The binding mechanism between cyclodextrins and pullulanase: A molecular docking, isothermal titration calorimetry, circular dichroism and fluorescence study

Two novel phosvitin peptides FGTEPDAK and IWGR: The dual effects and associated mechanisms for inhibiting α-amylase and alleviating insulin resistance in IR-HepG2 cells

Foodborne peptides have garnered significant attention for their potential in the intervention of type 2 diabetes mellitus (T2DM) through inhibition of α-amylase activity or alleviation of insulin resistance (IR). However, the poorly understood mechanisms constrain further advancement. This study aims to investigate the dual effects and potential mechanisms of Phe-Gly-Thr-Glu-Pro-Asp-Ala-Lys (FGTEPDAK) and Ile-Trp-Gly-Arg (IWGR) on α-amylase activity inhibition and IR alleviation. FGTEPDAK and IWGR were non-competitive inhibitors of α-amylase and bound to the non-active site of α-amylase through hydrogen bonding and hydrophobic interactions, resulting in the secondary structure transition and ultimately inhibited its activity. Furthermore, FGTEPDAK and IWGR improved glucose consumption by 57 % and 48 %, respectively, while also promoting glycogen synthesis by 53 % and 34 %, thus effectively alleviating IR in IR-HepG2 cells. FGTEPDAK and IWGR could strongly bind to their corresponding key targets to regulate the PI3K-AKT signaling pathway, and FGTEPDAK had a better regulate effect than IWGR.

Molecular and technical aspects on the interaction of bovine serum albumin with pyrazine derivatives: From molecular docking to spectroscopy study

In order to better understand the transport and action mechanism of flavor substance and proteins in human body, the interaction mechanism between pyrazine derivatives and bovine serum albumin (BSA) was studied by molecular dynamics simulation and a series of spectroscopic methods. In molecular docking, it was observed that the small molecules were surrounded by hydrophobic amino acid residues of the protein, and the main amino acid residues formed π-π interaction and hydrogen bond interaction with BSA. The results of fluorescence emission spectroscopy combined with thermodynamic analysis showed that static quenching was the main mechanism of the interaction between three pyrazine derivatives and BSA, which was dominated by hydrophobic interaction. Synchronous fluorescence spectroscopy and three-dimensional fluorescence spectroscopy combined with molecular dynamics simulation proved that the pyrazine derivatives changed the conformation of BSA. In summary, pyrazine derivatives can interact with BSA, and the complexation of the complex changes its spatial conformation. The research in this paper has positive significance for understanding the binding, transport, and metabolism of pyrazine compounds in the process of blood circulation and provides key data for the metabolism of pyrazine compounds in vivo. PRACTICAL APPLICATION: The interaction of pyrazine derivatives-BSA is studied by multi-spectra and MD. The fluorescence quenching of pyrazine derivatives-BSA is static quenching. The main force between pyrazine derivatives and BSA is hydrophobic force. There is only one site of association between pyrazine derivatives and BSA. Pyrazine derivatives have effects on conformation of BSA.

Inhibition of Human Colorectal Cancer by a Natural Product 7-Acetylhorminone and Interactions with BSA/HSA: Multispectral Analysis and In Silico and In Vitro Studies

We have semi-synthesized a natural product 7-acetylhorminone from crude extract of Premna obtusifolia (Indian headache tree), which is active against colorectal cancer after probation through computational screening methods as it passed through the set parameters of pharmacokinetics (most important nonblood-brain barrier permeant) and drug likeliness (e.g., Lipinski's, Ghose's, Veber's rule) which most other phytoconstituents failed to pass combined with docking with EGFR protein which is highly upregulated in the colorectal carcinoma cell. The structure of 7-acetylhorminone was confirmed by single crystal X-ray diffraction studies and 1H NMR, 13C NMR, and COSY studies. To validate the theoretical studies, first, in vitro experiments were carried out against human colorectal carcinoma cell lines (HCT116) which revealed the potent cytotoxic efficacy of 7-acetylhorminone and verified preliminary investigation. Second, the drugability of 7-acetylhorminone interaction with serum albumin proteins (HSA and BSA) is evaluated both theoretically and experimentally via steady-state fluorescence spectroscopic studies, circular dichroism, isothermal titration calorimetry, and molecular docking. In summary, this study reveals the applicability of 7-acetylhorminone as a potent drug candidate or as a combinatorial drug against colorectal cancer.

