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Recent advancements in experimental and computational methods for RNA secondary structure detection have revealed the crucial role of RNA structural elements in diverse molecular processes within living cells. It has been demonstrated that the secondary structure of the entire viral genome is often responsible for performing crucial functions in the viral life cycle and also influences virus evolution. To investigate the role of viral RNA secondary structure, alongside experimental techniques, the use of bioinformatics tools is important for analyzing various secondary structure patterns, including hairpin loops, internal loops, multifurcations, external loops, bulges, stems, and pseudoknots. Here, we have introduced a Python package for analyzing RNA secondary structure elements in viral genomes, which includes the recognition of common secondary structure patterns, the generation of descriptive statistics for these structural elements, and the provision of their basic properties. We applied the developed package to analyze the secondary structures of complete viral genomes collected from the literature, aiming to gain insights into viral function and evolution. Both the package and the collection of secondary structures of viral genomes are available at http://github.com/KazanovLab/RNAsselem ., Competing Interests: Declarations Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) primarily enters the cell by binding the virus's spike (S) glycoprotein to the angiotensin-converting enzyme 2 receptor on the cell surface, followed by proteolytic cleavage by host proteases. Studies have identified furin and transmembrane protease serine 2 proteases in priming and triggering cleavages of the S glycoprotein, converting it into a fusion-competent form and initiating membrane fusion, respectively. Alternatively, SARS-CoV-2 can enter the cell through the endocytic pathway, where activation is triggered by lysosomal cathepsin L. However, other proteases are also suspected to be involved in both entry routes. In this study, we conducted a genome-wide bioinformatics analysis to explore the capacity of human proteases in hydrolyzing peptide bonds of the S glycoprotein. Predictive models of sequence specificity for 169 human proteases were constructed and applied to the S glycoprotein together with the method for predicting structural susceptibility to proteolysis of protein regions. After validating our approach on extensively studied S2' and S1/S2 cleavage sites, we applied our method to each peptide bond of the S glycoprotein across all 169 proteases. Our results indicate that various members of the proprotein convertase subtilisin/kexin type, type II transmembrane family serine protease, and kallikrein families, as well as specific coagulation factors, are capable of cleaving S2' or S1/S2 sites. We have also identified a potential cleavage site of cathepsin L at the K790 position within the S2' loop. Structural analysis suggests that cleavage of this site induces conformational changes similar to the cleavage at the R815 (S2') position, leading to the exposure of the fusion peptide and subsequent fusion with the membrane. Other potential cleavage sites and the influence of mutations in common SARS-CoV-2 variants on proteolytic efficiency are discussed.IMPORTANCEThe entry of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) into the cell, activated by host proteases, is considerably more complex in coronaviruses than in most other viruses and is not fully understood. There is evidence that other proteases beyond the known furin and transmembrane protease serine 2 can activate the spike protein. Another example of uncertainty is the cleavage site for the alternative endocytic route of SARS-CoV-2 entrance, which is still unknown. Bioinformatics methods, modeling protease specificity and estimating the structural susceptibility of protein regions to proteolysis, can aid in studying this topic by predicting the involved proteases and their cleavage sites, thereby substantially reducing the amount of experimental work. Elucidating the mechanisms of spike protein activation is crucial for preventing possible future coronavirus pandemics and developing antiviral drugs., Competing Interests: The authors declare no conflict of interest.

Many viruses, including SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, enter host cells through a process of cell-viral membrane fusion that is activated by proteolytic enzymes. Typically, these enzymes are host cell proteases. Identifying the proteases that activate the virus is not a simple task but is important for the development of new antiviral drugs. In this study, we developed a bioinformatics method for identifying proteases that can cleave viral envelope glycoproteins. The proposed approach involves the use of predictive models for the substrate specificity of human proteases and the application of a structural analysis method for predicting the vulnerability of protein regions to proteolysis based on their 3D structures. Specificity models were constructed for 169 human proteases using information on their known substrates. A previously developed method for structural analysis of potential proteolysis sites was applied in parallel with specificity models. Validation of the proposed approach was performed on the SARS-CoV-2 spike protein, whose proteolysis sites have been well studied.

The importance of 3D protein structure in proteolytic processing is well known. However, despite the plethora of existing methods for predicting proteolytic sites, only a few of them utilize the structural features of potential substrates as predictors. Moreover, to our knowledge, there is currently no method available for predicting the structural susceptibility of protein regions to proteolysis. We developed such a method using data from CutDB, a database that contains experimentally verified proteolytic events. For prediction, we utilized structural features that have been shown to influence proteolysis in earlier studies, such as solvent accessibility, secondary structure, and temperature factor. Additionally, we introduced new structural features, including length of protruded loops and flexibility of protein termini. To maximize the prediction quality of the method, we carefully curated the training set, selected an appropriate machine learning method, and sampled negative examples to determine the optimal positive-to-negative class size ratio. We demonstrated that combining our method with models of protease primary specificity can outperform existing bioinformatics methods for the prediction of proteolytic sites. We also discussed the possibility of utilizing this method for bioinformatics prediction of other post-translational modifications.

While somatic mutations are known to be enriched in genome regions with non-canonical DNA secondary structure, the impact of particular mutagens still needs to be elucidated. Here, we demonstrate that in human cancers, the APOBEC mutagenesis is not enriched in direct repeats, mirror repeats, short tandem repeats, and G-quadruplexes, and even decreased below its level in B-DNA for cancer samples with very high APOBEC activity. In contrast, we observe that the APOBEC-induced mutational density is positively associated with APOBEC activity in inverted repeats (cruciform structures), where the impact of cytosine at the 3'-end of the hairpin loop is substantial. Surprisingly, the APOBEC-signature mutation density per TC motif in the single-stranded DNA of a G-quadruplex (G4) is lower than in the four-stranded part of G4 and in B-DNA. The APOBEC mutagenesis, as well as the UV-mutagenesis in melanoma samples, are absent in Z-DNA regions, owing to the depletion of their mutational signature motifs., Competing Interests: The authors declare no competing interests., (© 2022 The Author(s).)

