Novel Insights into the Therapeutic Effect of Amentoflavone Against Aeromonas hydrophila Infection by Blocking the Activity of Aerolysin

Aeromonas hydrophila (A. hydrophila) is an opportunistic and foodborne pathogen widely spread in the environments, particularly aquatic environments. Diseases caused by A. hydrophila in freshwater aquaculture result in huge economic losses every year. The increasing emergence of antibiotic resistance has limited the application of antibiotics in aquaculture. Aerolysin (AerA), the main virulence factor produced by A. hydrophila, has been identified as a promising target for developing drugs controlling A. hydrophila infection. Here, we found that the natural compound amentoflavone (AMF) with the MIC of 512 μg/mL against A. hydrophila could dose-dependently reduce the hemolysis of AerA, ranging from 0.5 to 4 μg/mL. Molecular docking and dynamics simulation results predicted that AMF could directly bind to domain 3 of AerA via Pro333 and Trp375 residues. Then, the binding sites were confirmed by fluorescence quenching assays. The results of heptamer formation demonstrated that the binding of AMF could affect the formation of oligomers and result in the loss of pore-forming activity. Cell viability assay showed that AerA after treatment with AMF ranging from 0.5 to 4 μg/mL could significantly reduce AerA-mediated cytotoxicity. Moreover, experimental therapeutics results showed that channel catfish infected with A. hydrophila and then administered with 20 mg/kg AMF at intervals of 12 h for 3 days could increase the survival rate by 35% compared with the positive control after a 10-day observation. These findings provided a novel approach to developing anti-infective drugs and a promising candidate for controlling A. hydrophila infection in aquaculture.

pH responsive fabrication of PVA-stabilized selenium nano formulation encapsulated with luteolin to reduce diabetic ureteral injury by decreasing NLRP3 inflammasome via Nrf2/ARE signaling

Diabetic ureteral injury (DUI) is a condition characterized by damage to the ureter, causing functional and morphological changes in the urinary system, which have a significant impact on a quality of life and requires appropriate medical treatment. The present study describes to novel design of luteolin (LT), a type of natural flavonoid, encapsulated selenium nanoparticles (Se NPs) to attain therapeutic potential for DUI. The physico-chemical characterizations of prepared Se NPs have benefitted zeta potential (-18 mV) and particle size (10-50 nm). In vitro assays were demonstrated the potential of LT-SeNPs by HEK 293 cells stimulated by STZ for DUI. Cytotoxicity assays on HEK 293 and NIH-3T3 showed >90% cell viability, which demonstrates the suitability of the nanoformulation for DUI treatment. The LT-SeNPs significantly inhibits the NLRP3 inflammasome through Nrf2/ARE pathway, which benefits for DUI treatment. The developed LT-SeNPs could be an effective formulation for the DUI therapy.

Food Antioxidants and Their Interaction with Human Proteins

Common to all biological systems and living organisms are molecular interactions, which may lead to specific physiological events. Most often, a cascade of events occurs, establishing an equilibrium between possibly competing and/or synergistic processes. Biochemical pathways that sustain life depend on multiple intrinsic and extrinsic factors contributing to aging and/or diseases. This article deals with food antioxidants and human proteins from the circulation, their interaction, their effect on the structure, properties, and function of antioxidant-bound proteins, and the possible impact of complex formation on antioxidants. An overview of studies examining interactions between individual antioxidant compounds and major blood proteins is presented with findings. Investigating antioxidant/protein interactions at the level of the human organism and determining antioxidant distribution between proteins and involvement in the particular physiological role is a very complex and challenging task. However, by knowing the role of a particular protein in certain pathology or aging, and the effect exerted by a particular antioxidant bound to it, it is possible to recommend specific food intake or resistance to it to improve the condition or slow down the process.

Galangin as a direct inhibitor of vWbp protects mice from Staphylococcus aureus-induced pneumonia

The surge in multidrug resistance in Staphylococcus aureus (S. aureus) and the lag in antibiotic discovery necessitate the development of new anti‐infective strategies to reduce S. aureus infections. In S. aureus, von Willebrand factor‐binding protein (vWbp) is not only the main coagulase that triggers host prothrombin activation and formation of fibrin cables but also bridges the bacterial cell wall and von Willebrand factor, thereby allowing S. aureus to bind to platelets and endothelial cells, playing a vital role in pathogenesis of S. aureus infections. Here, we have identified that galangin, a bioactive compound found in honey and Alpinia officinarum Hance, is a potent and direct inhibitor of vWbp by coagulation activity inhibition assay, thermal shift assay and biolayer interferometry assay. Molecular dynamic simulations and verification experiments revealed that the Trp‐64 and Leu‐69 residues are necessary for the binding of galangin to vWbp. Significantly, galangin attenuated S. aureus virulence in a mouse S. aureus‐induced pneumonia model. In addition, we also identified that galangin can enhance the therapeutic effect of latamoxef on S. aureus‐induced pneumonia. Taken together, the results suggest that galangin may be used for the development of therapeutic drugs or utilized as adjuvants to combine with antibiotics to combat S. aureus‐related infections.

Identification of Targeted Proteins by Jamu Formulas for Different Efficacies Using Machine Learning Approach

BACKGROUND

We performed in silico prediction of the interactions between compounds of Jamu herbs and human proteins by utilizing data-intensive science and machine learning methods. Verifying the proteins that are targeted by compounds of natural herbs will be helpful to select natural herb-based drug candidates.

METHODS

Initially, data related to compounds, target proteins, and interactions between them were collected from open access databases. Compounds are represented by molecular fingerprints, whereas amino acid sequences are represented by numerical protein descriptors. Then, prediction models that predict the interactions between compounds and target proteins were constructed using support vector machine and random forest.

RESULTS

A random forest model constructed based on MACCS fingerprint and amino acid composition obtained the highest accuracy. We used the best model to predict target proteins for 94 important Jamu compounds and assessed the results by supporting evidence from published literature and other sources. There are 27 compounds that can be validated by professional doctors, and those compounds belong to seven efficacy groups.

CONCLUSION

By comparing the efficacy of predicted compounds and the relations of the targeted proteins with diseases, we found that some compounds might be considered as drug candidates.

Mode of action and structural modelling of the interaction of formononetin with suilysin

AIMS

Suilysin is a critical pore-forming virulence factor of Streptococcus suis that has been demonstrated to substantially contribute to its pathogenicity. We have demonstrated that formononetin alleviates S. suis infection both in vivo and in vitro by targeting suilysin. However, the molecular mechanism of the effect is unclear. Our aim was to determine the molecular mechanism of the effect of formononetin on suilysin.

