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AcrB is the major multidrug exporter in Escherichia coli . Although several substrate-entrances have been identified, the specificity of these various transport paths remains unclear. Here we present evidence for a substrate channel (channel 3)  from the central cavity of the AcrB trimer, which is connected directly to the deep pocket without first passing the switch-loop and the proximal pocket . Planar aromatic cations, such as ethidium, prefer channel 3 to channels 1 and 2. The efflux through channel 3 increases by targeted mutations and is not in competition with the export of drugs such as minocycline and erythromycin through channels 1 and 2. A switch-loop mutant, in which the pathway from the proximal to the deep pocket is hindered, can export only channel 3-utilizing drugs. The usage of multiple entrances thus contributes to the recognition and transport of a wide range of drugs with different physicochemical properties. Multidrug transporters possess several drug binding sites. Here the authors describe a transport path specific for planar aromatic cations in the E. coli multi-drug transporter AcrB.

Chemo-mechanical deformation of structured DNA assemblies driven by DNA-binding ligands has offered promising avenues for biological and therapeutic applications. However, it remains elusive how to effectively model and predict their effects on the deformation and mechanical properties of DNA structures. Here, we present a computational framework for simulating chemo-mechanical change of structured DNA assemblies. We particularly quantify the effects of ethidium bromide (EtBr) intercalation on the geometry and mechanical properties of DNA base-pairs through molecular dynamics simulations and integrated them into finite-element-based structural analysis to predict the shape and properties of DNA objects. The proposed model captures various structural changes induced by EtBr-binding such as shape variation, flexibility modulation, and supercoiling instability. It enables a rational design of structured DNA assemblies with tunable shapes and mechanical properties by binding molecules. Chemo-mechanical deformation of structured DNA assemblies driven by DNA-binding ligands is promising for biological and therapeutic applications, but it is elusive how to effectively model and predict their effects on the deformation and mechanical properties of DNA structures. Here, the authors present a computational framework for simulating chemo-mechanical change of structured DNA assemblies, using ethidium bromide intercalation as an example.

Gold nanoparticles (AuNPs) have become frequently used materials in biotechnological and biomedical applications including cancer. They can be commonly synthesized by biological and chemical methods. In the present study, we synthesized Enterococcus -mediated AuNPs and evaluated their cytotoxicity in human colorectal cancer cell line (HT-29). AuNPs are synthesized intracellularly using Enterococcus sp. RMAA. Characterization of AuNPs has done using UV spectrophotometry and transmission electron microscope. Cytotoxicity was evaluated by MTT assay. Intercellular reactive oxygen species (ROS) expression and apoptosis-related morphology were evaluated by dichlorodihydrofluorescein diacetate and acridine orange/ethidium bromide staining via fluorescence microscopy. JC-1 staining and caspase 3 immunofluorescence expression were analyzed by confocal microscopy. Enterococcus sp. RMAA–mediated AuNPs are spherical and induced concentration-dependent cytotoxicity in HT-29 cells. AuNP treatments also induced ROS and caspase-3 expressions and reduced the mitochondrial membrane potential. Morphology related to apoptotic changes was also noticed after AuNP treatments in HT-29 cells. The present study revealed that Enterococcus -derived AuNPs induced apoptotic cell death in HT-29 cells and suggests that AuNPs could be used as a pro apoptotic agent for colon cancer treatment.

