The impact of crystallization conditions on structure‐based drug design: A case study on the methylene blue/acetylcholinesterase complex

Structure‐based drug design utilizes apoprotein or complex structures retrieved from the PDB. >57% of crystallographic PDB entries were obtained with polyethylene glycols (PEGs) as precipitant and/or as cryoprotectant, but <6% of these report presence of individual ethyleneglycol oligomers. We report a case in which ethyleneglycol oligomers' presence in a crystal structure markedly affected the bound ligand's position. Specifically, we compared the positions of methylene blue and decamethonium in acetylcholinesterase complexes obtained using isomorphous crystals precipitated with PEG200 or ammonium sulfate. The ligands' positions within the active‐site gorge in complexes obtained using PEG200 are influenced by presence of ethyleneglycol oligomers in both cases bound to W84 at the gorge's bottom, preventing interaction of the ligand's proximal quaternary group with its indole. Consequently, both ligands are ～3.0Å further up the gorge than in complexes obtained using crystals precipitated with ammonium sulfate, in which the quaternary groups make direct π‐cation interactions with the indole. These findings have implications for structure‐based drug design, since data for ligand‐protein complexes with polyethylene glycol as precipitant may not reflect the ligand's position in its absence, and could result in selecting incorrect drug discovery leads. Docking methylene blue into the structure obtained with PEG200, but omitting the ethyleneglycols, yields results agreeing poorly with the crystal structure; excellent agreement is obtained if they are included. Many proteins display features in which precipitants might lodge. It will be important to investigate presence of precipitants in published crystal structures, and whether it has resulted in misinterpreting electron density maps, adversely affecting drug design.     

亚甲蓝与多聚阴离子化合物结合反应的研究

对光谱探针亚甲蓝(MB)分别与硫酸化茯苓多糖(SP)、硫酸软骨素(CS)、透明质酸(HA)等多聚阴离子化合物相互作用的吸收光谱进行了比较研究,探讨了CS等多聚阴离子化合物与MB相互作用机理及其与MB结合的功能基团,计算了MB与SP、CS最大结合数分别为54和73。研究结果表明MB与多聚阴离子化合物的磺酸基发生明显的结合反应,与羧基不能发生明显的结合反应,多聚阴离子化合物与MB结合的功能基团是磺酸基。     

Kinetic and structural studies on the interactions of Torpedo californica acetylcholinesterase with two donepezil-like rigid analogues

Acetylcholinesterase inhibitors were introduced for the symptomatic treatment of Alzheimer’s disease (AD). Among the currently approved inhibitors, donepezil (DNP) is one of the most preferred choices in AD therapy. The X-ray crystal structures of Torpedo californica AChE in complex with two novel rigid DNP-like analogs, compounds 1 and 2, have been determined. Kinetic studies indicated that compounds 1 and 2 show a mixed-type inhibition against TcAChE, with K_i values of 11.12?±?2.88 and 29.86?±?1.12?nM, respectively. The DNP rigidification results in a likely entropy-enthalpy compensation with solvation effects contributing primarily to AChE binding affinity. Molecular docking evidenced the molecular basis for the binding of compounds 1 and 2 to the active site of β-secretase-1. Overall, these simplified DNP derivatives may represent new structural templates for the design of lead compounds for a more effective therapeutic strategy against AD by foreseeing a dual AChE and BACE-1 inhibitory activity.     

Attenuation of noise-induced hearing loss using methylene blue

The overproduction of reactive oxygen species (ROS) and reactive nitrogen species (RNS) has been known to contribute to the pathogenesis of noise-induced hearing loss. In this study, we discovered that in BALB/c mice pretreatment with methylene blue (MB) for 4 consecutive days significantly protected against cochlear injury by intense broad-band noise for 3 h. It decreased both compound threshold shift and permanent threshold shift and, further, reduced outer hair cell death in the cochlea. MB also reduced ROS and RNS formation after noise exposure. Furthermore, it protected against rotenone- and antimycin A-induced cell death and also reversed ATP generation in the in vitro UB-OC1 cell system. Likewise, MB effectively attenuated the noise-induced impairment of complex IV activity in the cochlea. In addition, it increased the neurotrophin-3 (NT-3) level, which could affect the synaptic connections between hair cells and spiral ganglion neurons in the noise-exposed cochlea, and also promoted the conservation of both efferent and afferent nerve terminals on the outer and inner hair cells. These findings suggest that the amelioration of impaired mitochondrial electron transport and the potentiation of NT-3 expression by treatment with MB have a significant therapeutic value in preventing ROS-mediated sensorineural hearing loss.     