METHODS AND RESULTS

The mechanism of interaction between formononetin and suilysin was investigated by molecular modelling. The results indicated that formononetin was bound at the junction of domain two and domain four of suilysin. The binding free energy values indicated that the A415, Y412, E414, N413, T61, T62 and G416 residues are critical for this binding, this observation was confirmed by the changes in the flexibility of these residues and the distances between these residues and formononetin. The inhibitory effect of formononetin on the pore-forming activity of suilysin, binding constant and binding free energy were significantly decreased by site-specific mutagenesis of Y412 and N413. Finally, we analysed the spatial configuration of suilysin before and after formononetin binding, the results indicated that the binding changed the conformation of suilysin, especially the angle between domain two and domain four, resulting in the disruption of cholesterol binding to suilysin and in the loss of pore-forming activity.

CONCLUSIONS

Formononetin is located at the junction of domain two and domain four of suilysin, and Y412 and N413 play critical roles in the binding. Formononetin binding changes the angle between domain two and domain four of suilysin, resulting in the loss of the pore-inducing activity of suilysin.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work will promote the application of formononetin to combat S. suis infections and may contribute to the development of new inhibitors or modification of existing inhibitors.

Luteolin decreases the pathogenicity of Aeromonas hydrophila via inhibiting the activity of aerolysin

Aeromonas hydrophila (A. hydrophila) can cause a number of diseases in both human and animals. A. hydrophila-related infections in aquaculture cause severe economic losses every year throughout the world. The emergence of antibiotic resistance that is due to the abuse of antibiotics has limited the application of antibiotics. Thus, novel approaches are needed to combat with treatment failure of antibiotics caused by resistant bacterial strains. Aerolysin plays a critical role in the pathogenesis of A. hydrophila and has been considered as a novel target for developing drugs based on anti-virulence strategies. Here, we reported that luteolin, a natural product with no anti-A. hydrophila activity, could reduce aerolysin-induced hemolysis by inhibiting aerolysin activity. The binding mode was simulated by molecular docking and dynamics simulation. Then the main binding sites were confirmed by fluorescence quenching assays. We found that luteolin could hindered the formation of functional heptamer of aerolysin according to the results of the oligomerization assay. Moreover, luteolin could protect A549 cells from aerolysin mediated cell death and increase the survival rate of A. hydrophila-infected channel catfish. These findings suggest a novel approach to developing drugs fighting against A. hydrophila, and luteolin can be a promising drug candidate for treatment of A. hydrophila-associated infections.

Indomethacin Increases Quercetin Affinity for Human Serum Albumin: A Combined Experimental and Computational Study and Its Broader Implications

Human serum albumin (HSA) is the most abundant carrier protein in the human body. Competition for the same binding site between different ligands can lead to an increased active concentration or a faster elimination of one or both ligands. Indomethacin and quercetin both bind to the binding site located in the IIA subdomain. To determine the nature of the HSA-indomethacin-quercetin interactions, spectrofluorometric, docking, molecular dynamics studies, and quantum chemical calculations were performed. The results show that the indomethacin and quercetin binding sites do not overlap. Moreover, the presence of quercetin does not influence the binding constant and position of indomethacin in the pocket. However, binding of quercetin is much more favorable in the presence of indomethacin, with its position and interactions with HSA significantly changed. These results provide a new insight into drug-drug interactions, which can be important in situations when displacement from HSA or other proteins is undesirable or even desirable. This principle could also be used to deliberately prolong or shorten the xenobiotics' half-life in the body, depending on the desired outcomes.

Baicalein mediates protection against Staphylococcus aureus-induced pneumonia by inhibiting the coagulase activity of vWbp

The emergence and spread of multidrug-resistant Staphylococcus aureus (S. aureus) necessitate the research on therapeutic tactics which are different from classical antibiotics in overcoming resistance andtreatinginfections. In S. aureus, von Willebrand factor-binding protein (vWbp) is one of the key virulence determinants because it mediates not only the activation of thrombin to convert fibrinogen to fibrin, thereby enabling S. aureus to escape from the host immune clearance, but also the adhesion of S. aureus to host cells. Thus, vWbp is regarded as a promising druggable target to treat S. aureus-associated infections. Here we identify that baicalein, a natural compound isolated from the Chinese herb Scutellaria baicalensis, can effectively block the coagulase activity of vWbp without inhibiting the growth of the bacteria. Through thermal shift and fluorescence quenching assays, we demonstrated that baicalein directly binds to vWbp. Molecular dynamics simulations and mutagenesis assays revealed that the Asp-75 and Lys-80 residues are necessary for baicalein binding to vWbp. Importantly, we demonstrated that baicalein treatment attenuates the virulence of S. aureus and protects mice from S. aureus-induced lethal pneumonia. In addition, baicalein can improve the therapeutic effect of penicillin G by 75% in vivo. These findings indicate that baicalein might be developed as a promising therapeutic agent against drug-resistant S. aureus infections.

Targeting staphylocoagulase with isoquercitrin protects mice from Staphylococcus aureus-induced pneumonia

Staphylocoagulase (Coa) is a virulence factor of Staphylococcus aureus (S. aureus) that promotes blood coagulation by activating prothrombin to convert fibrinogen to fibrin. Coa plays a crucial role in disease pathogenesis and is a promising target for the treatment of S. aureus infections. Here, we identified that isoquercitrin, a natural flavonol compound, can markedly reduce the activity of Coa at concentrations that have no effect on bacterial growth. Mechanistic studies employing molecular dynamics simulation revealed that isoquercitrin binds to Coa by interacting with Asp-181 and Tyr-188, thereby affecting the binding of Coa to prothrombin. Importantly, in vivo studies showed that isoquercitrin treatment significantly reduced the bacterial burden, pathological damage, and inflammation of lung tissue and improved the percentage of survival of mice infected with S. aureus Newman strain. These data suggest that isoquercitrin is a promising inhibitor of Coa that can be used for the development of therapeutic drugs to combat S. aureus infections.Key Points• Staphylocoagulase plays a key role in the pathogenesis of S. aureus infection.• We identified that isoquercitrin is a direct inhibitor of staphylocoagulase.• Isoquercitrin treatment can significantly attenuate S. aureus virulence in vivo.

Pterostilbene restores carbapenem susceptibility in New Delhi metallo-β-lactamase-producing isolates by inhibiting the activity of New Delhi metallo-β-lactamases

BACKGROUND AND PURPOSE

Bacteria producing New Delhi metallo-β-lactamase-1 (NDM-1) are an increasing clinical threat. NDM-1 can inactivate almost all β-lactams and is not sensitive to any existing β-lactamase inhibitors. To identify effective inhibitors of the NDM-1 enzyme and clarify the mechanism of action, a "lead compound" for developing more potent NDM-1 inhibitors needs to be provided.