A method of direct borylation of vinyl-substituted porphyrinoids (porphyrins and chlorins) has been developed based on the copper catalyzed vinylic C-H activation. Ni(II) complexes of meso - and β-vinylporphyrinoids have been transformed to the corresponding pinacolboronated derivatives with good yields and high ( E )-stereoselectivity. The method provides an easy and direct access to the valuable synthons which were shown to act as nucleophylic partners in the Suzuki cross-coupling building tetrapyrrole derivatives with π-conjugation through the carbon-carbon double bond.

Here, we investigated methods for carbene functionalization of porphyrinoids through metal catalyst-free thermal decomposition of their tosylhydrazones. For the first time, tetrapyrrolyl substituted carbenes were obtained via thermolysis of tosylhydrazones of the corresponding tetrapyrrolyl aldehydes and ketones in the presence of a base. The carbenes formed reacted thermally with substrates without a metal catalyst or light irradiation. Carbenes at the β-pyrrolic position of porphyrinoids reacted with styrene leading to cyclopropane derivatives of tetrapyrroles. Carbenes also reacted with 1,4-dioxane with their insertion into the C-H bond yielding a tetrapyrrole 1,4-dioxane conjugate. Thermolysis of tosylhydrazones of meso -formyl-β-octaalkylporphyrinoids led exclusively to the corresponding cyclopentane fused porphyrinoids via intramolecular carbene C-H insertion. A plausible reaction mechanism was discussed based on DFT calculations of the intermediates. The tetrapyrrolyl carbenes were found to be considerably more stable than other carbenes. The products of the functionalization of porphyrinoids via hydrazone formation and subsequent carbene reactions exhibited modified optical spectra. The method for carbene functionalization of porphyrinoids through thermal decomposition of their tosylhydrazones created a new synthetic pathway for tailoring the perimeter of tetrapyrrolic macrocycles. Moreover, this method allows the obtainment of dyes with controllable spectral optical properties. In particular, new tetrapyrrole derivatives possessing phytoporphyrin carbon skeletons which have not been accessible were obtained using a convenient straightforward procedure.

Since the discovery of the role of the APOBEC enzymes in human cancers, the mechanisms of this type of mutagenesis remain little understood. Theoretically, targeting of single-stranded DNA by the APOBEC enzymes could occur during cellular processes leading to the unwinding of DNA double-stranded structure. Some evidence points to the importance of replication in the APOBEC mutagenesis, while the role of transcription is still underexplored. Here, we analyzed gene expression and whole genome sequencing data from five types of human cancers with substantial APOBEC activity to estimate the involvement of transcription in the APOBEC mutagenesis and compare its impact with that of replication. Using the TCN motif as the mutation signature of the APOBEC enzymes, we observed a correlation of active APOBEC mutagenesis with gene expression, confirmed the increase of APOBEC-induced mutations in early-replicating regions and estimated the relative impact of transcription and replication on the APOBEC mutagenesis. We also found that the known effect of higher density of APOBEC-induced mutations on the lagging strand was highest in middle-replicating regions and observed higher APOBEC mutation density on the sense strand, the latter bias positively correlated with the gene expression level., (© The Author(s) 2021. Published by Oxford University Press on behalf of NAR Cancer.)

Bioinformatics-based prediction of protease substrates can help to elucidate regulatory proteolytic pathways that control a broad range of biological processes such as apoptosis and blood coagulation. The majority of published predictive models are position weight matrices (PWM) reflecting specificity of proteases toward target sequence. These models are typically derived from experimental data on positions of hydrolyzed peptide bonds and show a reasonable predictive power. New emerging techniques that not only register the cleavage position but also measure catalytic efficiency of proteolysis are expected to improve the quality of predictions or at least substantially reduce the number of tested substrates required for confident predictions. The main goal of this study was to develop new prediction models based on such data and to estimate the performance of the constructed models. We used data on catalytic efficiency of proteolysis measured for eight major human matrix metalloproteinases to construct predictive models of protease specificity using a variety of regression analysis techniques. The obtained results suggest that efficiency-based (quantitative) models show a comparable performance with conventional PWM-based algorithms, while less training data are required. The derived list of candidate cleavage sites in human secreted proteins may serve as a starting point for experimental analysis., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Photophysical and in vitro photocytotoxicity studies were performed for the photosensitizer Dimegine, a disodium salt 2.4-di(alpha-methoxyethyl)-deuteroporphyrin-IX with very low systemic toxicity. The singlet oxygen and luminescence quantum yield were Φ Δ  = 0,65 ± 0,06, and Φ ƒ =0,11 ± 0,01 respectively, and were independent of the excitation wavelength. The photobleaching coefficients for Dimegine dissolved in phosphate buffer (pH 7.4), and DMEM medium at concentration 2 μM/l and in phosphate buffer (pH 7.0) at concentration 10 μM/l were 16·10 -5 , 9·10 -5 and 2·10 -5 respectively. In vitro cellular distribution and photocytotoxicity was studied in two human (U87 - primary glioblastoma and HT1376 - bladder cancer) and two rat cell lines (RG2 - glioma, and AY27 - bladder carcinoma). Fluorescence microscopy analysis shows primary Dimegine accumulation as small fluorescent inclusion bodies around the nuclei, suggesting an apoptotic over a necrotic cell death mechanism. The PDT efficacy was slightly higher for the rat cell lines over the human-derived cell lines, with LD 50 values of 2,5 μM/l, 2.8 μM/l, 4.5 μM/l, 2.8 μM/l using 530 nm excitation wavelength for AY27, RG2, HT1376 and U87 respectively, and 1.8 μM/l, 2 μM/l, 5 μM/l, 2.4 μM/l using 625 nm excitation wavelength for AY27, RG2, HT1376 and U87 respectively. Comparison to literature data showed that Dimegine demonstrated improved phototherapeutic characteristics comparing to PpIX-mediated PDT., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Conjugates of 17α-substituted testosterone (1 and 2) and 17β-substituted epitestosterone (3 and 4) with pyropheophorbide a were synthesized. The scheme consisted of synthesis of 17α-hydroxy-3-oxopregn-4-en-21-oic and 17β-hydroxy-3-oxopregn-4-en-21-oic acids, and their coupling with pyropheophorbide a by means of either ethylene diamine, or 1,5-diamino pentane linkers. Mutual influence of steroidal and macrocyclic fragments in conjugates molecules was dependent on configuration of C17 and length of linker, that was established by analysis of 1 H NMR spectra and molecular models of conjugates. Studies of interaction of conjugates with prostate carcinoma cells revealed that their uptake and internalization were independent on the androgen receptor activity, but dependent on the structure of conjugates, decreasing in the following row: 3 > 4 ≥ 1 > 2. Conjugates significantly decreased the LNCaP and PC-3 cells growth at 96 h incubation. Epitestosterone derivatives 3 and 4 also showed superior anti-proliferative activity versus testosterone ones. Conformationally more rigid conjugates 1 and 3, comprising short linkers, were more active than those with long linkers; conjugate 3 was the most potent., (Copyright © 2018. Published by Elsevier Inc.)