Graphene oxide-methylene blue nanocomposite in photodynamic therapy of human breast cancer

The interaction of methylene blue (MB) as a photosensitizer with graphene oxide nano-sheets (GO) was examined in aqueous solution using UV-vis spectrophotometric techniques. MB–GO composites were prepared by mixing the solutions of GO nano-sheets and methylene blue due to interacting of the cationic methylene blue photosensitizer via electrostatic and π–π stacking or hydrophobic cooperative interactions. The cell killing potential of nanocomposite was examined on the MDA-MB-231 breast cancer cells in the absence and presence of red LED irradiation. The results demonstrated that the MB-GO nanocomposite has good performance in photodynamic therapy (PDT) during red LED irradiation. The cytotoxicity of nanocomposite caused reducing cell viability up to 20%. These effects would be due to the nano size structure of composite that could lead to effective cellular penetration. Also the significant difference has seen in lower concentrations of MB and MB-GO nanocomposite. The results show more than 40% increases in cell killing potential in lower concentrations of nanocomposite by using 2.5 μg/mL of each compound. The ratio of GO/MB can affect the interaction and higher ratios of graphene oxide (GO/MB > 1) can induce dimerization of MB. In lower concentrations and ratios of (GO/MB < 1) the free MB concentration increases and the electron shuttling effect of GO in photo activity decreases – which could affect the photocatalytic yield in PDT. The cell viability measurements confirm these effects on cancer cell killing potential of nanocomposite. According to microscopic and PDT assay results, the nanocomposite distribution and diffusion in cells enhanced the photochemical reaction yield in photodynamic therapy of MDA-MB-231 breast cancer cell line.     

Joint interaction of ethidium bromide and methylene blue with DNA. The effect of ionic strength on binding thermodynamic parameters

Large amount of data of experimental and theoretical studies have shown that ethidium bromide (EtBr) and methylene blue (MB) may bind to nucleic acids via three modes: intercalation between two adjacent base pairs, insertion into the plane between neighboring bases in the same strand (semi-intercalation), and outside binding with negatively charged backbone phosphate groups. The aim of the given research is to examine the behavior of these two ligands at both separate and joint DNA binding. The obtained experimental data show that the effect of simultaneous binding of EtBr and MB on double-stranded DNA has a non-additive effect of separate binding. The analyses of the melting thermodynamic parameters of DNA complexes with two bound ligands suggest competitive mechanism of interaction.     

Ionic imbalance and lack of effect of adjuvant treatment with methylene blue in the hamster model of leptospirosis

Leptospirosis in humans usually involves hypokalaemia andhypomagnesaemia and the putative mechanism underlying such ionic imbalances maybe related to nitric oxide (NO) production. We previously demonstrated thecorrelation between serum levels of NO and the severity of renal disease inpatients with severe leptospirosis. Methylene blue inhibits soluble guanylylcyclase (downstream of the action of any NO synthase isoforms) and was recentlyreported to have beneficial effects on clinical and experimental sepsis. Weinvestigated the occurrence of serum ionic changes in experimental leptospirosisat various time points (4, 8, 16 and 28 days) in a hamster model. We alsodetermined the effect of methylene blue treatment when administered as anadjuvant therapy, combined with late initiation of standard antibiotic(ampicillin) treatment. Hypokalaemia was not reproduced in this model: all ofthe groups developed increased levels of serum potassium (K). Furthermore,hypermagnesaemia, rather than magnesium (Mg) depletion, was observed in thishamster model of acute infection. These findings may be associated with anaccelerated progression to acute renal failure. Adjuvant treatment withmethylene blue had no effect on survival or serum Mg and K levels duringacute-phase leptospirosis in hamsters.     