EXPERIMENTAL APPROACH

Natural compounds were tested by enzyme inhibition screening to find potential inhibitors. MIC assays, growth curve assays, and time-kill assays were conducted to evaluate the in vitro antibacterial activity of pterostilbene and the combination of pterostilbene and meropenem. A murine thigh model and a mouse pneumonia model were used to evaluate the in vivo efficacy of combined therapy. Molecular modelling and a mutational analysis were used to clarify the mechanism of action.

KEY RESULTS

Pterostilbene significantly inhibited NDM-1 hydrolysis activity in enzyme inhibition screening assays and effectively restored the effectiveness of meropenem in vitro with NDM-expressing isolates in antibacterial activity assays. In addition, the combined therapy effectively reduced the bacterial burden in a murine thigh model and protected mice from pneumonia caused by Klebsiella pneumoniae. By means of molecular dynamics simulation, we observed that pterostilbene localized to the catalytic pocket of NDM-1, hindering substrate binding to NDM-1 and reducing NDM-1 activity.

CONCLUSIONS AND IMPLICATIONS

These findings indicated that pterostilbene combined with meropenem may offer a new safe and potential "lead compound" for the further development of NDM-1 inhibitors.

Binding characteristics of polyphenols as milk plasmin inhibitors

BACKGROUND

The potential use of polyphenols to improve the functional characteristics of dairy products has gained much attention. However, the effects of the polyphenols on naturally occurring enzymes in milk have not been studied extensively. Excess plasmin activity in dairy products might result in several quality defects. The objective of this study was to assess the ability of polyphenols to inhibit plasmin in milk using a molecular and kinetic approach.

RESULTS

Epicatechin gallate (ECG), epigallocatechin gallate (EGCG), quercetin (QUER), and myricetin (MYR) caused a significant decrease in plasmin activity by 60, 86, 65, and 90%, respectively. The inhibition rates were alleviated in the presence of milk proteins. EGCG, QUER, and MYR, exhibited noncompetitive inhibition against plasmin, whereas ECG caused a mixed-type inhibition. A decrease in the random structure of plasmin upon the complex formation with ECG, EGCG, QUER, and MYR was found. The other phenolics that were evaluated did not cause any significant changes in plasmin conformation. The observed inhibitory phenolic-plasmin interactions were dominated by H-bonds and electrostatic attractions. Green tea extract (GTE) rich in catechins also inhibited plasmin activity in the milk.

CONCLUSION

Significant changes in the secondary structure of plasmin upon binding of ECG, EGCG, QUER, and MYR led to diminished plasmin activity both in the absence and presence of milk proteins. These flavonoids with promising plasmin inhibitory potential could be used in new dairy formulations leading to controlled undesired consequences of plasmin activity. © 2019 Society of Chemical Industry.

Theaflavin-3,3´-digallate increases the antibacterial activity of β-lactam antibiotics by inhibiting metallo-β-lactamase activity

Metallo-β-lactamases (MBLs) are some of the best known β-lactamases produced by common Gram-positive and Gram-negative pathogens and are crucial factors in the rise of bacterial resistance against β-lactam antibiotics. Although many types of β-lactamase inhibitors have been successfully developed and used in clinical settings, no MBL inhibitors have been identified to date. Nitrocefin, checkerboard and time-kill assays were used to examine the enzyme behaviour in vitro. Molecular docking calculation, molecular dynamics simulation, calculation of the binding free energy and ligand-residue interaction decomposition were used for mechanistic research. The behaviour of the enzymes in vivo was investigated by a mouse infection experiment. We showed that theaflavin-3,3´-digallate (TFDG), a natural compound lacking antibacterial activities, can inhibit the hydrolysis of MBLs. In the checkerboard and time-kill assays, we observed a synergistic effect of TFDG with β-lactam antibiotics against methicillin-resistant Staphylococcus aureus BAA1717. Molecular dynamics simulations were used to identify the mechanism of the inhibition of MBLs by TFDG, and we observed that the hydrolysis activity of the MBLs was restricted by the binding of TFDG to Gln242 and Ser369. Furthermore, the combination of TFDG with β-lactam antibiotics showed effective protection in a mouse Staphylococcus aureus pneumonia model. These findings suggest that TFDG can effectively inhibit the hydrolysis activity of MBLs and enhance the antibacterial activity of β-lactam antibiotics against pathogens in vitro and in vivo.

Formation and Stabilization of Gold Nanoparticles in Bovine Serum Albumin Solution

The formation and growth of gold nanoparticles (AuNPs) were investigated in pH 7 buffer solution of bovine serum albumin (BSA) at room temperature. The processes were monitored by UV-Vis, circular dichroism, Raman and electron paramagnetic resonance (EPR) spectroscopies. TEM microscopy and dynamic light scattering (DLS) measurements were used to evidence changes in particle size during nanoparticle formation and growth. The formation of AuNPs at pH 7 in the absence of BSA was not observed, which proves that the albumin is involved in the first step of Au(III) reduction. Changes in the EPR spectral features of two spin probes, CAT16 and DIS3, with affinity for BSA and AuNPs, respectively, allowed us to monitor the particle growth and to demonstrate the protective role of BSA for AuNPs. The size of AuNPs formed in BSA solution increases slowly with time, resulting in nanoparticles of different morphologies, as revealed by TEM. Raman spectra of BSA indicate the interaction of albumin with AuNPs through sulfur-containing amino acid residues. This study shows that albumins act as both reducing agents and protective corona of AuNPs.

Aloe-emodin Attenuates Staphylococcus aureus Pathogenicity by Interfering With the Oligomerization of α-Toxin

α-toxin, an essential virulence factor secreted by Staphylococcus aureus (S. aureus), is a critical exotoxin in multiple infections. In this study, we found that aloe-emodin (AE), a natural compound lacking anti-S. aureus activity, could inhibit the hemolytic activity of α-toxin. Oligomerization assays, molecular dynamics simulations, and fluorescence-quenching analyses were used to determine the mechanism of this inhibition. The oligomerization of α-toxin was restricted by the engagement of AE with K110, T112, and M113 of the toxin, which eventually resulted in inhibition of the hemolytic activity. Lactate dehydrogenase and live/dead assays demonstrated that AE decreased the injury of human lung epithelial cells (A549) and mouse lung macrophages (MH-S) mediated by S. aureus. Furthermore, treatment with AE showed robust protective effects in mice infected by S. aureus. These findings suggest that AE effectively inhibited the pore-forming activity of α-toxin and showed a protective effect against S. aureus virulence in vitro and in vivo, which may provide a new strategy and new antibacterial agent for clinical treatment of S. aureus infections.

