Optimal Binding Site Research Articles

Network pharmacology and in vivo experiment-based strategy for investigating the mechanism of chronic prostatitis/chronic pelvic pain syndrome in QianLieJinDan tablets

BackgroundChronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a common urinary system disease that is prone to recurrence. It typically leads to varying degrees of pelvic pain and discomfort, as well as symptoms related to the urinary system in affected patients. QianLieJinDan tablets (QLJD), a traditional Chinese medicine, have shown promising therapeutic effects on CP/CPPS in clinical practice, but the underlying mechanisms of QLJD in treating CP/CPPS have not been determined. ObjectiveTo reveal the phytochemical characterization and multitarget mechanism of QLJD on CP/CPPS. MethodsThe concentrations of the components of QLJD were determined using UHPLC-Q Exactive Orbitrap-MS. Utilizing network pharmacology approaches, the potential components, targets, and pathways involved in the treatment of CP/CPPS caused by QLJD were screened. Molecular docking calculations were employed to assess the affinity between the components of the QLJD and potential targets, revealing the optimal molecular conformation and binding site. Finally, the therapeutic efficacy and potential underlying mechanisms of QLJD were investigated through pharmacological experiments. ResultsIn this study, a total of 35 components targeting 29 CP-related genes were identified, among which quercetin, baicalin, icariin, luteolin, and gallic acid were the major constituents. Enrichment analysis revealed that the potential targets were involved mainly in the regulation of cytokines, cell proliferation and apoptosis, and the oxidative stress response and were primarily associated with the cytokine‒cytokine receptor interaction pathway, the IL-17 signaling pathway, the Th17 cell differentiation pathway, and the JAK-STAT signaling pathway. In vivo experiments demonstrated that QLJD effectively attenuated the infiltration of CD3+ T cells and the expression of ROS in a CP/CPPS model rat prostate tissue. Furthermore, through the inhibition of IL-6 and STAT3 expression, QLJD reduced the differentiation of Th17 cells, thereby ameliorating pathological injury and prostatic index in prostate tissue. ConclusionThe potential of QLJD as an anti-CP/CPPS agent lies in its ability to interfere with the expression of IL-6 and STAT3, inhibit Th17 cell differentiation, reduce inflammatory cell infiltration in rat prostate tissue, and alleviate oxidative stress damage through its multi-component, multi-target, and multi-pathway effects.

Construction of ligand functionalized MIL-101(Fe)-R and mechanism of efficient removal of chlortetracycline hydrochloride: Experiment and DFT calculation

Functionalization of ligands is an effective strategy to enhance the adsorption performance of adsorbents. In this study, MIL-101(Fe)-R (R = -H, –OH, –NH2, and –NO2) was selected as a platform for systematically studying the impact of functionalization on the adsorption behavior of chlortetracycline (CTC). A series of characterizations were conducted on the prepared MIL-101(Fe)-R to clarify the influence of organic linkers on the microscopic morphology, pore structure, and surface functionality of the adsorbents. Additionally, the effects of different functional groups on the adsorption behavior of MIL-101(Fe)-R were compared to screen for MOFs with high efficiency in removing CTC. Experimental results showed that the maximum adsorption capacities (qm) of MIL-101(Fe), MIL-101(Fe)–NH2, MIL-101(Fe)–OH, and MIL-101(Fe)–NO2 were 418.980 mg/g, 559.854 mg/g, 187.387 mg/g, and 154.131 mg/g, respectively. Among them, MIL-101(Fe)–NH2 exhibited a higher mass transfer rate (reaching equilibrium in 15 min). Based on apparent adsorption behavior, adsorption kinetics, isotherm and thermodynamic studies, as well as FTIR and XPS characterizations before and after adsorption, the performance modulation mechanism of MIL-101(Fe)-R in CTC adsorption was discussed in detail. Combined with density functional theory (DFT) calculations, the host–guest interaction controlling the adsorption behavior was understood at the molecular level, demonstrating the optimal binding sites of the adsorbents. This study provides guidance for the design of efficient MOF adsorbents for antibiotic wastewater treatment.