Progress in cyclodextrins as important molecules regulating catalytic processes of glycoside hydrolases

Cyclodextrins (CDs) are important starch derivatives and commonly comprise α-, β-, and γ-CDs. Their hydrophilic surface and hydrophobic inner cavity enable regulation of enzyme catalysis through direct or indirect interactions. Clarifying interactions between CDs and enzyme is of great value for enzyme screening, mechanism exploration, regulation of catalysis, and applications. We summarize the interactions between CDs and glycoside hydrolases (GHs) according to two aspects: 1) CD as products, substrates, inhibitors and activators of enzymes, directly affecting the reaction process; 2) CDs indirectly affecting the enzymatic reaction by solubilizing substrates, relieving substrate/product inhibition, increasing recombinant enzyme production and storage stability, isolating and purifying enzymes, and serving as ligands in crystal structure to identify functional amino acid residues. Additionally, CD enzyme mimetics are developed and used as catalysts in traditional artificial enzymes as well as nanozymes, making the application of CDs no longer limited to GHs. This review concerns the regulation of GHs catalysis by CDs, and gives insights into research on interactions between enzymes and ligands.

The inhibition mechanism of bound polyphenols extracted from mung bean coat dietary fiber on porcine pancreatic α-amylase: kinetic, spectroscopic, differential scanning calorimetric and molecular docking

The inhibitory mechanisms of purified bound polyphenols extracted from mung bean coat dietary fiber (pMBDF-BP) on porcine pancreatic α-amylase (PPA) were investigated through inhibition kinetics, fluorescence spectroscopy, circular dichroism, differential scanning calorimetry and molecular docking. It was shown that pMBDF-BP exerted significant reversible inhibition on PPA in a mixed-type inhibition manner (IC50 = 18.57 ± 0.30 μg/mL), and the combination of the three major components exhibited a synergistic inhibitory effect on PPA. Further, pMBDF-BP bound to the active site or form a polyphenol-enzyme complex at the inactive site through hydrogen bonding and hydrophobic forces, via enhancing the hydrophobicity of the microenvironment surrounding tryptophan and tyrosine residues and promoting the secondary structure of PPA towards a more stable conformation, eventually reducing the enzyme activity. This study provided theoretical evidences for the utilization of bound polyphenols extracted from mung bean coat dietary fiber as a functional component in natural inhibitors of α-amylase.

Construction of the Gal-NH2/mulberry leaf polysaccharides-lysozyme/luteolin nanoparticles and the amelioration effects on lipid accumulation

Luteolin is a kind of natural flavonoid with great potential for lipid accumulation intervention. However, the poor water solubility and non-targeted release greatly diminish its efficiency. In this study, 4-aminophenyl β-D-galactopyranoside (Gal-NH2)/mulberry leaf polysaccharides- lysozyme/luteolin nanoparticles (Gal-MPL/Lut) were fabricated via amide reaction, self-assembly process and electrostatic interaction. The nanoparticles could hepatic-target of Lut and enhance action on liver tissue by specific recognition of asialoglycoprotein receptor (ASGPR). Physicochemical characterization of the nanoparticles showed a spherical shape with a uniform particle size distribution (77.8 ± 2.6 nm) with a polydispersity index (PDI) of 0.22 ± 0.06. Subsequently, in HepG2 cells model, administration with hepatic-targeted Gal-MPL/Lut nanoparticles promoted the cellular uptake of Lut, and regulated lipid metabolism manifested by remarkably inhibiting total cholesterol (TC) and triglyceride (TG) expression levels through the modulation of PI3K/SIRT-1/FAS/CEBP-α signaling pathway. This study provides a promising strategy for a highly hepatic-targeted therapy to ameliorate lipid accumulation using natural medicines facilitated by nano-technology.