Degradation of methylene blue using co-dopants Mg and Se in an hydroxyapatite composite

In this work, a comparative study was made of different magnesium ion content incorporated into hydroxyapatite (HAP) and modified with selenite ions, with the aim to develop the degradation performance of methylene blue. Although the dopant metal (Mg²⁺) was present at a relatively low ratio, it induced a change in the microstructure, morphology, surface area, external surface charge, particle size, and degradation performance. The effect of magnesium and selenium binary doping on microstructure and degradation of methylene blue was evaluated. The external surface charge measured by zeta potential clarified that the highest negativity was −11.8 mV and this was accomplished in 1.0 Mg/Se-HAP. Furthermore, the roughness average increased from 36.8 nm, reaching 59.2 nm upon the addition of Mg(II). Moreover, transmission electron microscope micrographs showed that compositions were formed as rod shapes. The process of degradation was optimized, showing effectiveness in methylene blue degradation of 62.4% after 150 min of exposure to visible light. Electrostatic attraction and H-bonding, and coordination played vital roles in the adsorption process. The recyclability of the as-prepared compositions demonstrated that the effectiveness had been reduced to ~54.2% after five times of re-use.     

In vitro evaluation of photodynamic activity of methylene blue against Trichophyton verrucosum azole-susceptible and -resistant strains

The intense search for the “Holy Grail” of antifungal therapy can be observed today. The searches are not limited only to discovery of potential antifungal drugs, but also new therapeutic strategies involving the use of chemosensitizers to achieve synergistic effect or physicochemical factors inducing stress conditions in fungal cells. In this study was examined in vitro effectiveness of photodynamic antifungal strategy with methylene blue using a light beam with a wavelength equal to 635 nm toward the Trichophyton verrucosum susceptible and itraconazole- and/or fluconazole-resistant strains. Methylene blue used at concentration equal to 5 μg/mL and in the presence of 40 J/cm² of light energy showed fungicidal effect toward the susceptible strains. However, for azole-resistant isolates, only the energy dose equal to 60 J/cm² at 5 μg/mL of methylene blue allowed to kill the pathogen. This study confirms that methylene blue induced by red light has a definite inhibitory effect on zoophilic dermatophytes.     

Induction of base-pair substitution and prameshift mutations in wild-type and repair-deficient strains of Salmonella typhimurium by the photodynamic action of methylene blue

Induction of back mutations to prototrophy by methylene blue (MB)-sensitized photodynamic (PD) treatment has been studied in wild-type and repair-deficient strains of Salmonella typhimurium carrying either the base-pair substitution mutation hisG46 or the frameshift mutation hisD3052. We found that reversion of the hisG46 mutation was increased in a strain carrying a uvrB deletion and decreased in a strain carrying a recA-type mutation. Reversion of the hisD3052 (frameshift) mutation, on the other hand, was decreased in both uvrB deletion and recA-type strains. The former results are consistent with the hypothesis that the majority of MB-sensitized PD-induced base-pair substitution mutations arise by a mechanism similar to that currently believed to be involved in UV mutagenesis. The latter results suggest that PD-induced frameshift mutations may arise in some other way, and two possible mechanisms involving sequential action of the excision repair and recombinational repair pathways are considered.     

Singlet oxygen quenchers and the photodynamic inactivation of E. coli ribosomes by methylene blue

$\text{E. coli}$ ribosomes are readily photoinactivated by methylene blue in the presence of air. A variety of singlet oxygen quenchers like NaN₃, 2,5-dimethylfuran, hydroquinone and ascorbic acid provide about 60% protection against this photoinactivation indicating that a major mechanism of ribosome inactivation proceeds through the formation of singlet oxygen, with small contributions (<40%) from other mechanisms. The singlet oxygen quenchers, 1,4-diazabicyclo [2.2.2] octane and triethylamine give unexpected results, in that they show no protection against photoinactivation.     

Fruit extract capped colloidal silver nanoparticles and their application in reduction of methylene blue dye

Green synthesis of silver nanoparticles (AgNPs) has become a promising environmentally benign synthetic route in nanoscience and nanotechnology during recent years. In the present work, we have developed an environment-friendly and low-cost method for synthesis of silver nanoparticles from silver nitrate using aqueous fruit extract of Dillenia indica. The as-synthesized nanoparticles were characterized by UV-Vis spectrophotometer, transmission electron microscopy (TEM) and X-ray diffraction (XRD). FTIR study was performed to know the interaction of bio-molecules present in the fruit extract with AgNPs. The catalytic application of the as-synthesized AgNPs was demonstrated against degradation of methylene blue (MB) in aqueous system. The absorption spectra of colloidal suspension of AgNPs showed characteristic surface plasmon resonance (SPR) band centred at a wavelength of 416?nm. TEM image showed that the AgNPs were almost spherical in shape having an average diameter of 10.78?±?.48?nm. XRD pattern and selected area electron diffraction (SAED) pattern with bright spots signify the crystalline nature of nanoparticles. The fruit extract-capped AgNPs was highly stable and have showed the effective catalytic activity in reduction of MB dye.     