Insight into the interaction of 5,6 epoxy-cholesterols with human serum albumin

5,6-Epoxy-cholesterols has been recently revealed to control metabolic pathway in breast cancer, which makes investigating their binding interaction with human serum albumin (HSA) an attractive field of research. The main aim of this article is to examine the binding interaction of 5,6 α-epoxy-cholesterol (5,6 α EC) and 5,6 β-epoxy-cholesterol (5,6 β- EC) with HSA using different spectroscopic methods and molecular modeling. These compounds interact with HSA via hydrophobic interactions and hydrogen bonds with binding constants 6.3 × 105 M−1 for 5,6 α-epoxy-cholesterol and 6.9 × 105 M−1 for 5,6 β-epoxy-cholesterol besides, the mechanism of the interaction can be attributed to static quenching. Circular dichroism data indicated that the α-helical content of HSA increased from 50.5 to 59.8 and 61.1 % after the addition of 5,6 α-ECs and 5,6 β-EC, respectively, with a ratio of 1:2. Thermodynamic analysis revealed that binding between 5,6-epoxy-cholesterols and HSA is spontaneous and entropy-driven. The molecular docking and esterase-like activity experiments were performed to envision a link between the experimental and theoretical results. The optimal binding site of 5,6-epoxy-cholesterols with HSA was located in subdomain IIA. Moreover, theoretical calculations were performed using the B3LYP function with the 6-311++G (d,p) basis set, indicating the HOMO-LUMO energy gap of 7.874 eV for 5,6 α-epoxy-cholesterol and 7.873 eV for 5,6 β-epoxy-cholesterol. The obtained findings are assumed to provide basic data for understanding the binding interactions of HSA with oxysterol compounds, which could help explore the pharmacokinetics and pharmacodynamics of oxysterol compounds.

Thermodynamic and functional changes of alpha-chymotrypsin after interaction with gallic acid

In the present study, the interaction mechanism between gallic acid (GA) and α-Chymotrypsin (α-CT) was investigated by employing a series ofspectroscopic methods, computational docking and molecular dynamic (MD) simulation. Fluorescence spectra analysis indicated the formation of a stable complex between GA and α-CT, where the quenching of the fluorescence emission was predominantly characterized by a static mechanism. TheCA obtained binding constants for the α-CT-GA complex were in the order of 103 M−1, indicating the moderate binding affinity of GA for α-CT. The corresponding CD findings showed that the interaction between GA and α-CT resulted in an alteration of the protein's secondary structure. The findings of the enzyme activity investigation clearly showed that the presence of GA led to a notable decline in the enzymatic activity of α-CT, highlighting GA's function as an effective inhibitor for α-CT. The molecular docking simulations revealed the optimal binding site for the GA molecule within the α-CT structure and MD simulations confirmed the stability of the α-CT-GA complex. This research expands our comprehension regarding the behavior of enzymes in the presence of small-molecule ligands and opens avenues for food safety.

Computational study of the mechanism of a polyurethane esterase A (PueA) from Pseudomonas chlororaphis.

The effective management of plastic waste has become a global imperative, given our reliance on a linear model in which plastics are manufactured, used once, and then discarded. This has led to the pervasive accumulation of plastic debris in landfills and environmental contamination. Recognizing this issue, numerous initiatives are underway to address the environmental repercussions associated with plastic disposal. In this study, we investigate the possible molecular mechanism of polyurethane esterase A (PueA), which has been previously identified as responsible for the degradation of a polyester polyurethane (PU) sample in Pseudomonas chlororaphis, as an effort to develop enzymatic biodegradation solutions. After generating the unsolved 3D structure of the protein by AlphaFold2 from its known genome, the enzymatic hydrolysis of the same model PU compound previously used in experiments has been explored employing QM/MM molecular dynamics simulations. This required a preliminary analysis of the 3D structure of the apo-enzyme, identifying the putative active site, and the search for the optimal protein-substrate binding site. Finally, the resulting free energy landscape indicates that wild-type PueA can degrade PU chains, although with low-level activity. The reaction takes place by a characteristic four-step path of the serine hydrolases, involving an acylation followed by a diacylation step. Energetics and structural analysis of the evolution of the active site along the reaction suggests that PueA can be considered a promising protein scaffold for further development to achieve efficient biodegradation of PU.

Icariin alleviates ferroptosis-related atherosclerosis by promoting autophagy in xo-LDL-induced vascular endothelial cell injury and atherosclerotic mice.