Pharmacokinetics and tissue distribution of N-(2-hydroxyphenyl)-2-propylpentanamide in Wistar Rats and its binding properties to human serum albumin

N-(2-hydroxyphenyl)-2-propylpentanamide (HO-AAVPA) is a novel valproic acid derivative that has shown anti-proliferative activity against epitheloid cervix carcinoma (HeLa), rhabdomyosarcoma (A204), and several breast cancer cell lines. The aim of this research was to evaluate the pharmacokinetic profile and tissue distribution of HO-AAVPA in Wistar rats, as well as its human serum albumin binding potential by experimental and in silico methods. A single dose of HO-AAVPA was given to male rats by intravenous, intragastric or intraperitoneal routes at doses of 25, 100, and 100 mg/kg, respectively. Then, blood samples were drawn at predetermined intervals of time, and the HO-AAVPA concentration in the plasma was quantified with a validated HPLC method. The elimination half-life (t1/2) was approximately 222 min, and the systemic clearance (CL) and apparent volume of distribution (Vd) were 2.20 mL/min/kg and 0.70 L/kg, respectively. The absolute oral bioavailability of HO-AAVPA was 33.8%, and the binding rate of HO-AAVPA with rat plasma proteins was between 66.2% and 83.0%. Additionally, in silico, UV and Raman spectroscopy data showed weak interactions between the test compound and human serum albumin. Thus, the results that were obtained demonstrated that despite its low oral bioavailability, the potential anticancer agent HO-AAVPA exhibits acceptable pharmacokinetic properties that would allow it to reach its site of action and exert its pharmacological effect in Wistar Rats, and it has a convenient profile for future assays to evaluate its human applications.

Analysis of the soybean metallothionein system under free radical stress: protein modification connected to lipid membrane damage

Metallothioneins are small Cys-rich peptides capable of coordinating metal ions, and proposed to be involved in radical stress. The four Zn(ii)-GmMT complexes of soybean (Glycine max) were recombinantly synthesised and exposed to oxidative (HO˙) and reductive (H˙ atoms and eaq-) stress conditions. Gamma-irradiation was used to simulate the endogenous formation of the reactive species in both aqueous solutions and unsaturated lipid vesicle suspensions, a biomimetic model that showed that tandem protein/lipid damage occurs, in particular under reductive radical stress. This is due to the formation of diffusible sulphur-centred radicals, which migrate from the aqueous phase to the lipid bilayer and are thus able to transform the cis double bond of the oleate moiety into the trans isomer. Among the amino acid residues present in GmMTs, Cys is one of the most sensitive residues towards the attack of free radicals, thus suggesting metal-clusters to be good interceptors of free radicals. Also Met, Tyr and Phe residues are sensitive amino acid sites of attack under both oxidative and reductive conditions. The modification of the Zn(ii)-GmMT complexes, in particular isoform 2, was monitored by Raman spectroscopy and mass spectrometry. Free radical stress on the Zn(ii)-GmMT complexes is able to induce significant structural changes such as partial deconstruction and/or rearrangement of the metal clusters, but not the complete demetallation of the proteins nor breaking of the backbone, thus confirming their capability to act as protectors under free radical stress conditions.

Magnolol restores the activity of meropenem against NDM-1-producing Escherichia coli by inhibiting the activity of metallo-beta-lactamase

The emergence of plasmid-mediated New Delhi metallo-β-lactamase-1 (NDM-1) in carbapenem-resistant Gram-negative pathogens is an increasing clinical threat. Here we report the discovery of an NDM-1 inhibitor, magnolol, through enzyme inhibition screening. We showed that magnolol significantly inhibited NDM enzyme activity (IC50 = 6.47 µg/mL), and it restored the activity of meropenem against Escherichia coli ZC-YN3, an NDM-1-producing E. coli isolate, in in vitro antibacterial activity assays. Magnolol lacked direct antibacterial activity, but compared with meropenem alone, it reduced the MICs of meropenem against E. coli ZC-YN3 by 4-fold and killed almost all the bacteria within 3 h. Molecular modeling and a mutational analysis demonstrated that magnolol binds directly to the catalytic pocket (residues 110 to 200) of NDM-1, thereby blocking the binding of the substrate to NDM-1 and leading to its inactivation. Our results demonstrate that the combination of magnolol and meropenem may have the potential to treat infections caused by NDM-1-positive, carbapenem-resistant Gram-negative pathogens.

Morin Protects Channel Catfish From Aeromonas hydrophila Infection by Blocking Aerolysin Activity

Aeromonas hydrophila (A. hydrophila) is an opportunistic bacterial pathogen widely distributed in the environments, particular aquatic environment. The pathogen can cause a range of infections in both human and animals including fishes. However, the application of antibiotics in treatment of A. hydrophila infections leads to the emergence of resistant strains. Consequently, new approaches need to be developed in fighting this pathogen. Aerolysin, the chief virulence factor produced by pathogenic A. hydrophila strains has been employed as target identifying new drugs. In our present study, we found that morin, a flavonoid without anti-bacterial activity isolated from traditional Chinese medicine, could directly inhibit the hemolytic activity of aerolysin. To determine the binding sites and the action of mechanism of morin against AerA, several assays were performed. Ser36, Pro347, and Arg356 were identified as the main binding sites affecting the conformation of AerA and resulted in block of the heptameric formation. Moreover, morin could protect Vero cells from cell injury mediated by aerolysin. In vivo study showed that morin could provide a protection to channel catfish against A. hydrophila infection. These results demonstrated that morin could be developed as a promising candidate for the treatment of A. hydrophila infections by decreasing the pathogenesis of A. hydrophila.

Erianin against Staphylococcus aureus Infection via Inhibiting Sortase A

With continuous emergence and widespread of multidrug-resistant Staphylococcus aureus infections, common antibiotics have become ineffective in treating these infections in the clinical setting. Anti-virulence strategies could be novel, effective therapeutic strategies against drug-resistant bacterial infections. Sortase A (srtA), a transpeptidase in gram-positive bacteria, can anchor surface proteins that play a vital role in pathogenesis of these bacteria. SrtA is known as a potential antivirulent drug target to treat bacterial infections. In this study, we found that erianin, a natural bibenzyl compound, could inhibit the activity of srtA in vitro (half maximal inhibitory concentration-IC₅₀ = 20.91 ± 2.31 μg/mL, 65.7 ± 7.2 μM) at subminimum inhibitory concentrations (minimum inhibitory concentrations-MIC = 512 μg/mL against S. aureus). The molecular mechanism underlying the inhibition of srtA by erianin was identified using molecular dynamics simulation: erianin binds to srtA residues Ile182, Val193, Trp194, Arg197, and Ile199, forming a stable bond via hydrophobic interactions. In addition, the activities of S. aureus binding to fibronectin and biofilm formation were inhibited by erianin, when co-culture with S. aureus. In vivo, erianin could improve the survival in mice that infected with S. aureus by tail vein injection. Experimental results showed that erianin is a potential novel therapeutic compound against S. aureus infections via affecting srtA.