Removal of methylene blue dye from aqueous solutions by natural clinoptilolite and clinoptilolite modified by iron oxide nanoparticles

Adsorption techniques are widely used to remove industrial wastewater contaminants, especially non-biodegradable colourants. In this study, Iranian zeolite clinoptilolite was synthesised using magnetic iron oxide as an inexpensive and efficient adsorbent. The results showed that using natural zeolite, the removal efficiency of 26.8.6% at pH?=?3 reached 48% at pH?=?9. However, the adsorption capacity of the modified clinoptilolite did not change by increasing pH; it ranged from 96.4% to 98.6%. Moreover, increase in the initial concentration of the dye did not have any effects on the removal efficacy of the modified clinoptilolite. Using natural zeolite, on the other hand, the adsorption capacity showed a significant decrease and reached less than 10% at the 200?mg/l dye concentration. At the optimal contact time of 45?min, the dye removal rate by the modified zeolite was more than 98% at the optimal dose of 0.5?g. Indeed, the adsorption isotherm complied with Freundlich equation. Overall, the results showed that in comparison to the natural zeolite, the adsorption capacity of the clinoptilolite modified by iron nanoparticles increased significantly due to the uniformity of the cavities and increase in the surface of the adsorbent.     

Enhancement of the binding affinity of methylene blue to site I in human serum albumin by cupric and ferric ions

In this work, the binding characteristics of methylene blue (MB) to human serum albumin (HSA) and the influence of Cu²⁺ and Fe³⁺ on the binding affinity of MB to HSA were investigated using fluorescence, absorption, circular dichroism (CD) spectroscopy and molecular modelling. The results of competitive binding experiments using the site probes ketoprofen and ibuprofen as specific markers suggested that MB was located in site I within sub‐domain IIA of HSA. The molecular modelling results agreed with the results of competitive site marker experiments and the results of CD spectra indicated that the interaction between MB and HSA caused the conformational changes in HSA. The binding affinity of MB to HSA was enhanced but to a different extent in the presence of Cu²⁺ and Fe³⁺, respectively, which indicated that the influence of different metal ions varied. Enhancement of the binding affinity of MB to HSA in the presence of Cu²⁺ is due to the formation of Cu²⁺–HSA complex leading to the conformational changes in HSA, whereas in the presence of Fe³⁺, enhancement of the binding affinity is due to the greater stability of the Fe³⁺–HSA–MB complex compared with the MB–HSA complex. Copyright © 2015 John Wiley & Sons, Ltd.     

A staining procedure for micronucleus test using new methylene blue and acridine orange: specimens that are supravitally stained with possible long-term storage

The micronucleus test has been widely used as an in vivo cytogenetic test. It employs two different kinds of supravital staining methods which use either new methylene blue (N) and Giemsa (G) or acridine orange (AO). We have developed a new staining procedure for the preparation of specimens supravitally stained with possible long-term storage, using both N and AO. This N/AO-staining method involves three steps; (1) combination of the target tissue or target cells with an equivalent volume of 0.5% solution of new methylene blue (N-staining step), (2) immediate smear of the mixture, followed by treatment with methanol for 10 min for fixation and removal of N and drying (referred to as fixed-decolorized specimens), and (3) staining with 0.007% solution of AO for 3 min, followed by washing with Sörensen's buffer (pH 6.8) and covering of specimens before observation (AO-staining step). To examine whether the N/AO-staining method is useful for the micronucleus test, comparisons were made between N-, N/AO-, and AO-stained specimens prepared supravitally from peripheral blood of rats with and without treatment of cyclophosphamide. The results indicate that N/AO-stained specimens can be supravitally observed after long-term storage with the same coloration and comparable frequencies of micronucleated reticulocytes with a positive response as AO-stained specimens, if the staining process is temporarily stopped before AO-staining (as fixed-decolorized specimens), or if the AO-staining step is repeated. The results also showed that separated reticulocyte types are supravitally stained in a similar fashion to N-stained specimens but not to AO-stained specimens, indicative of the preservation of the supravital feature of N-staining. Taken together these results suggest that the N/AO-staining procedure could offer an additional useful staining tool for the micronucleus test.     