Vascular endothelial cells (VECs) are located between the blood plasma and the vascular tissue, and the ferroptosis (iron-dependent programmed cell death) of VECs can lead to a range of cardiovascular diseases. Icariin is the main active ingredient of Epimedium brevicornum Maxim., which can improve endothelial cell dysfunction. In the present study, the protective effects of icariin on oxidised low-density lipoprotein (ox-LDL)-treated VECs and high-fat diet-fed Apolipoprotein E-deficient mice were investigated. Inflammatory fibrosis in tissues and inflammatory factors in serum and cell supernatants were detected, and mitochondrial membrane potential and the expression levels of ferroptosis-associated proteins were also detected. The results revealed that icariin reduced the endothelial atherosclerotic plaque area and collagen fibres in aortic sinus tissue, and increased the viability and mitochondrial membrane potential, whereas it reduced the reactive oxygen species levels of VECs. The nucleation of transcription factor EB (TFEB) and subsequent autophagy were negatively associated with ferroptosis in endothelial cells, and the more prominent the autophagy, the lower the levels of ferroptosis. Furthermore, by co-treating the cells with icariin and the two autophagy inhibitors, Bafilomycin A1 (blocking autophagosome and lysosome fusion) and 3-methyladenine (blocking autophagosome formation), respectively, the promoting effects of icariin on autophagy were found to be mediated through the process of autophagosome-lysosome fusion. In in vivo experiments, icariin reduced ferroptosis, alleviated atherosclerotic lesions and increased the rate of TFEB nucleation. Additionally, it was found that ARG304, THR308 and GLN311 were the optimal binding sites for the interaction between icariin and TFEB. Taken together, these results suggest that the fusion of autophagosomes and lysosomes promoted by icarrin enhances autophagy and thus reduces ferroptosis. Therefore, icariin may be a potential candidate for the prevention of ferroptosis of VECs and, thus, for the treatment of cardiovascular diseases.

Reducing the inherent auto-inhibitory interaction within the pegRNA enhances prime editing efficiency.

Prime editing systems have enabled the incorporation of precise edits within a genome without introducing double strand breaks. Previous studies defined an optimal primer binding site (PBS) length for the pegRNA of ∼13 nucleotides depending on the sequence composition. However, optimal PBS length characterization has been based on prime editing outcomes using plasmid or lentiviral expression systems. In this study, we demonstrate that for prime editor (PE) ribonucleoprotein complexes, the auto-inhibitory interaction between the PBS and the spacer sequence affects pegRNA binding efficiency and target recognition. Destabilizing this auto-inhibitory interaction by reducing the complementarity between the PBS-spacer region enhances prime editing efficiency in multiple prime editing formats. In the case of end-protected pegRNAs, a shorter PBS length with a PBS-target strand melting temperature near 37°C is optimal in mammalian cells. Additionally, a transient cold shock treatment of the cells post PE-pegRNA delivery further increases prime editing outcomes for pegRNAs with optimized PBS lengths. Finally, we show that prime editor ribonucleoprotein complexes programmed with pegRNAs designed using these refined parameters efficiently correct disease-related genetic mutations in patient-derived fibroblasts and efficiently install precise edits in primary human T cells and zebrafish.

Design, Synthesis, and Molecular Docking Study of Novel 3-Cyanopyridine Derivatives for the Anti-Cancer Drug Target Survivin Protein.

Through the optimization of the 3-cyanopyridine, 29 new compounds with a 3- Cyanopyridine structure were designed, synthesized, and characterized by NMR, IR, and mass spectrometry. The antitumor activity of the compounds in vitro was detected by the MTT method. In vitro anti-tumor experiments showed that some compounds exhibited good anti-cancer effects. The IC50 values of the compound 2-amino-6-(2,4-difluorophenyl)-4-(4-hydroxyphenyl) nicotinonitrile (10n) against human liver cancer (Huh7), human glioma (U251), and human melanoma (A375) cells were 5.9, 6.0 and 7.2 μM, respectively. The IC50 values of the compound 6-(2,4-difluorophenyl)- 4-(4-hydroxyphenyl)-2-oxo-1,2-dihydropyridine-3-carbonitrile (9o) against Huh7, U251 and A375 cells were 2.4, 17.5 and 7.2 μM, respectively, which were better than those of 10- hydroxycamptothecin and 5-fluorouracil. Analysis of the results of molecular dynamics simulation established that the BIR domain is the optimal binding site on the survivin protein, and the fingerprints of the eight most active compounds and the molecular docking to the survivin protein are analyzed. 3-Cyanopyridine is an excellent backbone for antitumor lead compounds, 10n and 9o, as derivatives of 3-Cyanopyridine are excellent survivin protein-targeting inhibitors worthy of further study. The key factor in inhibiting survivin protein through the action of amino acid Ile74.