Multiple sclerosis (MS) is a severe immune-mediated neurological disease characterized by neuroinflammation, demyelination, and axonal degeneration in the central nervous system (CNS). This is frequently linked to motor abnormalities and cognitive impairments. The pathophysiological hallmarks of MS include inflammatory demyelination, axonal injury, white matter degeneration, and the development of CNS lesions that result in severe neuronal degeneration. Several studies suggested downregulation of nuclear factor erythroid-2-related factor-2 (Nrf2)/Heme oxygenase-1 (HO-1) signaling is a causative factor for MS pathogenesis. Acetyl-11-keto-β-boswellic acid (AKBA) is an active pentacyclictriterpenoid obtained from Boswellia serrata, possessing antioxidant and anti-inflammatory properties. The present study explores the protective potential of AKBA on behavioral, molecular, neurochemical, and gross pathological abnormalitiesandhistopathological alterations by H&E and LFB staining techniques in an experimental model of multiple sclerosis, emphasizing the increase inNrf2/HO-1 levels in the brain. Moreover, we also examine the effect of AKBA on the intensity of myelin basic protein (MBP) in CSF and rat brain homogenate. Specific apoptotic markers (Bcl-2, Bax, andcaspase-3) were also estimated in rat brain homogenate. Neuro behavioralabnormalities in rats were examined using an actophotometer, rotarod test, beam crossing task (BCT),and Morris water maze (MWM). AKBA 50 mg/kg and 100 mg/kg were given orally from day 8 to 35 to alleviate MS symptoms in the EB-injected rats. Furthermore, cellular, molecular, neurotransmitter, neuroinflammatory cytokine, and oxidative stress markers in rat whole brain homogenate, blood plasma, and cerebral spinal fluid were investigated. This study shows that AKBA upregulates the level of antioxidant proteins such as Nrf2 and HO-1 in the rat brain. AKBA restores altered neurochemical levels, potentially preventing gross pathological abnormalities during MS progression.

Various detection methods of the specific product of reaction of superoxide (O 2 •− ) with hydroethidine (HE), namely 2-hydroxyethidium (2-OH-E + ), and with its mitochondria-targeted analog are described. The detailed protocol for quantification of 2-OH-E + , the unique product of HE/O 2 •− in cellular systems, is presented. The procedure includes cell lysis, protein precipitation using acidified methanol and HPLC analysis of the lysate. Using this protocol, we determined the intracellular levels of 2-OH-E + and E + in the range of 10 and 100 pmol per mg protein in unstimulated macrophage-like RAW 264.7 cells. In addition to HE, 2-OH-E + and E + , we detected several dimeric products of HE oxidation in cell lysates. As several oxidation products of HE are formed, the superoxide-specific product, 2-OH-E + needs to be separated from other HE-derived products for unequivocal quantification.

Pseudomonas aeruginosa and Escherichia coli are resistant to wide range of antibiotics rendering the treatment of infections very difficult. A main mechanism attributed to the resistance is the function of efflux pumps. MexAB-OprM and AcrAB-TolC are the tripartite efflux pump assemblies, responsible for multidrug resistance in P. aeruginosa and E. coli respectively. Substrates that are more susceptible for efflux are predicted to have a common pharmacophore feature map. In this study, a new criterion of excluding compounds with efflux substrate-like features was used, thereby refining the selection process and enriching the inhibitor identification process. An in-house database of phytochemicals was created and screened using high-throughput virtual screening against AcrB and MexB proteins and filtered by matching with the common pharmacophore models (AADHR, ADHNR, AAHNR, AADHN, AADNR, AAADN, AAADR, AAANR, AAAHN, AAADD and AAADH) generated using known efflux substrates. Phytochemical hits that matched with any one or more of the efflux substrate models were excluded from the study. Hits that do not have features similar to the efflux substrate models were docked using XP docking against the AcrB and MexB proteins. The best hits of the XP docking were validated by checkerboard synergy assay and ethidium bromide accumulation assay for their efflux inhibition potency. Lanatoside C and diadzein were filtered based on the synergistic potential and validated for their efflux inhibition potency using ethidium bromide accumulation study. These compounds exhibited the ability to increase the accumulation of ethidium bromide inside the bacterial cell as evidenced by these increase in fluorescence in the presence of the compounds. With this good correlation between in silico screening and positive efflux inhibitory activity in vitro, the two compounds, lanatoside C and diadzein could be promising efflux pump inhibitors and effective to use in combination therapy against drug resistant strains of P. aeruginosa and E. coli.

