Rational Design of Far-Red Archaerhodopsin-3-Based Fluorescent Genetically Encoded Voltage Indicators: from Elucidation of the Fluorescence Mechanism in Archers to Novel Red-Shifted Variants.

Genetically encoded voltage indicators (GEVIs) have found wide applications as molecular tools for visualization of changes in cell membrane potential. Among others, several classes of archaerhodopsin-3-based GEVIs have been developed and have proved themselves promising in various molecular imaging studies. To expand the application range for this type of GEVIs, new variants with absorption band maxima shifted toward the first biological window and enhanced fluorescence signal are required. Here, we integrate computational and experimental strategies to reveal structural factors that distinguish far-red bright archaerhodopsin-3-based GEVIs, Archers, obtained by directed evolution in a previous study (McIsaac et al., PNAS, 2014) and the wild-type archaerhodopsin-3 with an extremely dim fluorescence signal, aiming to use the obtained information in subsequent rational design. We found that the fluorescence can be enhanced by stabilization of a certain conformation of the protein, which, in turn, can be achieved by tuning the pK a value of two titratable residues. These findings were supported further by introducing mutations into wild-type archeorhodopsin-3 and detecting the enhancement of the fluorescence signal. Finally, we came up with a rational design and proposed previously unknown Archers variants with red-shifted absorption bands (λmax up to 640 nm) and potential-dependent bright fluorescence (quantum yield up to 0.97%).

Insertion of metal carbenes into the anilinic N-H bond of unprotected aminobenzenesulfonamides delivers low nanomolar inhibitors of human carbonic anhydrase IX and XII isoforms.

Herein we report the synthesis of a set of thirty-four primary sulfonamides generated via formal N-H-insertion of metal carbenes into anilinic amino group of sulfanilamide and its meta-substituted analog. Obtained compounds were tested in vitro as inhibitors of four physiologically significant isoforms of the metalloenzyme human carbonic anhydrase (hCA, EC 4.2.1.1). Many of the synthesized sulfonamides displayed low nanomolar Ki values against therapeutically relevant hCA II, IX, and XII, whereas they did not potently inhibit hCA I. Provided the promising activity profiles of the substances towards tumor-associated hCA IX and XII isozymes, single-concentration MTT test was performed for the entire set. Disappointingly, most of the discovered hCA inhibitors did not significantly suppress the growth of cancer cells either in normoxia or CoCl2 induced hypoxic conditions. The only two compounds exerting profound antiproliferative effect turned out to be modest hCA inhibitors. Their out of the range activity in cells is likely attributive to the presence of Michael acceptor substructure which can potentially act either through the inhibition of Thioredoxin reductases (TrxRs, EC 1.8.1.9) or nonspecific covalent binding to cell proteins.

Photosensitive Poly-l-lysine/Heparin Interpolyelectrolyte Complexes for Delivery of Genetic Drugs.

Photo-triggered release of biopharmaceutical drugs inside the cells is a challenging direction of modern science, which requires obtaining new polymeric systems. The interpolyelectrolyte complexes (IPECs) of poly-l-lysine with heparin capable of encapsulation of genetic constructions-such as model oligonucleotide, siRNA, and pDNA-were obtained. Poly-l-lysine to heparin ratios were optimized to provide the appropriate release kinetics of genetic material from the polyplex. In order to impart the obtained IPEC with photosensitive properties, the linker was synthesized as based on 4-brommethyl-3-nitrobenzoic acid. The conditions and kinetics of photosensitive linker destruction were carefully studied. The colloid particles of IPEC were modified with Cy3 probe and their cellular internalization was investigated by flow cytometry method. The efficacy of photosensitive IPECs as siRNA and pDNA delivery system was evaluated.

Arene-Ruthenium(II) Complexes Containing 11H-Indeno[1,2-b]quinoxalin-11-one Derivatives and Tryptanthrin-6-oxime: Synthesis, Characterization, Cytotoxicity, and Catalytic Transfer Hydrogenation of Aryl Ketones.