Engineering Plasmon-Enhanced Fluorescent Gold Nanoclusters Using Bovine Serum Albumin as a Novel Separation Layer for Improved Selectivity.

The combination of gold nanoclusters (AuNCs) with surface plasmonic metal nanomaterials is an effective and direct method to improve the photoluminescence efficiency of AuNCs. However, the plasmon-enhanced AuNC luminescence strategies usually utilize silica as the separation layer, which requires further functionalization because the silica layer has no functional groups for in situ bonding of AuNCs. Therefore, it appears as a crucial need to develop an appropriate separation layer for the preparation of plasmon-enhanced AuNC luminescent nanomaterials. In this work, employing bovine serum albumin (BSA) as a novel separation layer, we prepared gold nanoparticles (AuNPs)@BSA@Au35NCs by a controllable and in situ synthesis method. BSA can form a BSA layer on the surface of AuNPs through Au-S bonds. Meanwhile, BSA can reduce AuCl4- ions to generate Au35NCs. In comparison with pure BSA-AuNCs, the quantum yield of the AuNPs@BSA@Au35NCs was increased by nearly 7 times as a result of plasmonic coupling, and the time of in situ synthesis of Au35NCs was shortened by 8 h. More importantly, the preparation of the BSA layer was simple and time-saving without functionalization, in contrast to the previously reported silica layer. Moreover, the simulation calculation of different dimensions determined the optimal binding sites between Au35NCs and BSA, confirming that BSA can be an effective spatial spacer. Finally, it was found that the BSA layer between AuNPs and AuNCs can improve the specificity of AuNCs toward H2S, which is extremely difficult for pure BSA@AuNCs.

Tuning a high performing multiplexed-CRISPRi Pseudomonas putida strain to further enhance indigoidine production

In this study, a 14-gene edited Pseudomonas putida KT2440 strain for heterologous indigoidine production was examined using three distinct omic datasets. Transcriptomic data indicated that CRISPR/dCpf1-interference (CRISPRi) mediated multiplex repression caused global gene expression changes, implying potential undesirable changes in metabolic flux. 13C-metabolic flux analysis (13C-MFA) revealed that the core P. putida flux network after CRISPRi repression was conserved, with moderate reduction of TCA cycle and pyruvate shunt activity along with glyoxylate shunt activation during glucose catabolism. Metabolomic results identified a change in intracellular TCA metabolites and extracellular metabolite secretion profiles (sugars and succinate overflow) in the engineered strains. These omic analyses guided further strain engineering, with a random mutagenesis screen first identifying an optimal ribosome binding site (RBS) for Cpf1 that enabled stronger product-substrate pairing (1.6–fold increase). Then, deletion strains were constructed with excision of the PHA operon (ΔphaAZC-IID) resulting in a 2.2–fold increase in indigoidine titer over the optimized Cpf1-RBS construct at the end of the growth phase (∼6 h). The maximum indigoidine titer (at 72 h) in the ΔphaAZC-IID strain had a 1.5–fold and 1.8–fold increase compared to the optimized Cpf1-RBS construct and the original strain, respectively. Overall, this study demonstrated that integration of omic data types is essential for understanding responses to complex metabolic engineering designs and directly quantified the effect of such modifications on central metabolism.

Spectrophotometric determination of Zr(IV), Hg(II) and U(VI) in solution with their analytical applications: Structural characterization and molecular docking of the solid complexes