Oligopeptide Targeting Sortase A as Potential Anti-infective Therapy for Staphylococcus aureus

Sortase A (SrtA)-catalyzed anchorage of surface proteins in most Gram-positive bacteria is indispensable for their virulence, suggesting that this transpeptidase is a promising target for antivirulence therapy. Here, an oligopeptide, LPRDA, was identified as an effective inhibitor of SrtA via virtual screening based on the LPXTG substrate sequence, and it was found to inhibit SrtA activity in vitro and in vivo (IC₅₀ = 10.61 μM) by competitively occupying the active site of SrtA. Further, the oligopeptide treatment had no anti-Staphylococcus aureus activity, but it provided protection against S. aureus-induced mastitis in a mouse model. These findings indicate that the oligopeptide could be used as an effective anti-infective agent for the treatment of infection caused by S. aureus or other Gram-positive bacteria via the targeting of SrtA.

Effect of Oxidation and Protein Unfolding on Cross-Linking of β-Lactoglobulin and α-Lactalbumin

Oxidation and heat treatment can initiate changes in the amino acid composition, structure, solubility, hydrophobicity, conformation, function, and susceptibility to proteolysis of proteins. These can result in adverse consequences for mammals, plants, foodstuffs, and pharmaceuticals. This study investigated whether and how individual or combined treatment with heat, a commonly encountered factor in industrial processing, and H₂O₂ alters the structure and composition of two major milk whey proteins, α-lactalbumin and β-lactoglobulin, and mixtures of these. Thermal treatment induced reducible cross-links in isolated β-lactoglobulin, but not isolated α-lactalbumin under the conditions employed. Cross-linking occurred at lower temperatures and to a greater extent in the presence of low concentrations of H₂O₂. H₂O₂ did not induce cross-linking in the absence of heat. Mixtures of α-lactalbumin and β-lactoglobulin showed similar behavior, except that mixed α-lactalbumin-β-lactoglobulin dimers were detected. Cross-linking was associated with formation of sulfenic acids (RS-OH species), oxidation of methionine residues, cleavage of disulfide bonds in α-lactalbumin, altered conformation of disulfide bonds in β-lactoglobulin, alterations in the fluorescence intensity and maximum emission wavelength of endogenous tryptophan residues, and binding of the hydrophobic probe 8-anilinonaphthalenesulfonate. These data are consistent with increased unfolding and subsequent aggregation of the protein, with these changes being maximized in the presence of both heat and H₂O₂. The enhanced aggregation detected with H₂O₂ is consistent with additional pathways to aggregation above that induced by heat alone. These mechanistic insights provide potential strategies for modulating the extent and nature of protein modification induced by thermal and oxidant treatment.

Chalcone Attenuates Staphylococcus aureus Virulence by Targeting Sortase A and Alpha-Hemolysin

Staphylococcus aureus (S.aureus) resistance, considered a dilemma for the clinical treatment of this bacterial infection, is becoming increasingly intractable. Novel anti-virulence strategies will undoubtedly provide a path forward in combating these resistant bacterial infections. Sortase A (SrtA), an enzyme responsible for anchoring virulence-related surface proteins, and alpha-hemolysin (Hla), a pore-forming cytotoxin, have aroused great scientific interest, as they have been regarded as targets for promising agents against S. aureus infection. In this study, we discovered that chalcone, a natural small compound with little anti-S. aureus activity, could significantly inhibit SrtA activity with an IC₅₀ of 53.15 μM and Hla hemolysis activity with an IC₅₀ of 17.63 μM using a fluorescence resonance energy transfer (FRET) assay and a hemolysis assay, respectively. In addition, chalcone was proven to reduce protein A (SpA) display in intact bacteria, binding to fibronectin, formation of biofilm and S. aureus invasion. Chalcone could down-regulate the transcriptional levels of the hla gene and the agrA gene, thus leading to a reduction in the expression of Hla and significant protection against Hla-mediated A549 cell injury; more importantly, chalcone could also reduce mortality in infected mice. Additionally, molecular dynamics simulations and mutagenesis assays were used to identify the mechanism of chalcone against SrtA, which implied that the inhibitory activity lies in the bond between chalcone and SrtA residues Val168, Ile182, and Arg197. Taken together, the in vivo and in vitro experiments suggest that chalcone is a potential novel therapeutic compound for S. aureus infection via targeting SrtA and Hla.

Negligible interaction of [Ru(Phen)3]2+ with human serum albumin makes it promising for a reliable invivo assessment of the tissue oxygenation

The interaction between a ruthenium - based water soluble oxygen probe ([Ru(Phen)₃]²⁺, phen - phenanthroline) and human serum albumin (HSA) was investigated with the aim of describing the influence of HSA on the [Ru(Phen)₃]²⁺ luminescence properties. Nowadays, several oxygen sensitive luminescent probes are used to determine the oxygen level in different compartments of living organisms. However, they can interact, depending on their hydrophilic/hydrophobic characters, with various serum proteins, and/or lipids, during their utilization for invivo oxygen measurement. Since HSA is the most abundant serum protein in most biological organisms, its presence may affect the spectral properties of the employed probes and, consequently, the determination of the oxygen concentration. Having this in mind, we have applied several spectroscopic and calorimetric techniques to study [Ru(Phen)₃]²⁺ - HSA mixtures. Only a negligible effect of HSA on the absorption and luminescence spectra of [Ru(Phen)₃]²⁺ was observed. In addition, differential scanning calorimetric studies showed that [Ru(Phen)₃]²⁺ does not significantly influence HSA thermal stability. Importantly, [Ru(Phen)₃]²⁺ retained a reliable luminescence lifetime sensitivity to the oxygen concentration in solutions supplemented with HSA and in U87 MG cancer cells. Finally, the biodistribution of [Ru(Phen)₃]²⁺ in the presence of serum proteins in the blood stream of chick embryo's chorioallantoic membrane (CAM) was investigated. Fast [Ru(Phen)₃]²⁺ and similar extravasations were observed in the presence or absence of CAM-serum. We can conclude that HSA-[Ru(Phen)₃]²⁺ complex interaction does not significantly influence the potential of [Ru(Phen)₃]²⁺ to be a suitable candidate for a reliable oxygen probe in living organisms.