A series of novel mono- and binuclear arene-ruthenium(II) complexes [(p-cym)Ru(L)Cl] containing 11H-indeno[1,2-b]quinoxalin-11-one derivatives or tryptanthrin-6-oxime were synthesized and characterized by X-ray crystallography, IR, NMR spectroscopy, cyclic voltammetry, and elemental analysis. Theoretical calculations invoking singlet state geometry optimization, solvation effects, and noncovalent interactions were done using density functional theory (DFT). DFT calculations were also applied to evaluate the electronic properties, and time-dependent DFT was applied to clarify experimental UV-vis results. Cytotoxicity for cancerous and noncancerous human cell lines was evaluated with cell viability MTT assay. Complexes demonstrated a moderate cytotoxic effect toward cancerous human cell line PANC-1. The catalytic activity of the complexes was evaluated in transfer hydrogenation of aryl ketones. All complexes exhibited good catalytic activity and functional group tolerance.

Functionalized Pt(II) and Ir(III) NIR Emitters and Their Covalent Conjugates with Polymer-Based Nanocarriers.

Two NIR-emitting platinum [Pt(N^N^C)(phosphine)] and iridium [Ir(N^C)2(N^N)]+ complexes containing reactive succinimide groups were synthesized and characterized with spectroscopic methods (N^N^C, 1-phenyl-3-(pyridin-2-yl)benzo[4,5]imidazo[1,2-a]pyrazine, N^C, 6-(2-benzothienyl)phenanthridine, phosphine-3-(diphenylphosphaneyl)propanoic acid N-hydroxysuccinimide ether, and N^N, 4-oxo-4-((1-(pyridin-2-yl)-1H-1,2,3-triazol-4-yl)methoxy)butanoic acid N-hydroxysuccinimide ether). Their photophysics were carefully studied and analyzed using time-dependent density functional theory calculations. These complexes were used to prepare luminescent micro- and nanoparticles with the "core-shell" morphology, where the core consisted of biodegradable polymers of different hydrophobicity, namely, poly(d,l-lactic acid), poly(ε-caprolactone), and poly(ω-pentadecalactone), whereas the shell was formed by covalent conjugation with poly(l-lysine) covalently labeled with the platinum and iridium emitters. The surface of the species was further modified with heparin to reverse their charge from positive to negative values. The microparticles' size determined with dynamic laser scanning varies considerably from 720 to 1480 nm, but the nanoparticles' diameter falls in a rather narrow range, 210-230 nm. The species with a poly(l-lysine) shell display a high positive (>30 mV) zeta-potential that makes them essentially stable in aqueous media. Inversion of the surface charge to a negative value with the heparin cover did not deteriorate the species' stability. The iridium- and platinum-containing particles displayed emissions the spectral patterns of which were essentially similar to those of unconjugated complexes, which indicate retention of the chromophore nature upon binding to the polymer and further immobilization onto polyester micro- and nanoparticles for drug delivery. The obtained particles were tested to determine their ability to penetrate into different cells types: cancer cells, stem cells, and fibroblasts. It was found that all types of particles could effectively penetrate into all cells types under investigation. Nanoparticles were shown to penetrate into the cells more effectively than microparticles. However, positively charged nanoparticles covered with poly(l-lysine) seem to interact with negatively charged proteins in the medium and enter the inner part of the cells less effectively than nanoparticles covered with poly(l-lysine)/heparin. In the case of microparticles, the species with positive zeta-potentials were more readily up-taken by the cells than those with negative values.

Biological evaluation and molecular dynamics simulation of water-soluble fullerene derivative C60[C(COOH)2]3.

One of the most studied fullerene members, C60, has a potential of application in various fields of biomedicine including reactive oxygen species (ROS) scavenging activity, inhibiting of tumours development, inactivating of viruses and bacteria, as well as elaboration of diagnostic and targeted drug delivery tools. However, the hydrophobicity of this molecule impedes its practical use, therefore the actuality of the research devoted to functionalisation of fullerenes leading to amphiphilic derivatives remains important. In this work, the water-soluble carboxylated fullerene derivative C60[C(COOH)2]3 was studied. Extensive biomedical investigation of this compound, namely, the binding with human serum albumin (HSA), radical scavenging activity in the reaction with diphenylpicrylhydrazyl (DPPH) radical, photodynamic properties, cytotoxicity in human embryonic kidney (HEK293) cell line, erythrocytes' haemolysis, platelet aggregation, and genotoxicity in human peripheral mononuclear cells (PBMC) was conducted. Moreover, the dynamic and structural characteristics of C60[C(COOH)2]3-H2O binary system were obtained using molecular dynamic (MD) method, and size distribution of C60[C(COOH)2]3 associates was measured.