The study aimed at assessing the level of glutamate receptors antibodies (Abs) in blood serum and cerebrospinal fluid (CSF) of patients with spinal cord ischemia along with traditional diagnostic approaches., Material and Methods: Forty patients with spinal cord ischemia (10 with spinal stroke and 30 with subacute and chronic course of the disease) were enrolled. After exclusion of some participants, 27 patients continued the study. Comparison groups included 30 patients with ischemic stroke and 30 patients with radiculopathy. The control group consisted of 15 healthy volunteers. All participants underwent a neurological examination and spinal cord magnetic resonance imaging (MRI). Abs to glutamate receptors (NR2 subunits of NMDA-receptors, AMPA/kainate receptors) were measured by ELISA., Results: NR2 Abs in patients with spinal cord ischemia were significantly increased in serum (p=0.0001) and CSF (p=0.0005) compared to controls and comparison groups. The NR2 Abs reliably differentiated spinal cord ischemia compared to AMPA/kainate receptors and S100β protein. On the other hand, increased levels of Abs to the AMPA/kainate have been detected in patients with a more severe impairment associated with extensive white matter damage., Conclusion: The results show the potential of the Abs to glutamate receptors assessment in the diagnosis of spinal cord ischemia and severity of the process.

Aim: Study the effect of laser emission in the red spectrum on growth of methicillin- sensitive. and methicillin-resistant strains of Staphylococcus aureus, as well as photodynamic effect of photosensitizer photoditazin., Materials and Methods: Effect of light of semiconduc- tor red laser (X 660 nm, 100 mW/cm2) at 30,'60, 90 and 180 J/cm2 on growth of S. aureus colonies was determined. Time of exposure 5; 10, 15 and 30 minutes. In certain series of experiments bacterial cells were sensitized in advance by a Water. solution of photoditazin at a concentration of5xl0-6 M., Results: Red laser emission was established to cause a pronounced suppression of bacterial growth. This effect on standard S. aureus strain only took place dur- ing use of relatively high exposure doses (180 J/cm2). Photosensitivity of methicillin-resistant strain turned out to be significantly higher: bacteriostatic effect of red light was noted already at the dose of 60 J/cm2. Treatment of bacterial cells with photoditazin in advance signifi- cantly enhanced growth-inhibiting effect of laser light.

The features of porphyrins defining their functionality are related to their conformational flexibility. The degree of nonplanarity of metalloporphyrins depends directly on the number of substituents, their size and their location. The introduction of substituents in the meso positions of β-substituted porphyrins increases the steric interaction and leads to distortions of the porphyrin core. Increasing the distortion of the porphyrin core would augment the bathochromic (red) shift of the electronic absorption spectra. A new nonsymmetrical 2,3,7,8,12,13,17,18-octaethyl-5-[(methylimino)methyl]porphyrin complex of palladium(II), [Pd(C 38 H 47 N 5 )], was synthesized and characterized by NMR, mass spectrometry and X-ray analysis. The features of the electronic absorption spectrum of the synthesized complex are explained by the planarity of the porphyrin core and the π-system of the imino group orthogonal to it.

Aim: To study blood plasma concentrations of NR2-peptide in patients with ischemic stroke (IS) to assess its diagnostic value as a biomarker of cerebral ischemia and determine the dynamics of the biomarker during treatment with cortexin., Material and Methods: One hundred and twenty patients, aged from 18 to 70 years, including 36 with transient ischemic attack (TIA) and 84 with IS in the carotid territory (n=70) and vertebral/basilar territory with the Wallenberg-Zakharchenko syndrome (n=14), were enrolled. The National Institute of Health Stroke scale (NIHSS) was used to assess neurological status. Blood plasma concentration of NR2-peptide was measured in all patients at admission and after treatment. All laboratory results were compared with neuroimaging (MRI, CT) data., Results: Concentrations of NR2-peptide detected in all patients were higher than in controls (>1.5 ng/ml), p<0.0001. The direct correlation between NR2-peptide (from 3.38 ng/ml to 15.6 ng/ml) and ischemic lesion (from few to 80 mm) was observed. A decrease in NR2-peptide concentration (from 8.5 to 5,.9 ng/ml, p<0.0001) was noted in patients treated with cortexin after 10-day treatment course., Conclusion: NR2-peptide blood assay is a reliable hemotest of brain ischemia. Cortexin has a sufficient therapeutic efficacy.

Porphyrin complexes of ruthenium are widely used as models for the heme protein system, for modelling naturally occurring iron-porphyrin systems and as catalysts in epoxidation reactions. The structural diversity of ruthenium complexes offers an opportunity to use them in the design of multifunctional supramolecular assemblies. Coproporphyrins and metallocoproporphyrins are used as sensors in bioassay and the potential use of derivatives as multiparametric sensors for oxygen and H + is one of the main factors driving a growing interest in the synthesis of new porphyrin derivatives. In the coproporphyrin I Ru II complex catena-poly[[carbonylruthenium(II)]-μ-2,7,12,17-tetrakis[2-(ethoxycarbonyl)ethyl]-3,8,13,18-tetramethylporphyrinato-κ 5 N,N',N'',N''':O], [Ru(C 44 H 52 N 4 O 8 )(CO)] n , the Ru II centre is coordinated by four N atoms in the basal plane, and by axial C (carbonyl ligand) and O (ethoxycarbonylethyl arm from a neighbouring complex) atoms. The complex adopts a distorted octahedral geometry. Self-assembly of the molecules during crystallization from a methylene chloride-ethanol (1:10 v/v) solution at room temperature gives one-dimensional polymeric chains.