Biophysical exploration of protein-flavonol recognition: effects of molecular properties and conformational flexibility

The current work explores the biomolecular recognition of a series of flavonols by a protein and then uncovers the influences of the structural features of flavonols and the protein's own characteristics, e.g. the dynamics and flexibility, on the bioavailability of flavonols by using the pivotal biomacromolecule hemoglobin as a model. The experimental results revealed that flavonol may lead to a notable decrease in the steady-state fluorescence intensity of the β-37 Trp residue, and in the meantime the R-T transition of the protein transpired. Such noncovalent recognition forms the ground-state adduct, with an association intensity of 3.991 × 10(4) M(-1) in the reaction process, which has already been authenticated by the detailed analysis of time-resolved fluorescence and UV/vis absorption spectra. Furthermore, flavonol can form hydrogen bonds and π-conjugation effects with several amino acid residues on the polypeptide chain, for example, Trp-37, Arg-40, Asp-99 and Asn-102, and this event would induce self-regulation of the compact, regular conformation of the protein to a certain extent, which explicitly corroborates the results of circular dichroism. According to the study of molecular docking and structure-activity relationships, we could see that the recognition capacities of the protein-flavonols are inversely interrelated with the C log P values of the flavonol molecules. Moreover, the properties of the substituents in the structural B-ring unit of flavonols, i.e. polarity, position and number, will also prominently affect the degree of affinity and bioavailability of the protein-flavonol complexes. The analytical results of molecular dynamics (MD) simulation testified that the discussions of the structure-activity relationships are entirely logical, and the conformations of the amino acid residues forming noncovalent interactions tend to be stable in the MD simulation, as further elucidated from the dynamics data. Plainly, molecular recognition of the protein-flavonols might noticeably cause relatively large changes in protein flexibility, and then manifest different recognition strengths and corresponding biological activities. This issue will be carefully validated by the interpretation of root-mean-square fluctuation.

Phloretin Attenuates Listeria monocytogenes Virulence Both In vitro and In vivo by Simultaneously Targeting Listeriolysin O and Sortase A

The critical roles of sortase A (SrtA) and listeriolysin O (LLO) in Listeria monocytogenes pathogenicity render these two virulence factors as ideal targets for the development of anti-virulence agents against L. monocytogenes infection. Additionally, the structures of SrtA and LLO are highly conserved among the members of sortase enzyme family and cholesterol dependent toxin family. Here, phloretin, a natural polyphenolic compound derived from apples and pears that has little anti-L. monocytogenes activity, was identified to simultaneously inhibit LLO expression and neutralize SrtA catalytic activity. Phloretin neutralized SrtA activity by causing a conformational change in the protein's active pocket, which prevented engagement with its substrate. Treatment with phloretin simultaneously reduced L. monocytogenes invasion into host cells and blocked the escape of vacuole-entrapped L. monocytogenes into cytoplasm. Further, L. monocytogenes-infected mice that received phloretin showed lower mortality, decreased bacterial burden and reduced pathological injury. Our results demonstrate that phloretin is a promising anti-infective therapeutic for infections caused by L. monocytogenes due to its simultaneous targeting of SrtA and LLO, which may result in fewer side effects than those caused by other antibiotics.

Spectroscopic study of 3-Hydroxyflavone - protein interaction in lipidic bi-layers immobilized on silver nanoparticles

The interaction of 3-Hydroxyflavone with serum proteins (BSA and HSA) in lecithin lipidic bi-layers (PC) immobilized on silver nanoparticles (SNPs), was studied by fluorescence and Raman spectroscopy. BSA secondary structure was quantified with a deconvolution algorithm, showing a decrease in α-helix structure when lipids were added to the solution. The effect of temperature on the rate of the excited-state intra-molecular proton transfer and on the dual fluorescence emission of 3-HF in the HSA/PC/SNPs systems was discussed. Evaluation of the antioxidant activity of 3-HF in HSA/PC/SNPs systems was also studied. The antioxidant activity of 3-HF decreased in the presence of SNPs. The results are discussed with relevance to the secondary structure of proteins and of the 3-HF based nano-systems to a topical formulation useful in the oxidative stress process.

Molecular Mechanism of the Flavonoid Natural Product Dryocrassin ABBA against Staphylococcus aureus Sortase A

The intractability of bacterial resistance presents a dilemma for therapies against Staphylococcus aureus (S. aureus) infection. Effective anti-virulence strategies are urgently needed, reflecting the proliferation of resistant strains. Inhibitors of sortase A (SrtA), enzymes that anchor virulence-related surface proteins, are regarded as promising candidates for countermeasures against bacterial infections. In the present study, the inhibitory effect of dryocrassin ABBA (ABBA) against SrtA and its molecular basis has been examined. Fluorescence resonance energy transfer (FRET) assays were used to determine the inhibitory activity of ABBA against SrtA. To identify the mechanism underlying this activity, molecular dynamics simulations and mutagenesis assays were applied, and the results revealed that the direct engagement of SrtA via ABBA through binding to V166 and V168 significantly attenuated the catalytic activity of SrtA. Taken together, these findings indicated that ABBA is a potential novel antimicrobial agent for S. aureus infection via targeting SrtA.

The use of chlorogenic acid and its analogues as inhibitors: an investigation of the inhibition of sortase A of Staphylococcus aureus using molecular docking and dynamic simulation

OBJECTIVES

To use molecular docking and dynamic simulation to investigate the inhibitory action of chlorogenic acid (CHA) and its analogues against sortase A of Staphylococcus aureus.

RESULTS

Five novel, natural inhibitors with different activities were discovered for sortase A (SrtA). The inhibition mechanism of the novel inhibitors was consistent with the mechanism of CHA, which was reported previously by Wang et al. (Front Microbiol 6:1031, 2015). Based on structure-activity relationship analysis, the hydroxyl moiety (C1) of the inhibitors is critical in the catalytic region of SrtA, which could be confirmed by the calculation of the binding free energy between SrtA and the inhibitors.

CONCLUSIONS

The mechanism obtained by molecular dynamics simulation is thus useful for the development of novel, selective SrtA inhibitors.