Spectrophotometry was used to determine trace amounts of Zirconium(IV), Mercury(II) and Uranium(VI) in environmental, biological, pharmaceutical and industrial samples. The determination depend on the complexation reactions between albendazole reagent and metal ions [Zr(IV), Hg(II) and U(VI)] at 555 nm, 485 nm and 510 nm, respectively. The experimental conditions were explored to reach the optimum conditions for albendazole-metal ions interaction, including detection of a suitable wavelength, medium (pH), reagent concentration, surfactants effect, reaction time and temperature. Under optimum conditions, the complexes displayed apparent molar absorptivities of 0.8350 × 104, 0.6210 × 104 and 0.7012 × 104 L mol−1 cm−1; Sandell’s sensitivity of 0.01092, 0.03230 and 0.03394 µg cm−2 and with linearity ranges of 1.0–120.0, 3.0–200.0 and 1.0–150.0 µg mL−1 for the developed methods, respectively. Furthermore, Elemental analysis, thermal analysis (TGA, DTG), IR, 1HNMR, spectroscopies, electrical molar conductivity and magnetic moment measurements were used to determine the structures and characteristics of the complexes. A careful examination of the IR spectra revealed that the ligand interacted with all of the metal ions described as a bidentate via the oxygen of the carbonyl of the ester moiety and the nitrogen atom of the heterocyclic CN group. An octahedral geometry for Zr(IV), Hg(II) and U(VI) complexes has been postulated based on magnetic and electronic spectrum data. The band gap values indicated that these complexes were semi-conductors and belong to the same class of extremely effective solar materials. The albendazole ligand and its complexes have been biologically tested against a variety of bacterial and fungal strains, and molecular docking studies have been conducted to evaluate the optimal binding site and its inhibitory action.

Indirect mechanism of Au adatom diffusion on the Si(100) surface

Calculations of the diffusion of a Au adatom on the dimer reconstructed Si(100)-2x1 surface reveal an interesting mechanism that differs significantly from a direct path between optimal binding sites, which are located in between dimer rows. Instead, the active diffusion mechanism involves promotion of the adatom to higher energy sites on top of a dimer row and then fast migration along the row, visiting ca. a hundred sites at room temperature, before falling back down into an optimal binding site. This top-of-row mechanism becomes more important the lower the temperature is. The calculations are carried out by finding minimum energy paths on the energy surface obtained from density functional theory within the PBEsol functional approximation followed by kinetic Monte Carlo simulations of the diffusion over a range of temperature from 200 K to 900 K. While the activation energy for the direct diffusion mechanism is calculated to be 0.84 eV, the effective activation energy for the indirect mechanism is on average 0.56 eV.

Electrocatalysts for the Oxygen Reduction Reaction: From Bimetallic Platinum Alloys to Complex Solid Solutions

The oxygen reduction reaction has been the object of intensive research in an attempt to improve the sluggish kinetics that limit the performance of renewable energy storage and utilization systems. Platinum or platinum bimetallic alloys are common choices as the electrode material, but prohibitive costs hamper their use. Complex alloy materials, such as high-entropy alloys (HEAs), or more generally, multiple principal component alloys (MPCAs), have emerged as a material capable of overcoming the limitations of platinum and platinum-based materials. Theoretically, due to the large variety of active sites, this new kind of material offers the opportunity to identify experimentally the optimal binding site on the catalyst surface. This review discusses recent advances in the application of such alloys for the oxygen reduction reaction and existing experimental challenges in the benchmarking of the electrocatalytic properties of these materials.

Potential multiple bioactive components from Sinopodophyllum hexandrum explored by affinity ultrafiltration with four drug targets

Background: Sinopodophyllum hexandrum (S. hexandrum) is a typical Chinese herbal medicine with multiple components and pharmacological activities. However, the specific phytochemicals responsible for its anti-proliferative, anti-inflammatory and anti-viral effects remain unexplored. Purpose: This study aimed to explore the specific bioactive phytochemicals from S. hexandrum responsible for its multiple remarkable pharmacological in an effort to construct and decipher its empirical therapeutic roles. Study design: Bio-affinity ultrafiltration (AUF) with multiple drug targets corresponding to its empirical anti-proliferative, anti-inflammatory and anti-viral activities was developed to screen for potential bioactive ligands from S. hexandrum, and then in vitro bioactivity assays or molecular docking methods were used to verify those bioactive ligands. Methods: The integrative analytical strategy was developed to rapidly screen and identify bioactive ligands from S. hexandrum. The in vitro anti-proliferative, COX-2 and ACE2 inhibitory assays of ligands were further verified by SRB cell proliferation and cytotoxicity detection, COX-2 and ACE2 inhibitor screening kits, respectively. Molecular docking analysis was also implemented by the AutoDockTools 1.5.6 software. Results: Ten, seven, nine and nine phytochemicals were screened out and identified as the potential Topo I, Topo II, COX-2 and ACE2 ligands, respectively. Hereinto, podophyllotoxin and quercetin with higher EF values displayed strong inhibitory effects on A549 and HT-29 cells comparable with etoposide and 5-FU as the positive controls. Furthermore, compared with indomethacin at 0.73 ± 0.07 μM, kaempferol and podophyllotoxin with higher EF values exerted stronger inhibitory effects with IC50 values at 0.36 ± 0.02 μM and 10.49 ± 0.61 μM, respectively. Isorhamnetin with a higher EF value exerted stronger inhibitory effect against ACE2 with IC50 value at 118.46 ± 14.78 μM in contrast to podophyllotoxin with relatively lower EF value at > 970.00 μM. In addition, the optimal binding sites and mode of action between multiple drug targets and bioactive ligands were determined by molecular docking. Conclusion: This study showcased a quick and reliable experimental strategy for unveiling the underlying mechanism of S. hexandrum, which could also provide valuable information for better understanding the therapeutic targets and ligands of other herbal medicines.