Aim: To study an effect of cortexin on functional recovery and morphology of the spinal cord of rats with spinal cord ischemia., Material and Methods: Spinal cord ischemia was achieved by ligation of the infrarenal abdominal aorta in 16 rats stratified into two equal groups: the ligation of infrarenal aorta was performed in the control group, aorta ligation was performed also in the experimental group with preliminary intraperitoneally administration of cortexin in a dose of 0.15 mg/kg 30 min before procedure. Evaluation of neurologic deficit was performed by the Tarlov's scale. Morphological evaluation was made by analyzing the histological sections of the lumbar and sacral cord using the Nissl's method of coloring. Statistical analysis was performed as well., Results and Conclusion: A pronounced and significant effect of cortexin, which was clinically expressed in a decrease in neurological deficit (p=0.0095), morphologically in an increase in the number of normochromic neurons (р=0.01), and a decrease in shrunken neurons (р=0.0001) and shadow cells (р=0.0003), was noted. The results suggest a potential myeloprotective effect of cortexin. The drug can be considered in the context of treatment of vascular myelopathy.

Effects of disodium salt 2,4-di(1-metoxyethyl)-deuteroporphyrine-IX (Dimegin) and the light from Soret band (»395-405 nm) at the viability of microbial cells and at their potential to form microbial biofilms have been compared with traditional antiseptics. Irradiation of microbial cells of S. aureus, E. coli, C. albicans and others with diode light (power density 0.05 Wt/cm2) caused a bactericidial effect similar to that obtained with standard anticeptics (chlorhexidine and dioxidine). A comparative study of the effectiveness of Dimegin and Photoditazine (a soluble salt of chlorine e6) as photosensitizers have been performed using the test system of erythrocyte hemolysis in vitro under irradiation with light from the Sore band. Results have shown insignificant difference in the photodynamic effect with similar doses of absorbed light and preparation concentration.

This paper presents the evaluation results of the methods submitted to Challenge US: Biometric Measurements from Fetal Ultrasound Images, a segmentation challenge held at the IEEE International Symposium on Biomedical Imaging 2012. The challenge was set to compare and evaluate current fetal ultrasound image segmentation methods. It consisted of automatically segmenting fetal anatomical structures to measure standard obstetric biometric parameters, from 2D fetal ultrasound images taken on fetuses at different gestational ages (21 weeks, 28 weeks, and 33 weeks) and with varying image quality to reflect data encountered in real clinical environments. Four independent sub-challenges were proposed, according to the objects of interest measured in clinical practice: abdomen, head, femur, and whole fetus. Five teams participated in the head sub-challenge and two teams in the femur sub-challenge, including one team who tackled both. Nobody attempted the abdomen and whole fetus sub-challenges. The challenge goals were two-fold and the participants were asked to submit the segmentation results as well as the measurements derived from the segmented objects. Extensive quantitative (region-based, distance-based, and Bland-Altman measurements) and qualitative evaluation was performed to compare the results from a representative selection of current methods submitted to the challenge. Several experts (three for the head sub-challenge and two for the femur sub-challenge), with different degrees of expertise, manually delineated the objects of interest to define the ground truth used within the evaluation framework. For the head sub-challenge, several groups produced results that could be potentially used in clinical settings, with comparable performance to manual delineations. The femur sub-challenge had inferior performance to the head sub-challenge due to the fact that it is a harder segmentation problem and that the techniques presented relied more on the femur's appearance.

The chemical synthesis of six lipophilic conjugates of chlorins was carried out, in which lipophilic fragment (either hexadecyl- or cholest-5-en-3β-yloxyethyl-) bound to 13(1)-, 15(2)-, 17(3)-positions of macrocycle by formation of related carboxamides. Structure of synthesized conjugates was studied by spectral methods and molecular modeling. Lipophilic conjugates of chlorins, being mixed with egg yolk phosphatidyl choline, formed mixed micelles stable in aqueous media under physiological conditions. Mixed micelles of conjugates with phosphatidyl choline differing in stoichiometric compositions were prepared and characterized by absorption spectra, electron microscopy and laser scattering. These micelles were found to bind and internalized by human breast carcinoma MCF-7 cells. The presented data reveal that modification of macrocycle with lipophilic substituents, solubilization of obtained conjugates in aqueous medium as mixed micelles with phospholipids, and transfer of mixed micelles to cells is simple approach for targeting of chlorin derivatives, which apparently may be used in photodynamic therapy., (Copyright © 2013. Published by Elsevier Ltd.)

The recombinant producer of Rhodospirillum rubrum L-asparaginase (RrA) was received and purification procedure of RrA was developed. It was shown that RrA has following biochemical and catalytic characteristics: K(m) for L-asn 0.22 MM, pH optimum 9.2; temperature optimum 54 degrees C; pI = 5.1 +/- 0.3; L-gln activity seems to be low-to-negligible. K562, DU145 and MDA-MB-231 cellular lines displayed significant sensitivity towards the enzyme (IC50 = 1.80; 9.19 and 34.62 ME/ml, respectively. In comparison with L-asparaginases from E. coli II type (EcA) and Erwinia carotovora (EwA) cytotoxicity of RrA seems to be higher than EwA, but lower than EcA. 10-fold i.p. RrA administration (4000 ME/kg per day) in L5178y bearing mice showed T/C = 172%. The received results show that RrA belongs to I type cellular L-asparaginases with low L-gln activity and the high antiproliferative effect.

We describe a novel technique for heme removal and replacement in the heme domain of P450BM-3 (BMP). The method was applied to obtain the aluminum-protoporphyrin IX (Al-PP) substituted derivative of BMP (Al-BMP). The overall yield of the purified Al-BMP was about 15% as related to the initial amount of the hemeprotein. Al-BMP possesses extensive fluorescence in the 550-650 nm region with excitation in the porphyrin absorbance bands. The protein was shown to bind substrates of P450BM-3 (palmitic, arachidonic, and cis-parinaric acids) with affinities similar to those of the native enzyme (3-6 µM). However, the substrate-induced changes in fluorescence of Al-PP reveal the existence of a second, low-affinity substrate-binding site, which cannot be detected by the spin shift in the native, heme-containing BMP. Using fluorescence resonance energy transfer, we have demonstrated that Al-BMP forms a complex with the flavoprotein domain of P450BM-3 labeled with 7-ethylamino-3-(4'-maleimidylphenyl)-4-methylcoumarin maleimide, revealing the affinity similar to that of native BMP (Kd = 5 µM at 0.06 M ionic strength). Therefore, aluminum-substituted BMP may serve as a valuable tool in studies on the mechanisms of interactions of P450s with their substrates and protein partners., (© 2013 International Union of Biochemistry and Molecular Biology, Inc.)