From random to rational: A discovery approach to selective subnanomolar inhibitors of human carbonic anhydrase IV based on the Castagnoli-Cushman multicomponent reaction.

By exploiting the power of multicomponent chemistry, a relatively small, diverse set of primary sulfonamides was synthesized and screened against a panel of human carbonic anhydrases to reveal a low-nanomolar, albeit non-selective hCA IV lead inhibitor. Investigation of the docking poses of this compound identified a hydrophilic pocket unique to hCA IV and conveniently positioned near the carboxylate functionality of the initial lead. Various residues capable of forming hydrogen bonds as well as salt bridges were placed in this pocket via a carboxamides linkage, which led to drastic improvement of potency and selectivity towards hCA IV. This improvement of the desired inhibitory profile was rationalized by the new contacts as had been envisioned. These new tool compounds were shown to possess selective, dose-dependent cytotoxicity against human glioma T98G cell line. The latter showed a substantially increased hCA IV mRNA expression under hypoxic conditions.

Pyridazinone-substituted benzenesulfonamides display potent inhibition of membrane-bound human carbonic anhydrase IX and promising antiproliferative activity against cancer cell lines.

An expanded set of pyridazine-containing benzene sulfonamides was investigated for inhibition of four human carbonic anhydrase isoforms, which revealed a pronounced inhibition trend toward hCA IX, a cancer-related, membrane-bound isoform of the enzyme. Comparison of antiproliferative effects of these compounds against cancer (PANC-1) and normal (ARPE-19) cells at 50 µM concentration narrowed the selection of compounds to the eight which displayed selective growth inhibition toward the cancer cells. More detailed investigation in concentration-dependent mode against normal (ARPE-19) and two cancer cell lines (PANC-1 and SK-MEL-2) identified two lead compounds one of which displayed a notable cytotoxicity toward pancreatic cancer cells while the other targeted the melanoma cells. These findings significantly expand the knowledge base concerning the hCA IX inhibitors whose inhibitory potency against a recombinant enzyme translates into selective anticancer activity under hypoxic conditions which are aimed to model the environment of a growing tumor.

Attachment of a 5-nitrofuroyl moiety to spirocyclic piperidines produces non-toxic nitrofurans that are efficacious in vitro against multidrug-resistant Mycobacterium tuberculosis.

A selectively antimycobacterial compound belonging to the nitrofuran class of antimicrobials has been developed via conjugation of the nitrofuran moiety to a series of spirocyclic piperidines through an amide linkage. It proved to have comparable activity against drug-sensitive (H37Rv) strain as well as multidrug-resistant, patient-derived strains of Mycobacterium tuberculosis. The compound is druglike, showed no appreciable cytotoxicity toward human retinal pigment epithelial cell line ARPE-19 in concentrations up to 100 µM and displayed low toxicity when evaluated in mice.

Non-natural 2H-azirine-2-carboxylic acids: an expedient synthesis and antimicrobial activity.

Non-natural 2H-azirine-2-carboxylic acids were obtained in high yields by FeCl2-catalyzed isomerization of 5-chloroisoxazoles to azirine-2-carbonyl chlorides followed by their hydrolysis. The 3-aryl- and 3-heteroaryl-substituted acids are stable during prolonged storage, exhibit antibacterial activity against ESKAPE pathogens and show a low level of cytotoxicity.

Continued exploration of 1,2,4-oxadiazole periphery for carbonic anhydrase-targeting primary arene sulfonamides: Discovery of subnanomolar inhibitors of membrane-bound hCA IX isoform that selectively kill cancer cells in hypoxic environment.

An expanded set of diversely substituted 1,2,4-oxadiazole-containing primary aromatic sulfonamides was synthesized and tested for inhibition of human carbonic anhydrase I, II, IX and XII isoforms. The initial biochemical profiling revealed a significantly more potent inhibition of cancer-related, membrane-bound isoform hCA IX (reaching into submicromolar range), on top of potent inhibition of hCA XII that is another cancer target. The observed structure-activity relationships have been rationalized by molecular modeling. Comparative single-concentration profiling of the carbonic anhydrase inhibitors synthesized for antiproliferative effects against normal (ARPE-19) and cancer (PANC-1) cell lines under chemically induced hypoxia conditions revealed several candidate compounds selectively targeting cancer cells. More in-depth characterization of these leads revealed two structurally related compounds that showed promising selective cytotoxicity against pancreatic cancer (PANC-1) and melanoma (SK-MEL-2) cell lines.

