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Progress in RNA metabolism and function studies relies largely on molecular imaging systems, including those comprising a fluorogenic dye and an aptamer-based fluorescence-activating tag. G4 aptamers of the Mango family, typically combined with a duplex/hairpin scaffold, activate the fluorescence of a green light-emitting dye TO1-biotin and hold great promise for intracellular RNA tracking. Here, we report a new Mango-based imaging platform. Its key advantages are the tunability of spectral properties and applicability for visualization of small RNA molecules that require minimal tag size. The former advantage is due to an expanded (green-to-red-emitting) palette of TO1-inspired fluorogenic dyes, and the truncated duplex scaffold ensures the latter. To illustrate the applicability of the improved platform, we tagged Mycobacterium tuberculosis sncRNA with the shortened aptamer-scaffold tag. Then, we visualized it in bacteria and bacteria-infected macrophages using the new red light-emitting Mango-activated dye.

A method of direct borylation of vinyl-substituted porphyrinoids (porphyrins and chlorins) has been developed based on the copper catalyzed vinylic C–H activation.

Rose Bengal (RB) is an anionic xanthene dye with multiple useful biological features, including photosensitization properties. RB was studied extensively as a photosensitizer, mostly for antibacterial and antitumor photodynamic therapy (PDT). The application of RB to virus inactivation is rather understudied, and no RB derivatives have been developed as antivirals. In this work, we used a synthetic approach based on a successful design of photosensitizing antivirals to produce RB derivatives for virus photoinactivation. A series of n-alkyl-substituted RB derivatives was synthesized and evaluated as antiviral photosensitizers. The compounds exhibited similar 1O2 generation rate and efficiency, but drastically different activities against SARS-CoV-2, CHIKV, and HIV; with comparable cytotoxicity for different cell lines. Submicromolar-to-subnanomolar activities and high selectivity indices were detected for compounds with C4-6 alkyl (SARS-CoV-2) and C6-8 alkyl (CHIKV) chains. Spectrophotometric assessment demonstrates low aqueous solubility for C8-10 congeners and a significant aggregation tendency for the C12 derivative, possibly influencing its antiviral efficacy. Initial evaluation of the synthesized compounds makes them promising for further study as viral inactivators for vaccine preparations.

Perylene-based compounds are attracting significant attention due to their high broad-spectrum antiviral activity against enveloped viruses. Despite unambiguous results of in vitro studies and high selectivity index, the poor water solubility of these compounds prevented in vivo evaluation of their antiviral properties. In this work, we synthesized a series of compounds with a perylene pharmacophore bearing positively charged substituents to improve the aqueous solubility of this unique type of antivirals. Three types of charged groups were introduced: (1) quaternary morpholinium salts (3a–b); (2) a 2′-O-l-valinyl-uridine hydrochloride residue (8), and (3) a 3-methylbenzothiazolium cation (10). The synthesized compounds were evaluated based both on antiviral properties in vitro (CHIKV, SARS-CoV-2, and IAV) and on solubility in aqueous media. Compound 10 has the greatest aqueous solubility, making it preferable for pre-evaluation by intragastrical administration in a mouse model of lethal influenza pneumonia. The results indicate that the introduction of a positively charged group is a viable strategy for the design of drug candidates with a perylene scaffold for in vivo studies.

Progress in the studies of RNA metabolism and function relies largely on molecular imaging systems, including those comprising a fluorogenic dye and an aptamer-based fluorescence-activating tag. G4 aptamers of Mango family, typically combined with a duplex/hairpin scaffold, activate fluorescence of a green-emitting dye TO1-biotin and hold great promise for intracellular RNA tracking. Here, we report a new Mango-based imaging platform. Its key advantages are tunability of spectral properties and applicability for visualization of small RNA molecules that require minimal tag size. The former advantage is due to an expanded (green-to-red-emitting) palette of TO1-inspired fluorogenic dyes, and the latter is ensured by the truncated duplex scaffold. To illustrate applicability of the improved platform, we tagged Mycobacterium tuberculosis sncRNA with the shortened aptamer-scaffold tag and visualized it in bacteria and bacteria-infected macrophages using the new red light-emitting Mango-activated dye.

In order to increase the bioavailability of water-insoluble pyropheophorbide-a (PPP-a) methyl ester, its liposomal form is prepared and the physicochemical and photochemical properties of this form are studied. The quantum yield of 1O2 is found to have a bell-shaped dependence on the concentration of PPP-a in the lipid phase of liposomes with the maximum at 31.6 µmol/g of lipids. The IR spectroscopy shows the photoinduced formation of aldehyde groups in the lipid phase of liposomes. The intracellular accumulation of PPP-a is confirmed by confocal microscopy.