Accumulation of photosensibilisators - derivatives of E6 chlorines ("Radachlorine", "Photoditazine", "Zelevsky's balsam") in the mucous membrane and selection of most effective sources of emission have been investigated in 30 patients with rhinosinusitis and 10 with tonsillitis. As a source of emission we used light emitting diode (LED) matrix device "ACT" (wavelength approximately 405 nm (Sore band)) and a laser device LAHTA-"MILON"-ML500-SP (wavelength 662 nm). Drug accumulation in the mucous membrane and changes of their concentrations after emission were evaluated by changes of fluorescence, measured with a LESA-01-BIOSPEC spectrometer. The percent of fluorescence decrease ranged from 50% to 92.7%. This suggests intensive disintegration of photosensibilisators, and consequently, high therapeutic activity of this method. Effectiveness of this method is also confirmed by clinical results.

A panel of phosphorescent oligoarginine conjugates of tetracarboxylic Pt(II)-coproporphyrin I dye (PtCP), monosubstituted with long peptides or tetra-substituted with short peptides and having different linkers and peripheral groups, is described. Their photophysical properties, cell loading efficiency, and mechanisms of transport into the cell were investigated and compared. The conjugates were seen to rely on endocytotic mechanisms of cell entry, which are different from that of the unconjugated oligoarginine peptide, and show diverse patterns of intracellular distribution. On the basis of this study, the tetra-substituted PtCP conjugate displaying whole cell distribution was selected for the sensing of intracellular O(2). This probe has been tested in biological experiments on a fluorescence plate reader, including the monitoring of in situ oxygenation of respiring cells and their responses to metabolic stimulation. Similar conjugates of the phosphorescent Pd(II)-coprorphyrin and fluorescent coproporphyrin-ketone were also synthesized and assessed for the sensing of low levels intracellular O(2) and ratiometric pH-sensing, respectively. The results produced and the structure-activity relationships determined can facilitate the rational design of new bioconjugates of porphyrin dyes tailored to specific applications.

Isatin (indole-dione-2,3) is an endogenous indole that exhibits a wide spectrum of biological and pharmacological activities. Physiologically relevant concentrations of isatin (ranged from 1 nM to 10 M) did not influence basal activity of soluble human platelet guanylate cyclase (sGC), but caused a bell-shaped inhibition of the NO-activated enzyme. Inhibition of the NO-dependent activation by isatin did not depend on a chemical nature of the NO donors. The inhibitory effects of ODC (a heme-dependent inhibitor of sGC) and isatin were non-additive suggesting that the inhibitory effect of isatin may involve the heme binding domain (possibly heme iron) and experiments with hemin revealed some isatin-dependent changes in its spectrum. Isatin also inhibited sGC activation by the allosteric activator YC-1. It is suggested that the bell shaped inhibition of the NO-dependent activation of sGC by isatin may be attributed to complex interaction of isatin with the heme binding domain and the allosteric YC-1-binding site of sGC.

Aim: To study long-term prognosis in patients with non-ST elevation acute myocardial infarction (AMI) with reference to changes in myocardial tissue dopplerography (MTD) in the course of treatment., Material and Methods: MTD echocardiography was conducted in 88 non-ST elevation AMI (mean age 58.0-9.8 years) and 34 healthy volunteers (mean age 58.0 +/- 9.8 years). Measurements were made of the velocity of systolic, early and late diastolic peaks at 4 levels of interventricular septum, anterior, lateral and inferior walls of the left ventricle (LV). MTD was repeated before the discharge from hospital. The patients were followed up for 10-18 months after the discharge., Results: By MTD results the patients were divided into 3 subgroups: 1--an asymmetric decrease of MTD values--17(19.3%) patients who had a 20% reduction of the systolic and early diastolic peak velocity compared to healthy controls on one or two adjacent LV walls; subgroup 2--a diffuse decline of MTD values--61 (69.3%) patients. Their velocity of systolic and early diastolic peaks was subnormal on all the walls, all levels of estimation; subgroup 3--10 (11.4%) patients without MTD changes. These proportions changed in the course of treatment: the number of patients with a diffuse decrease of MTD values reduced to 31 (35.3%), the number of patients with an asymmetric MTD decrease rose to 37 (42%), and with unchanged MTD rose to 20 (22.7%) patients. The rate of development of congestive cardiac failure (CCF) and asymptomatic LV dysfunction in the long-term period was significantly higher in the subgroup with retained diffuse decrease of MTD values., Conclusion: The treatment of non-ST elevation AMI reduces the number of patients with a diffuse decrease of MTD values and elevates the number of patients with asymmetric decrease of MTD and unchanged MTD. Persistence of MTD diffuse changes is an unfavourable prognostic factor in relation to CCF and LV silent dysfunction.

Data are presented on the results of photodynamic treatment (PDT) of mice DBA2 with transplantable lympho-leukemia P-388. Different regimens of photosensitizer Dimegin and emission were used. Both intravenous PDT and in combination with local PDT should be recommended.