Synergistic antifungal mechanism of effective components from essential oil against Penicillium roqueforti

Essential oil (EO) has significant antifungal activity. However, there is limited information on the mechanism of the synergistic antifungal effect of the effective components of EO against fungi. In the present study, molecular electrostatic potential and molecular docking were used for the first time to investigate the synergistic antifungal mechanism of eugenol and citral small molecule (CEC) against Penicillium roqueforti. The results showed that the CEC treatment made the activity of β-(1,3)-glucan synthase (GS) and chitin synthase (CS) decreas by 20.2% and 11.1%, respectively, and the contents of which decreased by 85.0% and 27.9%, respectively compared with the control group. Molecular docking revealed that CEC small molecules could bind to GS and CS through different amino acid residues, inhibiting their activity and synthesis. The CEC can combine with tryptophan, tyrosine, and phenylalanine in the cell membrane, causing damage to the cell membrane. The binding sites between small molecules and amino acids were mainly around the OH group. In addition, CEC affected the energy metabolism system and inhibited the glycolysis pathway. Simultaneously, CEC treatment reduced the ergosterol content in the cell membrane by 58.2% compared with the control group. Finally, changes in β-galactosidase, metal ion leakage, and relative conductivity confirmed the destruction of the cell membrane, which resulted in the leakage of cell contents. The above results showed that CEC can kill P. roqueforti by inhibiting energy metabolism and destroying the integrity of the cell membrane.

In Vitro Inhibitory Effects of Polyphenols from Flos sophorae immaturus on α-Glucosidase: Action Mechanism, Isothermal Titration Calorimetry and Molecular Docking Analysis

Flos sophorae immaturus (FSI) is considered to be a natural hypoglycemic product with the potential for a-glucosidase inhibitory activity. In this work, the polyphenols with α-glucosidase inhibition in FSI were identified, and then their potential mechanisms were investigated by omission assay, interaction, type of inhibition, fluorescence spectroscopy, circular dichroism, isothermal titration calorimetry and molecular docking analysis. The results showed that five polyphenols, namely rutin, quercetin, hyperoside, quercitrin and kaempferol, were identified as a-glucosidase inhibitors with IC₅₀ values of 57, 0.21, 12.77, 25.37 and 0.55 mg/mL, respectively. Quercetin plays a considerable a-glucosidase inhibition role in FSI. Furthermore, the combination of quercetin with kaempferol generated a subadditive effect, and the combination of quercetin with rutin, hyperoside and quercitrin exhibited an interference effect. The results of inhibition kinetics, fluorescence spectroscopy, isothermal titration calorimetry and molecular docking analysis showed that the five polyphenols were mixed inhibitors and significantly burst the fluorescence intensity of α-glucosidase. Moreover, the isothermal titration calorimetry and molecular docking analysis showed that the binding to α-glucosidase was a spontaneous heat-trapping process, with hydrophobic interactions and hydrogen bonding being the key drivers. In general, rutin, quercetin, hyperoside, quercitrin and kaempferol in FSI are potential α-glucosidase inhibitors.

Cyclodextrins: Only Pharmaceutical Excipients or Full-Fledged Drug Candidates?

Cyclodextrins, representing a versatile family of cyclic oligosaccharides, have extensive pharmaceutical applications due to their unique truncated cone-shaped structure with a hydrophilic outer surface and a hydrophobic cavity, which enables them to form non-covalent host-guest inclusion complexes in pharmaceutical formulations to enhance the solubility, stability and bioavailability of numerous drug molecules. As a result, cyclodextrins are mostly considered as inert carriers during their medical application, while their ability to interact not only with small molecules but also with lipids and proteins is largely neglected. By forming inclusion complexes with cholesterol, cyclodextrins deplete cholesterol from cellular membranes and thereby influence protein function indirectly through alterations in biophysical properties and lateral heterogeneity of bilayers. In this review, we summarize the general chemical principles of direct cyclodextrin-protein interactions and highlight, through relevant examples, how these interactions can modify protein functions in vivo, which, despite their huge potential, have been completely unexploited in therapy so far. Finally, we give a brief overview of disorders such as Niemann-Pick type C disease, atherosclerosis, Alzheimer's and Parkinson's disease, in which cyclodextrins already have or could have the potential to be active therapeutic agents due to their cholesterol-complexing or direct protein-targeting properties.