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

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.

Emerging and re-emerging viruses periodically cause outbreaks and epidemics all over the world, eventually leading to global events such as the current pandemic of the novel SARS-CoV-2 coronavirus infection COVID-19. Therefore, an urgent need for novel antivirals is crystal clear. Here we present the synthesis and evaluation of an antiviral activity of phenoxazine-based nucleoside analogs divided into three groups: (1) 8-alkoxy-substituted, (2) acyclic, and (3) carbocyclic. The antiviral activity was assessed against a structurally and phylogenetically diverse panel of RNA and DNA viruses from 25 species. Four compounds (11a-c, 12c) inhibited 4 DNA/RNA viruses with EC50 ≤ 20 μM. Toxicity of the compounds for the cell lines used for virus cultivation was negligible in most cases. In addition, previously reported and newly synthesized phenoxazine derivatives were evaluated against SARS-CoV-2, and some of them showed promising inhibition of reproduction with EC50 values in low micromolar range, although accompanied by commensurate cytotoxicity., Graphical abstract Image 1

Solid paraffin briquettes are one of the most modern types of rodenticide baits, because they protect it from the environmental exposure and do not reduce palatability of rodents. This paper proposes a simple universal method for the determination of brodifacoum, bromadiolone and difenacoum in solid briquettes, which are a mixture of paraffin, poison and filler, which can be used as grain, flour and the like. The difficulty in the analysis of baits containing paraffin, is to get rid of it. For this, we propose to use hexane-acetonitrile extraction in the system. Paraffin dissolves in hexane, while brodifacoum, bromadiolone and difenacoum do not. The resulting two-phase system was separated using a separatory funnel and the bottom fraction was collected. If any fillers were present in the sample, they were filtered until the mixture was separated, the residue was washed with acetonitrile. Before introducing the sample into the chromatograph, it was filtered twice with PTFE filters with a porosity of 0.45 µm. The best separation was achieved using a Thermo Acclaim® Surfactant column using acetonitrile and 0.1 M aqueous ammonium acetate solution (pH 5.4) as the mobile phase in a gradient elution mode. All three poisons were detected at a wavelength of 264 nm. This method has a sensitivity of 0.028 mg. The linearity range is from 0.00067 to 0.01%. The recovery rate for bromadiolone is 94%, for brodifacoum, 98%, and for difenacoum, 90%.

G-quadruplexes (G4) represent one class of non-canonical secondary nucleic acid structures that are currently regarded as promising and attractive targets for anti-cancer, anti-viral and antibacterial therapy. Herein, we probe a new i-clamp-inspired phenoxazine scaffold for designing G4-stabilizing ligands. The length of the protonated aminoalkyl tethers ('arms') of the phenoxazine-based ligand was optimized in silico. Two double-armed ligands differing in the relative orientation of their arms and one single-armed ligand were synthesized. The two-armed ligands significantly enhanced the thermal stability of the G-quadruplex structures (increasing the melting temperature by up to 20 °C) and displayed G4 selectivity over duplex DNA. The ligands look promising for biological studies and the phenoxazine scaffold could be a starting point for designing new G4-interacting compounds.

A new approach to functionalize porphyrinoids was developed based on the Vilsmeier formylation followed by the azine formation and a new class of the compounds namely azines of porphyrinoids was obtained. Variously substituted azine porphyrins, chlorins and their dyads were synthesized, and their structural and electronic parameters were studied with X-ray diffraction analysis, electronic absorption and emission spectra, electrochemistry and DFT calculations. Azine represents a very peculiar bridge with an unclear conjugation ability affecting optical properties of chromophores. This work was aimed to reveal azine properties and the influence of the azine bridge on the chromophores linked. The results of investigation allowed to conclude that azine bridge can partly be regarded as a conjugation switch with a high threshold level of switching, where limited conjugation in the ground state can be greatly increased at higher energy states of the azine molecule.