Biogenic Ferrihydrite Nanoparticles Produced by Klebsiella oxytoca: Characterization, Physicochemical Properties and Bovine Serum Albumin Interactions.

The synthesis of nanoparticles inside microorganisms is an economical alternative to chemical and physical methods of nanoparticle synthesis. In this study, ferrihydrite nanoparticles synthesized by Klebsiella oxytoca bacterium in special conditions were characterized by scanning electron microscopy (SEM), energy-dispersive X-ray analysis (EDS), small-angle X-ray (SAXS), UV-Vis spectroscopy, fluorescence, fluorescence resonance energy transfer (FRET), and molecular docking. The morphology and the structure of the particles were characterized by means of SEM and SAXS. The elemental content was determined by means of the EDS method. The absorption properties of the ferrihydrite nanoparticles were investigated by UV-Vis spectroscopy. The binding mechanism of the biogenic ferrihydrite nanoparticles to Bovine Serum Albumin (BSA) protein, studied by fluorescence, showed a static and weak process, combined with FRET. Protein denaturation by temperature and urea in the presence of the ferrihydrite nanoparticles demonstrated their influence on the unfolding process. The AutoDock Vina and UCSF Chimera programs were used to predict the optimal binding site of the ferrihydrite to BSA and to find the location of the hydrophobic cavities in the sub-domain IIA of the BSA structure.

Engineering the C4 pathway of Corynebacterium glutamicum for efficient production of 5-aminolevulinic acid

5-aminolevulinic acid (5-ALA) plays an important role in the fields of medicine and agriculture. 5-ALA can be produced by engineered Escherichia coli and Corynebacterium glutamicum. We systematically engineered the C4 metabolic pathway of C. glutamicum to further improve its ability to produce 5-ALA. Firstly, the hemA gene encoding 5-ALA synthase (ALAS) from Rhodobacter capsulatus and Rhodopseudomonas palustris were heterologously expressed in C. glutamicum, respectively. The RphemA gene of R. palustris which showed relatively high enzyme activity was selected. Screening of the optimal ribosome binding site sequence RBS5 significantly increased the activity of RphemA. The ALAS activity of the recombinant strain reached (221.87±3.10) U/mg and 5-ALA production increased by 14.3%. Subsequently, knocking out genes encoding α-ketoglutarate dehydrogenase inhibitor protein (odhI) and succinate dehydrogenase (sdhA) increased the flux of succinyl CoA towards the production of 5-ALA. Moreover, inhibiting the expression of hemB by means of sRNA reduced the degradation of 5-ALA, while overexpressing the cysteine/O-acetylserine transporter eamA increased the output efficiency of intracellular 5-ALA. Shake flask fermentation using the engineered strain C. glutamicum 13032/∆odhI/∆sdhA-sRNAhemB- RBS5RphemA-eamA resulted in a yield of 11.90 g/L, which was 57% higher than that of the original strain. Fed-batch fermentation using the engineered strain in a 5 L fermenter produced 25.05 g/L of 5-ALA within 48 h, which is the highest reported-to-date yield of 5-ALA from glucose.

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.

