn decreased with the treatment of FA. In addition, analysis of pepsin activity assay measurements confirmed that FA reduced enzymatic activity of pepsin within the investigated concentrations. This work studied the inhibitory effects and revealed mechanisms of the interaction between FA and pepsin in vitro, and suggested that FA could be a potential component to affect the structure and properties of digestive enzyme.

Understanding of the mechanism of extracellular polymeric substances of aerobic granular sludge against tetracycline from the perspective of fluorescence properties

Aerobic granular sludge (AGS) exhibited an excellent removal efficiency and a high tolerance in the treatment of antibiotics wastewater. Extracellular polymeric substances (EPS) of AGS with abundant binding sites might serve as the first barrier to prevent the direct contact of antibiotics and cells, thereby keeping the stability of AGS. In this study, the investigations in the fluorescence properties and the molecular weight of AGS-EPS after interaction with tetracycline (TC) were combined to reveal the resistance mechanism of AGS-EPS against TC. The two-dimensional correlation spectroscopy (2D-COS) was utilized to analyze the interaction priority of the AGS-EPS components with TC. Results showed that TC interacted with proteins and humic acid in AGS-EPS by forming a complex through hydrogen bond and van der Waals force. Compared with humic acid, TC could preferentially interact with proteins and form more stable complexes. Moreover, the components with the larger molecular weight in AGS-EPS interact with TC prior to which with smaller molecular weight. Significantly, TC exhibited the potential of binding with the divalent cation of AGS-EPS and caused the conformation changes of the protein. Therefore, AGS-EPS could resist the TC at a certain concentration range by trapping antibiotics, while over-loaded TC would cause the instability of AGS due to the limited interaction site of AGS-EPS and the destructive effect of antibiotics on AGS-EPS. This study provided a theoretical basis for understanding the interaction mechanism between antibiotics and AGS-EPS and offered a reference for AGS to maintain the stability of granules under the threat of antibiotics.

Cholesterol-lowering drugs the simvastatin and atorvastatin change the protease activity of pepsin: An experimental and computational study

In this study, the effect of long-term use drugs of cholesterol-lowering atorvastatin and simvastatin on the activity and molecular structure of pepsin as important gastric enzyme was investigated by various experimental and computational methods. Based on the results obtained from fluorescence experiments, both drugs can bond to pepsin and quench the fluorescence intensity of protein through the static quenching mechanism. Also analysis of the thermodynamic parameters of binding the drugs to pepsin showed that the main forces in the complex formation for both are hydrophobic interactions and van der Waals forces. The effects of the drugs on the enzymatic activity of pepsin were then investigated and results showed that in the presence of both drugs the catalytic activity of the enzyme was significantly increased in lower (0.3-0.6 mM) concentrations however about the atorvastatin, increasing the concentration (0.9 mM) decreased the protease activity of pepsin. Also as a result of the FTIR studies, it was found that binding of the drugs to protein did not significant alteration in the structure of the protein. In order to obtain the atomic details of drug-protein interactions, the computational calculations were performed. The results in good agreement with those obtained from the experimental for interaction; confirm that the drugs both are bind to a cleft near the active site of the protein without any change in the structure of pepsin. Overall from the results obtained in this study, it can be concluded that both simvastatin and atorvastatin can strongly bond to a location close to the active site of pepsin and the binding change the enzymatic activity of protein.

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.

Molecular mechanism of the interaction between resveratrol and trypsin via spectroscopy and molecular docking

Mechanism of the interaction between resveratrol and trypsin and its effect on their biological activity.