Research on cell-penetrating peptides for the intracellular delivery of porphyrin compounds has mainly focused on the use of trans-activator of transcription (TAT)-derived peptides and, to a lesser extent, on proline-rich peptides and phosphorescent metalloporphyrins. In this article, we describe a novel phosphorescent oxygen-sensitive probe for intracellular use which comprises a bactenecin 7 peptide fragment (15-24) conjugated with the uncharged monofunctional derivative of Pt(II) coproporphyrin I (PEPP0). This probe provides efficient loading of various mammalian cells, including PC12, HCT116, SH-SY5Y and HeLa, via cell-type-dependent uptake mechanisms. The conjugate displays a similar distribution in cytoplasm and mitochondria which allows local oxygen levels to be monitored. Respiratory responses of PC12 cells loaded with the conjugate, measured on a time-resolved fluorescent reader, showed significant cell deoxygenation in response to uncoupling by carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone and external hypoxia. Treatment with mitochondrial inhibitors led to a decrease in cell deoxygenation. Although the biophysical properties of this conjugate are similar to those of the phosphorescent intracellular oxygen-sensitive probes described previously, it possesses a number of advantages, including ease of synthesis, high loading efficiency and reliability in physiological experiments with cells. This intracellular probe can be employed for the measurement of intracellular O(2) levels in samples containing mammalian cells using the phosphorescence quenching technique. In addition, the responses to metabolic stimuli can be assessed in a wide range of cells, as can the levels of relative cell oxygenation under external hypoxia., (© 2010 The Authors Journal compilation © 2010 FEBS.)

Synthesis of 13'[(cholest-5-en)-3beta-yloxyethoxycarbamoyl]-chlorin e6 starting from methylpheophorbide and 3beta(2-hydroxy)-ethoxycholest-5-ene is presented, as well as the preparation of related copper complex. Both conjugates obtained may be simply incorporated in phosphatidyl choline vesicles., (2010 Elsevier Ltd. All rights reserved.)

Several new derivatives of the phosphorescent Pt(II)-coproporphyrin (PtCP) were evaluated with respect to the sensing of intracellular oxygen by phosphorescence quenching. Despite the more favorable molecular charge compared to PtCP, self-loading into mammalian cells was rather inefficient for all the dyes, while cell loading by facilitated transport using transfection reagents produced promising results. The PtCP-NH(2) derivative, which gave best loading efficiency and S/N ratio, was investigated in detail including the optimisation of loading conditions, studies of sub-cellular localization, cytotoxicity, oxygen sensitivity and long-term signal stability. Being spectrally similar to the macromolecular MitoXpress™ probe currently used in this application, the PtCP-NH(2) demonstrated higher loading efficiency and phosphorescent signals, suitability for several problematic cell lines and a slightly increased lifetime scale for the physiological range (0-200 μM O(2)). In physiological experiments with different cell types, mitochondrial uncouplers and inhibitors performed on a time-resolved fluorescence plate reader, this probe produced the anticipated profiles of intracellular oxygen concentration and responses to cell stimulation. Therefore, PtCP-NH(2) represents a convenient probe for the experiments and applications in which monitoring of cellular oxygen levels is required.

Probing of molecular oxygen in mammalian cells is important for the analysis of mitochondrial function, metabolic responses, and energetic status of the cells. We describe a new panel of intracellular O(2)-sensitive probes based on phosphorescent porphyrin dyes conjugated to cell-penetrating peptides. The probes comprising the uncharged derivatives of Pt(II)-coproporphyrin I covalently linked to positively charged TAT-derived peptides are shown to effectively load live mammalian cells without any transfection reagents. The probes work well with all cell types tested, show similar subcellular localization, and produce characteristic responses to cell stimulation with mitochondrial uncouplers and inhibitors. They provide a simple and versatile tool for O(2) monitoring in live cells and in tissue, and an alternative to the existing O(2) probes which require facilitated transport into the cell., (Copyright 2009 Elsevier Inc. All rights reserved.)

A simple, minimally invasive methodology for the analysis of intracellular oxygen in populations of live mammalian cells is described. Loading of the cells with the phosphorescent O(2)-sensing probe, MitoXpress, is achieved by passive liposomal transfer or facilitated endocytosis, followed by monitoring in standard microwell plates on a time-resolved fluorescent reader. Phosphorescence lifetime measurements provide accurate, real-time, quantitative assessment of average oxygen levels in resting cells and their alterations in response to stimulation. Analytical performance of the method is examined, optimized, and then demonstrated with different suspension and adherent cell lines including Jurkat, PC12, A549, HeLa, SH-SY5Y, and C2C12, by monitoring responses to mitochondrial uncouplers, inhibitors, plasma membrane depolarization, and Ca(2+) effectors. The assay provides relevant, information-rich data on cellular function and metabolism. It allows monitoring of small, rapid, and transient changes in cell respiration and screening of new chemical entities.

The development and application of a methodology for measurement of oxygen within single mammalian cells are presented, which employ novel macromolecular near infrared (NIR) oxygen probes based on new metalloporphyrin dyes. The probes, which display optimal spectral characteristics and sensitivity to oxygen, excellent photostability, and low cytotoxicity and phototoxicity, are loaded into cells by simple transfection procedures and subsequently analyzed by high-resolution fluorescence microscopy. The methodology is demonstrated by sensing intracellular oxygen in different mammalian cell lines, including A549, Jurkat, and HeLa, and monitoring rapid and transient changes in response to mitochondrial uncoupling by valinomycin and inhibition by antimycin A. Furthermore, the effect of ryanodine receptor-mediated Ca(2+) influx on cellular oxygen uptake is shown by substantial changes in the level of intracellular oxygen. The results demonstrate the ability of this technique to measure small, rapid, and transient changes in intracellular oxygen in response to different biological effectors. Moreover, this technique has wide ranging applicability in cell biology and is particularly useful in the study of low oxygen environments (cellular hypoxia), mitochondrial and cellular (dys)function, and for therapeutic areas, such as cardiovascular and neurological research, metabolic diseases, and cancer.

Quenching of phosphorescent platinum(II) and palladium(II) coproporphyrin (MeCP) labelled oligonucleotides was investigated. Strong hybridization-specific quenching was observed in duplex DNA structures with a variety of quenchers and with two identical porphyrin labels when in close proximity. Classical resonance energy transfer mechanism was ruled out, since quenching did not correlate with spectral overlaps and lifetime changes were insignificant. Quenching of MeCP by the free quenchers in solution revealed that porphyrin-porphyrin quenching is predominantly static while other dyes quench dynamically. The results suggest that the quenching in DNA duplex proceeds via direct contact.