Hydroxamic acids represent a group of weak organic acids, both naturally occurring and synthetically derived, characterized by the general formula RC(= O)N(R’OH). In this study, we investigated the binding behavior of N-m-tolyl-4-chlorophenoxyaceto hydroxamic acid with calf thymus DNA (ct-DNA) and torula yeast RNA (t-RNA) through a combination of techniques including UV–visible spectroscopy, fluorescence emission analysis, viscometry, and computational simulations using AutoDock4 software. Our findings reveal that the mode of binding between the compound and the nucleic acids is consistent with intercalation. Competitive binding experiments demonstrated that the complex competes effectively with ethidium bromide (EB) for binding to ct-DNA/t-RNA, displacing EB from its binding sites. Additionally, the introduction of the compound into the DNA-EB system resulted in a quenching of fluorescence emission peaks. Analysis of absorption spectra indicated a red shift and hypochromic shift when the compound interacted with DNA, further supporting the intercalative binding mode. The calculated binding constant (K b ) value for the compound is 6.62 × 10 4  M −1 and 5.40 × 10 3  M −1 indicating a strong interaction with ct-DNA and t-RNA respectively. We determined the Stern–Volmer constants for ct-DNA and t-RNA as 9.96 × 10 4  M −1 and 8.13 × 10 5  M −1 , respectively. The binding free energy values for ct-DNA/t-RNA were calculated to be − 3.741 × 10 7 and − 5.425 × 10 8  kcal/mol, respectively. Viscometric studies corroborated the UV results, showing a continuous increase in relative viscosity of ct-DNA/t-RNA solutions with the addition of the optimal hydroxamic acid concentration. Furthermore, we assessed the antioxidant activity of the compound using DPPH-radical scavenging and β-carotene linoleic acid assays. Gel electrophoresis results demonstrated the compound's remarkable efficacy in preventing DNA damage. Collectively, all experimental evidence supports the conclusion that N-m-tolyl-4-chlorophenoxyaceto hydroxamic acid binds to ct-DNA/t-RNA through an intercalative mechanism, which is consistent with our molecular docking simulations.

Background Pyroptosis is a novel programmed cell death. It is identified as caspase-1 dependent and characterized by plasma-membrane rupture and release of proinflammatory intracellular contents inculuding IL-1 beta and IL-18. Pyroptosis is distinct from other forms of cell death, especially apoptosis that is characterized by nuclear and cytoplasmic condensation and is elicited via activation of a caspase cascade. In pyroptosis, gasdermin D (GSDMD) acts as a major executor, while NLRP3 related inflammasome is closely linked to caspase-1 activation. Given that pyroptosis has played a critical role in the progression of non-alcoholic steatohepatitis (NASH), here, we investigated whether the regulation of pyroptosis activation is responsible for the protective role of monounsaturated oleic acids in the context of hepatocellular lipotoxicity. Methods Human hepatoma cell line HepG2 cells were exposed to palmitic acid (PA) with or without oleic acids (OA) or/and endoplasmic reticulum (ER) stress inhibitor tauroursodeoxycholic acid (TUDCA) for 24 h. Besides, the cells were treated with the chemical ER stressor tunicamycin (TM) with or without OA for 24 h as well. The expressions of pyroptosis and ER stress related genes or proteins were determined by real-time PCR, Western blot or immunofluorescence. The morphology of pyroptosis was detected by acridine orange and ethidium bromide (AO/EB) staining. The release of IL-1 beta and tumor necrosis factor alpha (TNF-α) was determined by ELISA. Sprague–Dawley (SD) rats were fed with high fat diet (HFD) for 16 w, then, HFD was half replaced by olive oil to observe the protective effects of olive oil. The blood chemistry were analyzed, and the liver histology and the expressions of related genes and proteins were determined in the liver tissues. Results We demonstrated that PA impaired the cell viability and disturbed the lipid metabolism of HepG2 cells (P < 0.01) , but OA robustly rescued cells from cell death (P < 0.001) . More importantly, we found that instead of cell apoptosis, PA induced significant pyroptosis, evidenced by remarkably increased mRNA and protein expressions of inflammasome marker NLRP3, Caspase-1 and IL-1beta, as well as cell membrane perforation driving protein GSDMD (P < 0.05) . Furthermore, we demonstrated that the PA stimulated ER stress was causally related to pyroptosis. The enhanced expressions of ER stress markers CHOP and BIP were found subcellular co-located to pyroptosis markers NLRP3 and ASC. Additionally,TM was able to induce pyroptosis like PA did, and ER stress inhibitor TUDCA was able to inhibit both PA and TM induced ER stress as well as pyroptosis. Furthermore, we demonstrated that OA substantially alleviated either PA or TM induced ER stress and pyroptosis in HepG2 cells (P < 0.01) . In vivo, only olive oil supplementation did not cause significant toxicity, while HFD for 32 w obviously induced liver steatosis and inflammation in SD rats (P < 0.05) . Half replacement of HFD with olive oil (a mixed diet) has remarkably ameliorated liver abnormalities, and particularly inhibited the protein expressions of either ER stress and pyroptosis markers (P < 0.05) . Conclusion Palmitic acid induced predominant pyroptosis in HepG2 cells, and ER stress may be responsible for the induction of pyroptosis and subsequent cell death. Monounsaturated oleic acids were able to ameliorate hepatocellular lipotoxicity both in vitro and in vivo, and OA mediated inhibition of ER stress and pyroptosis may be the underlying mechanisms.