Fabrication and Characterization of Antifungal Hydroxypropyl-β-Cyclodextrin/Pyrimethanil Inclusion Compound Nanofibers Based on Electrospinning

Pyrimethanil (PMT) is an anilinopyrimidine bactericide with poor water solubility, which limits its applications. To improve the physical and chemical properties of PMT, hydroxypropyl-β-cyclodextrin/pyrimethanil inclusion compound nanofibers (HPβCD/PMT-IC-NFs) were fabricated via electrospinning. A variety of analytical techniques were used to confirm the formation of the inclusion compound. Scanning electron microscopy image displayed that HPβCD/PMT-IC-NF was homogeneous without particles. Thermogravimetric analysis indicated that the formation of the inclusion compound improved the thermostability of PMT. In addition, the phase solubility test illustrated that the inclusion compound formed by PMT and HPβCD had a stronger water solubility. The antifungal effect test exhibited that HPβCD/PMT-IC-NF had better antifungal properties. The release experiment confirmed that HPβCD/PMT-IC-NF had a sustained-release effect, and the release curve conformed to the first-order kinetic model equation. In short, the fabrication HPβCD/PMT-IC-NF inhibited improved solubility and thermostability of PMT, thus promoting the development of pesticide dosage form to water-based and low-pollution direction.

Formation of protein corona on interaction of pepsin with chitin nanowhiskers in simulated gastric fluid

Protein corona (PC) usually changes the physicochemical properties of nanoparticles (NPs) and determines their ultimate fate in the physiological environment. As NPs are widely used in food, it is important to obtain a deep understanding of PC formation in the gastrointestinal fluid. Herein, we explored the adsorption of pepsin to chitin nanowhiskers (CNWs) and their interactions in simulated gastric fluid. Results suggest that the binding of pepsin reduced the surface potential of CNWs from 22.4 ± 0.15 to 12.9 ± 0.51 mV and caused their aggregation. CNWs quenched the fluorescence of pepsin and induced slightly changes in its secondary structure containing a reduction in the β-sheet content (∼ 3%) and an increase in the random coils (∼ 2%). The isothermal titration calorimetry (ITC) data suggested that the interaction forces between CNWs and pepsin were mainly hydrogen bonds and van der Waals forces.

Application of molecular docking in elaborating molecular mechanisms and interactions of supramolecular cyclodextrin

The cyclodextrin (CD)-based supramolecular nanomedicines have attracted growing interest because of their superior characteristics, including desirable biocompatibility, low toxicity, unique molecular structure and easy functionalization. The smart structures of CD impart host-guest interaction for meeting the multifunctional needs of disease therapy. However, it faces challenges in formulation design and inclusion mechanism clarification of the functional supramolecular assemblies owing to the complicated structures and mechanisms. Fortunately, molecular docking helps the researchers to comprehend the interaction between the drug and the target molecule for achieving high-through screening from the database. In this review, we summarized the category and characteristics of molecular docking along with the properties and applications of CD. Significantly, we highlighted the application of molecular docking in elaborating molecular mechanisms and simulating complex structures at molecular levels. The issues and development of CD and molecular docking were also presented to provide beneficial reference and new insights for supramolecular nano-systems.

Inhibitory effects of phenolic glycosides from Trollius chinensis Bunge on α-glucosidase: inhibition kinetics and mechanism

Two undescribed phenolic glycosides, trochinenols B-C (1-2), together with four known analogues (3-6), were isolated from the functional tea Trollius chinensis Bunge and their α-glucosidase inhibitory kinetics and mechanism were...

Microbial starch debranching enzymes: Developments and applications

Starch debranching enzymes (SDBEs) hydrolyze the α-1,6 glycosidic bonds in polysaccharides such as starch, amylopectin, pullulan and glycogen. SDBEs are also important enzymes for the preparation of sugar syrup, resistant starch and cyclodextrin. As the synergistic catalysis of SDBEs and other starch-acting hydrolases can effectively improve the raw material utilization and production efficiency during starch processing steps such as saccharification and modification, they have attracted substantial research interest in the past decades. The substrate specificities of the two major members of SDBEs, pullulanases and isoamylases, are quite different. Pullulanases generally require at least two α-1,4 linked glucose units existing on both sugar chains linked by the α-1,6 bond, while isoamylases require at least three units of α-1,4 linked glucose. SDBEs mainly belong to glycoside hydrolase (GH) family 13 and 57. Except for GH57 type II pullulanse, GH13 pullulanases and isoamylases share plenty of similarities in sequence and structure of the core catalytic domains. However, the N-terminal domains, which might be one of the determinants contributing to the substrate binding of SDBEs, are distinct in different enzymes. In order to overcome the current defects of SDBEs in catalytic efficiency, thermostability and expression level, great efforts have been made to develop effective enzyme engineering and fermentation strategies. Herein, the diverse biochemical properties and distinct features in the sequence and structure of pullulanase and isoamylase from different sources are summarized. Up-to-date developments in the enzyme engineering, heterologous production and industrial applications of SDBEs is also reviewed. Finally, research perspective which could help understanding and broadening the applications of SDBEs are provided.