Protein-Flavonoid Interaction Studies by a Taylor Dispersion Surface Plasmon Resonance (SPR) Technique: A Novel Method to Assess Biomolecular Interactions

Flavonoids are common polyphenolic compounds widely distributed in fruits and vegetables. These pigments have important pharmacological relevance because emerging research suggests possible anti-cancer and anti-inflammatory properties as well other beneficial health effects. These compounds are relatively hydrophobic molecules, suggesting the role of blood transport proteins in their delivery to tissues. In this study, we assess the binding interactions of four flavonoids (kaempferol, luteolin, quercetin, and resveratrol) with human serum albumin (HSA), the most abundant protein in the blood, and with glutathione S-transferase pi isoform-1 (GSTP1), an enzyme with well-characterized hydrophobic binding sites that plays an important role in detoxification of xenobiotics with reduced glutathione, using a novel Taylor dispersion surface plasmon resonance (SPR) technique. For the first time, HSA sites revealed a high-affinity binding site for flavonoid interactions. Out of the four flavonoids that we examined, quercetin and kaempferol showed the strongest equilibrium binding affinities (K_D) of 63 ± 0.03 nM and 37 ± 0.07 nM, respectively. GSTP1 displayed lower affinities in the micromolar range towards all of the flavonoids tested. The interactions of flavonoids with HSA and GSTP1 were studied successfully using this novel SPR assay method. The new method is compatible with both kinetic and equilibrium analyses.

Structural and electronic determinants of flavonoid binding to human serum albumin: an extensive ligand-based study

The most prominent features responsible for binding of flavonoid aglycones to the IIA region of human serum albumin (HSA) were determined based onin vitrofluorescence measurements and density functional theory calculations.

Identification of the Flavonoid Luteolin as a Repressor of the Transcription Factor Hepatocyte Nuclear Factor 4α

Hepatocyte nuclear factor 4α (HNF4α) is a nuclear receptor that regulates the expression of genes involved in the secretion of apolipoprotein B (apoB)-containing lipoproteins and in glucose metabolism. In the present study, we identified a naturally occurring flavonoid, luteolin, as a repressor of HNF4α by screening for effectors of the human microsomal triglyceride transfer protein (MTP) promoter. Luciferase reporter gene assays revealed that the activity of the MTP gene promoter was suppressed by luteolin and that the mutation of HNF4α-binding element abolished luteolin responsiveness. Luteolin treatment caused a significant decrease in the mRNA levels of HNF4α target genes in HepG2 cells and inhibited apoB-containing lipoprotein secretion in HepG2 and differentiated Caco2 cells. The interaction between luteolin and HNF4α was demonstrated using absorption spectrum analysis and luteolin-immobilized beads. Luteolin did not affect the DNA binding of HNF4α to the promoter region of its target genes but suppressed the acetylation level of histone H3 in the promoter region of certain HNF4α target genes. Short term treatment of mice with luteolin significantly suppressed the expression of HNF4α target genes in the liver. In addition, long term treatment of mice with luteolin significantly suppressed their diet-induced obesity and improved their serum glucose and lipid parameters. Importantly, long term luteolin treatment lowered serum VLDL and LDL cholesterol and serum apoB protein levels, which was not accompanied by fat accumulation in the liver. These results suggest that the flavonoid luteolin ameliorates an atherogenic lipid profile in vivo that is likely to be mediated through the inactivation of HNF4α.

Methylene Blue Doped Films of Wool Keratin with Antimicrobial Photodynamic Activity

In this work, keratin films doped with different amounts of methylene blue (MB) were developed in order to prepare new biodegradable and biocompatible materials for tissue engineering and wound healing, able to exert antimicrobial photodynamic activity upon irradiation with visible light. Preliminary results indicated that the swelling ratio, as well as the MB release, increases by increasing the pH. Moreover, the generation of reactive oxygen species (ROS) and singlet oxygen can be easily triggered and controlled by a fine-tuning of the irradiation time and MB concentration in the films. As concerns the photodynamic effects on keratin, the ROS attack does not induce any significant photodegradation on the protein, even if a slight photo-oxidation of sulfonated amino acids occurs. Finally, the film with the highest MB concentration (400 μg per gram of keratin) displays a significant photobactericidal activity against Staphylococcus aureus with a bacterial reduction that increases by increasing the irradiation time. In particular, the irradiation of KFMB400 film incubated with S. aureus at a concentration of 10(8) cfu mL(-1) determined the 99.9% killing rate and the killing effect increased proportionally with irradiation time.

Phage-AgNPs complex as SERS probe for U937 cell identification

The early diagnosis of malignancy is the most critical factor for patient survival and the treatment of cancer. In particular, leukemic cells are highly heterogeneous, and there is a need to develop new rapid and accurate detection systems for early diagnosis and monitoring of minimal residual disease. This study reports the utilization of molecular networks consisting of entire bacteriophage structure, displaying specific peptides, directly assembled with silver nanoparticles as a new Surface Enhanced Raman Spectroscopy (SERS) probe for U937 cells identification in vitro. A 9-mer pVIII M13 phage display library is screened against U937 to identify peptides that selectively recognize these cells. Then, phage clone is assembled with silver nanoparticles and the resulting network is used to obtain a SERS signal on cell-type specific molecular targets. The proposed strategy could be a very sensitive tool for the design of biosensors for highly specific and selective identification of hematological cancer cells and for detection of minimal residual disease in a significant proportion of human blood malignancy.

The Spectroscopy Study of the Binding of an Active Ingredient of Dioscorea Species with Bovine Serum Albumin with or without Co(2+) or Zn(2+)

Diosgenin (DIO) is the active ingredient of Dioscorea species. The interaction of DIO with bovine serum albumin (BSA) was investigated through spectroscopic methods under simulated physiological conditions. The fluorescence quenching data revealed that the binding of DIO to BSA without or with Co(2+) or Zn(2+) was a static quenching process. The presence of Co(2+) or Zn(2+) both increased the static quenching constants K SV and the binding affinity for the BSA-DIO system. In the sight of the competitive experiment and the negative values of ΔH (0) and ΔS (0), DIO bound to site I of BSA mainly through the hydrogen bond and Van der Waals' force. In addition, the conformational changes of BSA were studied by Raman spectra, which revealed that the secondary structure of BSA and microenvironment of the aromatic residues were changed by DIO. The Raman spectra analysis indicated that the changes of conformations, disulfide bridges, and the microenvironment of Tyr, Trp residues of BSA induced by DIO with Co(2+) or Zn(2+) were different from that without Co(2+) or Zn(2+).