The influence of protoporphyrin IX derivatives--2,4-di(1-methoxyethyl)-deuteroporphyrin IX disodium salt (dimegin) and hematoporphyrin IX (HP)--on the activation of human platelet soluble guanylate cyclase by sodium nitroprusside was investigated. Dimegin and HP, like 1-benzyl-3-(hydroxymethyl-2-furyl)indazole (YC-1), produce synergistic effects on the activation of soluble guanylate cyclase by sodium nitroprusside. The synergistic activation of the enzyme by the combination of 10 microM sodium nitroprusside and 5 microM dimegin (or 5 microM HP) was 190 +/- 19 and 134 +/- 10%, respectively. The synergistic activation of guanylate cyclase by 3 microM YC-1 and 10 microM sodium nitroprusside was 255 +/- 19%. Dimegin and HP had no effect on the activation of guanylate cyclase by YC-1; they did not change the synergistic effect of YC-1 (3 microM) and sodium nitroprusside (10 microM) on guanylate cyclase activity. The synergistic activation of NO-stimulated guanylate cyclase activity by dimegin and HP represents a new biochemical effect of these compounds that may have important pharmacotherapeutic and physiological significance.

Photodynamic therapy (PDT) is frequently accompanied by induction of systemic immunosuppression. Photochemical mechanisms underlying this effect are not completely understood. Here, we demonstrate the immunosuppressive activity of photooxidation products of protoporphyrin IX dimethyl ester (PPIX) in a murine model of contact hypersensitivity (CHS) to 2,4-dinitrofluorobenzene (DNFB). Intravenous injection of the preirradiated solution of PPIX to mice resulted in fluence-dependent suppression of the CHS. The samples of photodecomposed PPIX with suppressive effect on the CHS contained chlorin-type products, namely, two isomers of photoprotoporphyrin (pPP1 and pPP2) as main photoproducts. Concentration-dependent suppression of the CHS was also induced when purified pPP1 or pPP2 were injected to mice intravenously. These purified photoproducts exerted equal immunosuppressive activity. The highest suppression of the CHS was induced when pPP1 was injected 20 h before sensitization with DNFB. The lowest suppression was at its injection time 24 h before challenge. The pPP1-induced suppression of the CHS was adoptively transferable and was associated with generation of cells with suppressive functions. These suppressor cells inhibited the efferent phase of the CHS. Our results strongly indicate that induction of systemic immunosuppression by PDT with PPIX may proceed through photobleaching of photosensitizer and generation of photoprotoporphyrins, which can affect T cell immunity.

Phosphorescent platinum(II) coproporphyrin label (PtCP) is evaluated for the detection of cellular proteases by time-resolved fluorescence in homogeneous format. An octameric peptide containing the recognition motif for the caspase-3 enzyme was dual labeled with a new maleimide derivative of PtCP and with the dark quencher dabcyl. Following photophysical characterization, the quenched substrate was employed in cleavage assays for caspase-3 using Jurkat and HL60 cell lines treated with proapoptotic stimuli performed on a commercial plate reader. Dose-response and time course assays for the drug camptothecin were obtained for comparison with conventional fluorometric detection.

[structure: see text] A racemic mixture of the ethane-bridged bis(zinc octaethylchlorin) was successfully resolved for the first time to yield two enantiomers that exhibit substantial CD signals in the regions of chlorin B and Q transitions. The absolute configuration of the corresponding enantiomers was assigned and the origin of its high optical activity was rationalized through a combined spectral, crystallographic, and theoretical analysis.

Chlorin e(6) and its derivatives are promising sensitizers for photodynamic therapy (PDT). In order to compare the photodynamic effects of 8 novel derivatives of chlorin e(6) and to explore some mechanisms of their effects at the cellular level, we studied PDT-induced changes in bioelectric activity of crayfish mechanoreceptor neuron that was used as a sensitive experimental model. Neurons were insensitive to red laser irradiation (632.8 nm; 0.3 W/cm(2)) or to photosensitizers alone, but changed firing rate and died under the photodynamic effect of nanomolar concentrations of sensitizers. The dynamics of neuron responses depended on photosensitizer type and concentration. The dependence of neuron lifetime on photosensitizer concentration allowed comparing efficiencies of different photosensitizers. Radachlorin was the most potent photosensitizer comparable with mTHPC. High photodynamic efficiency of some chlorin e(6) derivatives was related to weak dependence of neuron lifetime on sensitizer concentration, indicating to the initiation of 2-3 secondary processes such as free radical membrane damage by one absorbed photon. Photodynamic efficiency of sensitizers depended on amphiphilicity influencing their intracellular localization.

In this paper we describe the preparation of a series of new phosphorescent labelling reagents, based on monosubstituted palladium(II) coproporphyrin-I and the isothiocyanato reactive group. The labelling reagents differ with respect to the chemical composition of the linker unit that combines the reactive group and the porphyrin chromophore. Altogether, seven different labelling reagents are prepared. The new labelling reagents are conjugated with monoclonal mouse IgG to yield label conjugates with variable degrees of conjugation. The effect is studied of linker unit on: (a) the conjugation reaction kinetics; (b) the biological activity of the resulting IgG conjugates; and (c) the efficiency of phosphorescence emission. The results show that an increase in the length of the linker unit has a positive effect on both the reactivity of the label and the biological activity of the resulting conjugates. In addition, the results indicate that the labels with the most hydrophilic linker units exhibit the highest phosphorescence emission efficiencies., (Copyright 2003 John Wiley & Sons, Ltd.)

A comparative analysis of the ability of 4-(1-methyl-3-hydroxybutyl)-deuteroporphyrin-IX (I) and 2,4-di-(1-methyl-3-hydroxybutyl)-deuteroporphyrin-IX (II) to photosensitize hemolysis of human erythrocytes was performed. The photohemolytic efficiency of dye I was shown to be about 60 times higher than that of dye II. It was found that a part of each dye tightly binds to erythrocyte membranes and is not removed by washing. A method for estimating the share of the dye tightly bound to the membrane (beta) was proposed, which takes into account the shielding effect produced by the free dye and the photohemolytic efficiency of the bound dye. It was shown that the beta values for dyes I and II are 86 and 61% and correlate with the coefficients of distribution of the dyes in the octanol/water system (20.7 and 17.0, respectively).