Nowadays modified oligonucleotides are widely used in diagnostics and as novel therapeutics. Introduction of modified or unnatural residues into oligonucleotides allows fine tuning of their binding properties to complementary nucleic acids and leads to improved stability both in vitro and in vivo. Previously it was demonstrated that insertion of phenoxazine nucleotides with various groups in C9-position into oligonucleotides leads to a significant increase of duplex stability with complementary DNA and RNA. Here the synthesis of a novel G-clamp nucleoside analogue (G8AE-clamp) bearing 2-aminoethyl tether at C8-atom is presented. Introduction of such modified residues into oligonucleotides lead to enhanced specificity of duplex formation towards complementary DNA and RNA targets with increased thermal and 3'-exonuclease stability. According to CD-spectroscopy studies G8AE-clamp does not substantially disrupt helix geometry. Primers containing G8AE-clamp demonstrated superior sensitivity in qPCR detection of dsRNA of Kemerovo virus in comparison to native oligonucleotides.

The phenoxazine scaffold is widely used to stabilize nucleic acid duplexes, as a part of fluorescent probes for the study of nucleic acid structure, recognition, and metabolism, etc. Here we present the synthesis of phenoxazine-based nucleoside derivatives and their antiviral activity against a panel of structurally diverse viruses: enveloped DNA herpesviruses varicella zoster virus (VZV) and human cytomegalovirus, enveloped RNA tick-borne encephalitis virus (TBEV), and non-enveloped RNA enteroviruses. Studied compounds were effective against DNA and RNA viruses reproduction in cell culture. 3-(2′-Deoxy-β-D-ribofuranosyl)-1,3-diaza-2-oxophenoxazine proved to be a potent inhibitor of VZV replication with superior activity against wild type than thymidine kinase deficient strains (EC50 0.06 and 10 μM, respectively). This compound did not show cytotoxicity on all the studied cell lines. Several compounds showed promising activity against TBEV (EC50 0.35–0.91 μM), but the activity was accompanied by pronounced cytotoxicity. These compounds may be considered as a good starting point for further structure optimization as antiherpesviral or antiflaviviral compounds.

Non-canonical DNA structures are widely used for regulation of gene expression, in DNA nanotechnology and for the development of new DNA-based sensors. I-motifs (iMs) are two intercalated parallel duplexes that are held together by hemiprotonated C-C base pairs. Previously, iMs were used as an accurate sensor for intracellular pH measurements. However, iM stability is moderate, which in turn limits its in vivo applications. Here, we report the rational design of a new substituted phenoxazine 2′-deoxynucleotide (i-clamp) for iM stabilization. This residue contains a C8-aminopropyl tether that interacts with the phosphate group within the neighboring chain without compromising base pairing. We studied the influence of i-clamp on pH-dependent stability for intra- and intermolecular iM structures and found the optimal positions for modification. Two i-clamps on opposite strands provide thermal stabilization up to 10–11°C at a pH of 5.8. Thus, we developed a new modification that shows significant iM-stabilizing effect both at strongly and mildly acidic pH and increases iM transition pH values. i-Clamp can be used for tuning iM-based pH probes or assembling extra stable iM structures for various applications.

Regioselective bromination of methyl pyropheophorbide a at the C32-position of the terminal double bond has been carried out as a one-pot two-step addition/elimination process. The elimination occurs with 100% stereoselectivity and bromovinyl 4 has E-configuration of the C3-double bond. The reactivity of unsaturated bromide 4 has been evaluated in the series of the Pd -catalyzed coupling reactions.

Chlorhexidine digluconate has been widely used in lenticular compositions, skin antiseptics and other ready-to-use disinfectants. This is due to its low toxicity, as well as a wide range of antimicrobial effects. A commonly used method for the analysis of commercially available chlorhexidine digluconate (usually available as a 20% aqueous solution) is high-performance liquid chromatography. In this article, the main methods of analysis used to determine chlorhexidine digluconate in disinfectants and skin antiseptics are considered. A new simple technique for the determination of chlorhexidine digluconate in technical products and disinfectants based on acid-base titration in alcohol-ketone is developed. It is shown that in this medium hydrochloric acid interacts with two nitrogen atoms of the chlorhexidine digluconate molecule. The end point of the titration is established by the transition of the blue color to green in the presence of bromophenol blue. The range of measured concentrations is from 0.1 to 2.0 mass%. The relative error of the method is 2.5% with the confidence probability P = 0.95. A comparison of the diode array detector and the charged aerosol detector for the determination of chlorhexidine digluconate has been performed. It is shown that a charged aerosol detector can be used to analyze chlorhexidine digluconate in cases where it is difficult to analyze with an ultraviolet or diode array detector. However, the sensitivity of the detector of charged aerosols is significantly lower than that of the diode matrix, and the linearity range is smaller. All methods were tested on model samples, as well as on samples of disinfectants, skin antiseptics, soaps and wipes with antibacterial effect.