Molecular modeling reveals the novel inhibition mechanism and binding mode of three natural compounds to staphylococcal α-hemolysin

α-Hemolysin (α-HL) is a self-assembling, channel-forming toxin that is produced as a soluble monomer by Staphylococcus aureus strains. Until now, α-HL has been a significant virulence target for the treatment of S. aureus infection. In our previous report, we demonstrated that some natural compounds could bind to α-HL. Due to the binding of those compounds, the conformational transition of α-HL from the monomer to the oligomer was blocked, which resulted in inhibition of the hemolytic activity of α-HL. However, these results have not indicated how the binding of the α-HL inhibitors influence the conformational transition of the whole protein during the oligomerization process. In this study, we found that three natural compounds, Oroxylin A 7-O-glucuronide (OLG), Oroxin A (ORA), and Oroxin B (ORB), when inhibiting the hemolytic activity of α-HL, could bind to the “stem” region of α-HL. This was completed using conventional Molecular Dynamics (MD) simulations. By interacting with the novel binding sites of α-HL, the ligands could form strong interactions with both sides of the binding cavity. The results of the principal component analysis (PCA) indicated that because of the inhibitors that bind to the “stem” region of α-HL, the conformational transition of α-HL from the monomer to the oligomer was restricted. This caused the inhibition of the hemolytic activity of α-HL. This novel inhibition mechanism has been confirmed by both the steered MD simulations and the experimental data obtained from a deoxycholate-induced oligomerization assay. This study can facilitate the design of new antibacterial drugs against S. aureus.

A conformational study of hydroxyflavones by vibrational spectroscopy coupled to DFT calculations

The conformational preferences of a series of hydroxyflavones were studied by Raman and FTIR spectroscopies, coupled to Density Functional Theory calculations. Special attention was paid to the effect of hydroxyl substitution, due to its importance on the biological activity of these compounds. Their conformational preferences were found to be determined mainly by the orientation of the hydroxylic groups at C(7) and within the catechol moiety, leading to the occurrence of distinct conformers in the solid state. A complete assignment of the experimental spectra was carried out for these molecules, in the light of their most stable conformers and the corresponding predicted vibrational pattern.

A comparison study on the binding of hesperetin and luteolin to bovine serum albumin by spectroscopy

Binding mechanism of luteolin (LUT) and hesperetin (HES) to bovine serum albumin (BSA) was investigated at 288,298,310K and pH=7.40 by UV absorption spectroscopy, fluorescence quenching and synchronous fluorescence spectroscopy. Under simulated physiological conditions, the fluorescence data indicated that hesperetin binding to BSA mainly occurs through a static mechanism. In contrast, binding of luteolin to BSA is a combined quenching process while static quenching is prevailing. Linear interval of the Stern-Volmer plot of LUT-BSA for the concentration ratio of LUT to BSA ranged from 0.5 to 1.25 was obtained. The thermodynamic parameters obtained from the Van't Hoff equation indicated that electrostatic force was the predominant force in the LUT-BSA and HES-BSA complex. The inner filter effect was eliminated to get accurate data. The conformational changes of BSA caused by LUT and HES were observed in the UV absorption. Results of fluorescence quenching and synchronous fluorescence showed that degree of luteolin-BSA quenching was higher than hesperetin-BSA quenching, which indicated that the 4'-hydroxide radical was more helpful to the ligand binding to proteins than 4'-methoxyl group for flavones.

Oroxylin A inhibits hemolysis via hindering the self-assembly of α-hemolysin heptameric transmembrane pore

Alpha-hemolysin (α-HL) is a self-assembling, channel-forming toxin produced by most Staphylococcus aureus strains as a 33.2-kDa soluble monomer. Upon binding to a susceptible cell membrane, the monomer self-assembles to form a 232.4-kDa heptamer that ultimately causes host cell lysis and death. Consequently, α-HL plays a significant role in the pathogenesis of S. aureus infections, such as pneumonia, mastitis, keratitis and arthritis. In this paper, experimental studies show that oroxylin A (ORO), a natural compound without anti-S. aureus activity, can inhibit the hemolytic activity of α-HL. Molecular dynamics simulations, free energy calculations, and mutagenesis assays were performed to understand the formation of the α-HL-ORO complex. This combined approach revealed that the catalytic mechanism of inhibition involves the direct binding of ORO to α-HL, which blocks the conformational transition of the critical “Loop” region of the α-HL protein thereby inhibiting its hemolytic activity. This mechanism was confirmed by experimental data obtained from a deoxycholate-induced oligomerization assay. It was also found that, in a co-culture system with S. aureus and human alveolar epithelial (A549) cells, ORO could protect against α-HL-mediated injury. These findings indicate that ORO hinders the lytic activity of α-HL through a novel mechanism, which should facilitate the design of new and more effective antibacterial agents against S. aureus.

The mechanism controlling protein-ligand interactions is one of the most important processes in rational drug design. X-ray crystallography is a traditional tool used to investigate the interaction of ligands and proteins in a complex. However, protein crystallography is inefficient, and the development of crystal technology and research remains unequally distributed. Thus, it seems impractical to explore the structure of the α-hemolysin-ORO monomer complex by crystallography. Therefore, we used molecular dynamics simulations to investigate the receptor-ligand interaction in the α-HL-ORO monomer complex. In this study, we found that oroxylin A (ORO), a natural compound with little anti-S. aureus activity, can inhibit the hemolytic activity of α-HL at low concentrations. Through molecular docking and molecular dynamics simulations, we determined the potential binding mode of the protein-ligand interaction. The data revealed that ORO directly binds to α-HL, an interaction that blacks the conformational transition of the critical “Loop” region in α-HL and thus prevents the formation of the α-HL heptameric transmembrane pore, which ultimately inhibits the hemolytic activity of α-HL. This mechanism was confirmed by experimental data. Furthermore, we demonstrated that ORO could protect against α-HL-mediated injury in human alveolar epithelial (A549) cells.

Molecular insight into the inhibition mechanism of cyrtominetin to α-hemolysin by molecular dynamics simulation

The protein α-hemolysin (α-HL) is a self-assembling exotoxin that binds to the membrane of a susceptible host cell. In this paper, experimental studies show that cyrtominetin (CTM) can inhibit the hemolytic activity of α-HL. To understand how CTM can affect hemolytic activity, molecular dynamics simulations were carried out for α-HL-CTM complex and these results were compared with the crystal structure of monomeric α-HL. With this approach, the analysis revealed that the inhibition of CTM involves CTM directly binding to α-HL. Due to the binding of CTM, the conformation of the critical "Loop" region was restrained. This mechanism was confirmed by the experimental data. These findings indicate that CTM hinders the lysis activity of α-HL through a novel mechanism.

Universal metal-semiconductor hybrid nanostructured SERS substrate for biosensing

We demonstrate here a novel high surface area GaN nanowall network substrate with plasmonic Ag nanodroplets, that can be employed as a highly sensitive, reproducible, and charge independent SERS substrate. The uniformity of the size and distribution of the Ag droplets and the absence of linker ligands result in large near-field intensity, while the GaN nanowall network morphology provides multiple reflections for signal enhancement. FDTD calculations simulate the observed hot-spot distribution and reiterate the higher performance of this hybrid substrate over conventional ones. Our studies on oppositely charged proteins provide a proof of concept for employing this as a versatile charge independent label free SERS substrate for trace biomolecule detection.