Syntheses of octaethylporphine-diketone (OEPDK) and its platinum(II) and palladium(II) complexes (PtOEPDK, PdOEPDK) were optimized, and the dyes were isolated in a pure form in preparative quantities. They were characterized by the NMR, UV-VIS absorption and emission spectroscopy. Electronic spectra of these dyes (absorption and luminescence) were investigated in detail, and compared to corresponding porphyrins and porphyrin-monoketones. OEPDK showed a strong fluorescence at about 700 nm, while PtOEPDK and PdOEPDK showed very weak room-temperature phosphorescence in the region of 850-1100 nm and practically no fluorescence. Protonation mechanisms were studied for these dyes. Protonation at sites other than pyrrole nitrogen atoms was shown to occur, corresponding protomeric spectral forms are presented. The possibilities of the use of porphyrin-diketones as longwave fluorescent and phosphorescent probes are discussed.

The photodynamic effects of 6 new deuteroporphyrin IX derivatives with different amphiphilicity and lipophilicity, as well as effects of known hematoporphyrin derivatives Photofrin II and Photoheme on isolated crayfish mechanoreceptor neurons were studied. After 30 min photosensitization, neurons were irradiated with He-Ne laser (632.8 nm, 0.3 W/cm(2)), and changes in their firing frequency were recorded. Neuron firing was shown to be very sensitive to photodynamic effect of the studied deuteroporphyrin IX derivatives causing irreversible firing abolition at pikomolar concentrations while Photoheme and Photofrin II were effective in the nanomolar range. The most effective sensitizers were 4-(1-methyl-3-hydroxybutyl)- and 4-(1-methyl-2-acetyl-3-oxobutyl)-deuteroporphyrins. Extinction and amphiphilicity were shown to be the most important properties determining photodynamic efficiency of the studied photosensitizers., (Copyright 2001 Academic Press.)

A liposome preparation of a porphyrin photosensitizer for photodynamic therapy of tumors (PDT) was obtained. The in vitro efficiency of the photosensitizer was enhanced 2.5-fold through the liposome formulation. The composition and some properties of the new preparation were studied. An algorithm for a complex approach to the prediction of photosensitizer efficiencies by model experiments in vitro was developed. This approach is based on the use of two models: the determination of coefficient of distribution between n-octanol and a phosphate buffer, pH 7.4, and the determination of the cytotoxic effect on the culture of CaOv ovarian adenocarcinoma cells.

The deuteroporphyrin-IX derivative Dimegin [2,4-di-(alpha-methoxyethyl)-deuteroporphyrin IX] was investigated with respect to cellular uptake, intracellular localization and cell survival following photodynamic treatment in human cell lines derived from the skin (SCL1 and SCL2, squamous cell carcinoma; HaCaT keratinocytes; N1 fibroblasts). Using flow cytometry, we determined the cellular fluorescence as a marker of the uptake of Dimegin after incubation for 24 h. The intracellular localization of Dimegin was analysed using fluorescence microscopy and co-staining with fluorescent dyes specific for cell organelles. Following irradiation with an incoherent light source (580-740 nm) using a light dose of 24 J/cm2, phototoxicity was determined by means of trypan blue dye exclusion, MTT assays and growth curves. The relative Dimegin fluorescence of the different cell lines declined as follows: SCL1 > HaCaT > N1 > SCL2. Intracellular localization of Dimegin was found in the mitochondria. For all cell lines Dimegin concentrations above 15 microM yielded a significant phototoxic effect. The EC50 for SCL1 cells was 8.9 +/- 2.0 microM Dimegin. The EC50 for the cell lines increased as follows: SCL1 < HaCaT < N1 < SCL2, thus correlating with the cellular fluorescence of Dimegin. The results of the MTT assay were confirmed by trypan blue dye exclusion assay and growth curves. In conclusion, the study shows that Dimegin is an effective photosensitizer with a rapid mechanism of action in vitro, resulting in an immediate loss of plasma membrane integrity following irradiation.

Antibodies conjugated with porphyrins and metalloporphyrins have a great potential for applications in fluorescence or phosphorescence immunoassays as well as in photodynamic therapy, radioimaging and internal radiation therapy of cancer. Here we describe how the new preactivated metalloporphyrin, palladium (II) coproporphyrin I-tetra-N-hydroxysuccinimide ester, can be covalently attached to mouse monoclonal and rabbit anti-human ferritin antibodies. The advantages of the proposed reagent over the previously reported carboxylic porphyrins coupled through carbodiimide activation are indicated. Conformational changes in antibodies caused by each of the two methods were assessed from their binding to the antigen (a probe for the antibody Fv domain) and anti-IgG antibodies probing the global conformation of the CH2 domain in the Fc fragment. Porphyrin coupling through carbodiimide activation resulted in a decrease in both functional activities of modified antibodies even at low levels of modification. In contrast, when the N-hydroxysuccinimide (NHS) derivative of porphyrin was used, enhancement of the antigen-binding affinity of porphyrin-antibody conjugates occurred due to an increase in the conformational mobility (flexibility) of the modified antibodies. The stimulatory effect of conjugation was maximal when one porphyrin molecule was coupled to an antibody molecule. Coupling of NHS-activated porphyrin at pH 7.4, 7.8 and pH 8.5 suggested that the high efficiency of the reaction at pH 8.5 could be attributed predominantly to the formation of antibody aggregates, only 50% of which were covalently cross-linked. The lowest percentage of aggregates in porphyrin-antibody conjugates was found at pH 7.4 and a molar reagent-to-protein ratio in the 10:1-40:1 range. Thus, the use of the NHS-activated carboxylic porphyrin provides a mild, simple and convenient procedure for preparing antibody conjugates with enhanced antigen-binding affinity.

Monoclonal antibodies against Pd-coproporphyrin I have been obtained. The antibody specificity for free as well as for conjugated Pd-coproporphyrin I is characterized. Affinity constants are estimated for 3 monoclonal antibodies effectively interacting with free Pd-coproporphyrin I. A comparative study on the binding of monoclonal antibodies with analogues and derivatives of Pd-coproporphyrin I has revealed that the antigen is mainly located inside the antibody paratope. The protein adjoins complementary to the metalloporphyrin in such a manner that antibodies obtained discern only isomer I, and to some degree, isomer III of coproporphyrin.