Drug efflux is a common resistance mechanism found in bacteria and cancer cells, but studies providing comprehensive functional insights are scarce. In this study, we performed deep mutational scanning (DMS) on the bacterial ABC transporter EfrCD to determine the drug efflux activity profile of more than 1,430 single variants. These systematic measurements revealed that the introduction of negative charges at different locations within the large substrate binding pocket results in strongly increased efflux activity toward positively charged ethidium, whereas additional aromatic residues did not display the same effect. Data analysis in the context of an inward-facing cryogenic electron microscopy structure of EfrCD uncovered a high-affinity binding site, which releases bound drugs through a peristaltic transport mechanism as the transporter transits to its outward-facing conformation. Finally, we identified substitutions resulting in rapid Hoechst influx without affecting the efflux activity for ethidium and daunorubicin. Hence, single mutations can convert EfrCD into a drug-specific ABC importer. Deep mutational scanning revealed the drug efflux activity profile of more than 1,430 single variants, enabling the identification of critical residues that regulate the activity of the bacterial drug efflux pump EfrCD in response to different drugs.

In this work, a novel chromatin-loaded chitosan polyvinyl alcohol composite was developed as a simple, efficient and environmentally friendly adsorbent for the efficient removal of ethidium bromide (EtBr). SEM images showed that the composites were characterized by dense porous and uniformly distributed morphology. The BET analysis showed the presence of mesopores and macropores in the composites. FTIR and XRD results showed that the chromatin was uniformly dispersed in the chitosan-polyvinyl alcohol carrier through hydrogen bonding. The fluorescence microscopy images showed the change of fluorescence effect before and after the adsorption of the material, which indicated that the chromatin was uniformly distributed in the composites and had a good adsorption effect. The optimal experimental conditions were T = 30℃, t = 120 min, pH = 7.4, m = 0.2 g when the composite with only 5% chromatin content had the ability to adsorb EtBr efficiently (minimum concentration 2 mg·L −1 : adsorption rate 99%; maximum concentration 20 mg·L −1 : adsorption rate 90%).The adsorption kinetics and thermodynamics showed that the EtBr adsorption kinetics of the composite conformed to the pseudo-second-order kinetic model (0.995 <  R 2  < 0.999) and the Freundlich isothermal model, and was a spontaneous process (Δ H  < 0). This study on the immobilization of chromatin will provide a new way and reference for the application of chromatin in the treatment of EtBr pollutants. Graphical abstracts