A polychromatic staining method for epoxy embedded tissue: a new combination of methylene blue and basic fuchsine for light microscopy

A simple and rapid method is described for staining semithin sections of material embedded in epoxy resin for observing tissues prior to transmission electron microscopy. The method is suitable for tissue fixed with a glutaraldehyde-formaldehyde mixture and postfixed in osmium tetroxide. No etching or oxidizing procedures are necessary. Sections 0.5-0.8 µm thick are dried onto a slide and stained with either 0.75% methylene blue and 0.25% azure B or 0.5% methylene blue and 0.5% azure II in 0.5% aqueous borax and heated over a flame for 8-10 sec. The slides are rinsed with water, then stained the same way with 0.1% basic fuchsine in 5% aqueous ethanol. Cytoplasm stains blue; nuclei darker blue; collagen, mucus and elastin pink to red; fat and intracellular lipid droplets gray-green.     

A polychromatic staining method for epoxy embedded tissue: a new combination of methylene blue and basic fuchsine for light microscopy

A simple and rapid method is described for staining semithin sections of material embedded in epoxy resin for observing tissues prior to transmission electron microscopy. The method is suitable for tissue fixed with a glutaraldehyde-formaldehyde mixture and postfixed in osmium tetroxide. No etching or oxidizing procedures are necessary. Sections 0.5–0.8 µm thick are dried onto a slide and stained with either 0.75% methylene blue and 0.25% azure B or 0.5% methylene blue and 0.5% azure II in 0.5% aqueous borax and heated over a flame for 8–10 sec. The slides are rinsed with water, then stained the same way with 0.1% basic fuchsine in 5% aqueous ethanol. Cytoplasm stains blue; nuclei darker blue; collagen, mucus and elastin pink to red; fat and intracellular lipid droplets gray-green.     

Kinetics of Torpedo californica acetylcholinesterase inhibition by bisnorcymserine and crystal structure of the complex with its leaving group

Natural and synthetic carbamates act as pseudo-irreversible inhibitors of AChE (acetylcholinesterase) as well as BChE (butyrylcholinesterase), two enzymes involved in neuronal function as well as in the development and progression of AD (Alzheimer's disease). The AChE mode of action is characterized by a rapid carbamoylation of the active-site Ser(200) with release of a leaving group followed by a slow regeneration of enzyme action due to subsequent decarbamoylation. The experimental AD therapeutic bisnorcymserine, a synthetic carbamate, shows an interesting activity and selectivity for BChE, and its clinical development is currently being pursued. We undertook detailed kinetic studies on the activity of the carbamate bisnorcymserine with Tc (Torpedo californica) AChE and, on the basis of the results, crystallized the complex between TcAChE and bisnorcymserine. The X-ray crystal structure showed only the leaving group, bisnoreseroline, trapped at the bottom of the aromatic enzyme gorge. Specifically, bisnoreseroline interacts in a non-covalent way with Ser(200) and His(440), disrupting the existing interactions within the catalytic triad, and it stacks with Trp(84) at the bottom of the gorge, giving rise to an unprecedented hydrogen-bonding contact. These interactions point to a dominant reversible inhibition mechanism attributable to the leaving group, bisnoreseroline, as revealed by kinetic analysis.     

A blue chemiluminescence in the reaction of umbelliferone with hypochlorite

A strongly fluorescing 7-hydroxycoumarin (umbelliferone, U) oxidized in dilute (10 μmol/L-0, 1 mol/L) aqueous solution with CIO^? or CIO^? + H₂O₂ (but not with H₂O₂ alone) produces a strong chemiluminescence (CL). Light emission kinetics depends on the pH of solution (4.0–10.5) and the reaction has a low activation energy E_a = 31 ± 2 kJ/mol (285–310 K). The spectrum covers the fluorescence of umbelliferone (400–550 nm, λ_max 460nm). No red emission typical of ¹Δg, ¹Σ⁺g (O₂)₂ is observed either in the umbelliferone +CIO^? or the umbelliferone +CIO^? + H₂O₂ solution. The possible mechanism of CL and concomitant degradative oxidation of umbelliferone is discussed.