Formononetin/methyl-β-cyclodextrin inclusion complex incorporated into electrospun polyvinyl-alcohol nanofibers: Enhanced water solubility and oral fast-dissolving property

Improving solubility and administration route of isoflavone formononetin (FMN) are critical factors to improve its bioavailability in the oral cavity. This study fabricated fast-dissolving nanofibers containing FMN/methyl-β-cyclodextrin (FMN/Me-β-CD) inclusion complex. The solubility of FMN could be increased by approximately 50 times at 20 mM aqueous Me-β-CD. Interactions and thermodynamic parameters of the host-guest inclusion complex were studied by a fluorescence quenching method. The structure and mechanisms of the complex were further studied by molecular docking and molecular dynamics. Finally, polyvinyl-alcohol (PVA) nanofibrous webs containing the FMN/Me-β-CD inclusion complex were fabricated by electrospinning. The dissolution test demonstrated that the FMN/Me-β-CD/PVA nanofibers can be dissolved in artificial saliva within approximately 2 s. This study shows the potential of Me-β-CD inclusion and electrospinning to improve solubility and administration route of isoflavones.

Transformation of fluopyram during enzymatic hydrolysis of apple and its effect on polygalacturonase and apple juice yield

China is one of the largest apple-growing areas in the world. Fluopyram (FLP) is a novel pesticide that has been widely used in agriculture. This work investigated the behavior of pesticides during enzymatic hydrolysis of apple juice and its effect on polygalacturonase (PG), apple juice yield, and flavor. The study findings revealed that 27.5% to 34.2% FLP was degraded during the enzymatic hydrolysis of apple. The three degradation products (P1, P2, and P3) were identified by a hybrid ion trap-orbitrap mass spectrometer. Based on toxicity assessment, it was found that carcinogenicity was higher for P2 and P3 than for FLP. Furthermore, FLP affected the yield and flavor of apple juice. FLP reduced yield by 4.8%, because FLP inhibited the activity of PG. Through molecular docking, it was found that there was an interaction between the active center of PG and FLP, resulting in a reduction in catalytic ability.

Investigation of the transformation and toxicity of trichlorfon at the molecular level during enzymic hydrolysis of apple juice

Trichlorfon is one of the most widely used organophosphorus pesticides in agriculture. In this study, the extent of transformation of trichlorfon to dichlorvos (DDVP), during the polygalacturonase (PG) treatment of apple pulp was monitored. A transformation pathway is proposed for trichlorfon molecules, based on density functional theory (DFT) calculations. The transformation of trichlorfon involves hydroxyl substitution and cleavage, which was confirmed by molecular electrostatic potential (MEP) and frontier molecular orbital (FMO) theory. In addition, the toxicity of trichlorfon and its transformed products was analyzed using Ecological Structure Activity Relationships (ECOSAR) software. The binding sites of the two pesticides are located in the hydrophobic grooves of the acetylcholinesterase (AChE) active site region and both pesticides form hydrophobic interactions and hydrogen bonds with a large number of surrounding amino acid residues. DDVP binds more strongly with AChE, so it is a better AChE inhibitor and more toxic than trichlorfon.

Development of pullulanase mutants to enhance starch substrate utilization for efficient production of β-CD

The inhibitory effect of β-CD on pullulanase which hydrolyzes α-1,6 glycosidic bond in starch to release more available linear substrates, limited substrate utilization thus influencing the yield of β-CD. Here, an aspartic acid residue (D465) which interacted with cyclodextrin ligand by hydrogen bond, was mutated to explore its contribution to bind inhibitors and obtain mutants with lower affinity to β-CD. Enzyme activity results showed that mutants D465E and D465N retained higher activity than wild-type pullulanase in presence of 10 mM β-CD. Circular dichroism spectra and fluorescence spectra results showed that D465 was related to structure stability. Chain length distribution results confirmed the improvement of substrate utilization by the addition of D465E. The conversion rate from potato starch, cassava starch, and corn starch into β-CD, increased to 56.9%, 55.4% and 54.7%, respectively, when synchronous using β-CGTase and D465E in the production process.