In vitro and in vivo inhibitory effect of anthocyanin-rich bilberry extract on α-glucosidase and α-amylase

The inhibition of glycosidase activity is regarded as an effective treatment for diabetes mellitus. Bilberry (Vaccinium myrtillus L.) fruit has a high content of anthocyanins with various biological activities. The objective of this study was to investigate the inhibitory activity of anthocyanin-rich bilberry extract (BE) on α-glucosidase and α-amylase and their interaction mechanisms in vitro. The IC50 values of BE with regard to α-glucosidase and α-amylase inhibition were 0.31 ± 0.02 and 4.06 ± 0.12 mg/mL, respectively. The enzyme kinetics revealed that BE acts as a mixed-type inhibitor against α-glucosidase and α-amylase. Moreover, the fluorescence of two glucosidases showed significant quenching by BE. FTIR spectra and differential scanning calorimetry (DSC) indicated that BE changed the enzyme structure and decreased its stability. A morphological observation of starch granules found that BE inhibited the activity of α-amylase to postpone the hydrolysis of starch. Furthermore, the in vivo study further showed that BE had a hypoglycaemic effect. The most suitable conformation (main anthocyanidins of BE) and optimal binding site (α-glucosidase, α-amylase) were assayed by molecular docking. In conclusion, this study revealed that BE could be a potential glycosidase inhibitor.

Biochemical and Computational Studies of the Interaction between a Glucosamine Derivative, NAPA, and the IKKα Kinase.

The glucosamine derivative 2-(N-Acetyl)-L-phenylalanylamido-2-deoxy--D-glucose (NAPA), was shown to inhibit the kinase activity of IKK, one of the two catalytic subunits of IKK complex, decreasing the inflammatory status in osteoarthritis chondrocytes. In the present work we have investigated the inhibition mechanism of IKK by NAPA by combining computational simulations, in vitro assays and Mass Spectrometry (MS) technique. The kinase in vitro assay was conducted using a recombinant IKK and IKKtide, a 20 amino acid peptide substrate derived from IkB kinase protein and containing the serine residues Ser32 and Ser36. Phosphorylated peptide production was measured by Ultra Performance Liquid Chromatography coupled with Mass Spectrometry (UPLC-MS), and the atomic interaction between IKK and NAPA has been studied by molecular docking and Molecular Dynamics (MD) approaches. Here we report that NAPA was able to inhibit the IKK kinase activity with an IC50 of 0.5 mM, to decrease the Km value from 0.337 mM to 0.402 mM and the Vmax from 0.0257 mM·min to 0.0076 mM·min. The computational analyses indicate the region between the KD, ULD and SDD domains of IKK as the optimal binding site explored by NAPA. Biochemical data indicate that there is a non-significant difference between Km and Ki whereas there is a statistically significant difference between the two Vmax values. This evidence, combined with computational results, consistently indicates that the inhibition is non-competitive, and that the NAPA binding site is different than that of ATP or IKKtide.

Membrane dynamics simulation and virtual screening reveals potential dual natural inhibitors of endothelin receptors for targeting glaucomatous condition

Glaucoma is the second leading cause of blindness in the world and is characterized by the loss of retinal ganglion cells (RGC) over a period of time, leading to complete blindness. Recently, endothelin has been identified as an important factor that influences intraocular pressure IOP, OBF, and direct RGC damage. Targeting the endothelin receptor signaling pathway in glaucoma is considered to be highly beneficial, as it can effectively modulate IOP, OBF, and RGC damage, the key factors which are essential to modulate the disease progression holistically. Currently, synthetic drugs like Bosentan, BQ-123, and prostaglandin analogues are available as endothelin receptor antagonists, which are extensively used in the treatment of cardiovascular and other conditions like systemic hypertension. However, the usage of these drugs in glaucoma is limited due to toxicity and poor bioavailability in the ocular milieu. Thus, there is a need for potential natural compounds as endothelin receptor antagonists that acts as dual inhibitors by targeting both ETA and ETB and are highly efficient with the least toxicity. Hence, this study is intended to prioritize endothelin receptor antagonists by structural bioinformatics approaches involving molecular modeling, molecular dynamics, and molecular docking studies. Subsequently, High throughput virtual screening (HTVS) vs. Natural compound databases targeting the optimal binding sites of both ETA and ETB. Following this, the common hits were subjected to binding free energy calculations (MMGBSA) and ADMETox analysis. Finally, the most potential hits were analyzed for MD based binding stability analysis and binding free energy. Similarly, the known synthetic inhibitors were also docked to the receptors and the results were analyzed. From this study, it was inferred that among the natural compounds dataset (8929 compounds), only 4 common compounds were identified as hits. Among these, only one compound ST075640 surpassed all the prioritization criteria including MMGBSA, ADMETox prediction, dual inhibitory potential (ETA & ETB), and also in structural comparative analysis with bosentan it showed similar efficiency. Thus, the validated hit shall prove to be effective in modulating endothelin mediated IOP, OBF, and RGC damage in glaucomatous condition.