Cholesterol-imprinted macroporous monoliths: Preparation and characterization.

The development of sorbents for selective binding of cholesterol, which is a risk factor for cardiovascular disease, has a great importance for analytical science and medicine. In this work, two series of macroporous cholesterol-imprinted monolithic sorbents differing in the composition of functional monomers (methacrylic acid, butyl methacrylate, 2-hydroxyethyl methacrylate and ethylene dimethacrylate), amount of a template (4, 6 and 8 mol%) used for molecular imprinting, as well as mean pore size were synthesized by in situ free-radical process in stainless steel housing of 50 mm × 4.6 mm i.d. All prepared materials were characterized regarding to their hydrodynamic permeability and porous properties, as well as examined by BET and SEM methods. Imprinting factors, apparent dynamic dissociation constants, the maximum binding capacity, the number of theoretical plates and the height equivalent to a theoretical palate of MIP monoliths at different mobile phase flow rates were determined. The separation of a mixture of structural analogues, namely, cholesterol and prednisolone, was demonstrated. Additionally, the possibility of using the developed monoliths for cholesterol solid-phase extraction from simulated biological solution was shown.

Immobilized enzyme reactors based on monoliths: Effect of pore size and enzyme loading on biocatalytic process.

Macroporous monolithic columns with different mean pore size (from 360 to 2020 nm) and appropriate flow-through properties were synthesized using free radical in situ copolymerization of glycidyl methacrylate, 2-hydroxyethyl methacrylate and ethylene dimethacrylate. In order to predict the composition of porogen mixture to generate the pores in the interested size interval, the Hildebrand theory was used. Ribonuclease A and its specific low- and macromolecular substrates cytidine-2',3'-cyclic monophosphate sodium salt and RNA were applied as model system. The effect of mean pore size of macroporous monoliths used for enzyme immobilization on molecular recognition and biocatalytic characteristics was examined. The monitoring of RNA degradation was performed using anion-exchange HPLC on monolithic CIM DEAE analytical column. The high efficiency of heterogeneous biocatalysts obtained comparatively to the catalytic reaction of RNA degradation in solution was demonstrated. Additionally, the series of six monolithic immobilized enzyme reactors with different amount of biocatalyst was prepared and studied regarding to the biocatalytic properties at recirculation mode at two experimental variants, e.g. (i) fixed range of concentrations of circulated substrate solutions, and (ii) fixed range of substrate/enzyme molar ratios.

Polyester-based microparticles of different hydrophobicity: the patterns of lipophilic drug entrapment and release.

The paper is devoted to the investigation of the effect of polyester hydrophobicity and ability for crystallisation on lipophilic drug loading and release from microparticles fabricated on the base of these polymers. Poly(l-lactic acid), poly(d, l-lactic acid) and poly (lactic acid-co-glycolic acid) were synthesised by ring-opening polymerisation using stannous octoate as catalyst, while poly(caprolactone) (PCL) and poly(ω-pentadecalactone) (PPDL) formation was catalysed by lipase. The particles were formed via single emulsion evaporation/diffusion method. The particles obtained were studied using SEM, XRD and DSC methods. The degradation of particles based on different polyesters, entrapment and release of a model hydrophobic drug (risperidone®) were thoroughly studied. The effect of particles hydrophobicity and crystallinity on these parameters was of most interest. The drug entrapment is greater for the hydrophobic polymers. Drug release was more rapid from crystalline particles (PLLA, PCL, PPDL), than from amorphous PDLLA and PLGA ones.

Hydrogel Layers on the Surface of Polyester-Based Materials for Improvement of Their Biointeractions and Controlled Release of Proteins.

The modification of bioresorbable polyester surfaces in order to alter their biointeractions presents an important problem in biomedical polymer science. In this study, the covalent modification of the surface of poly(lactic acid)-based (PLA-based) films with poly(acryl amide) and sodium alginate hydrogels was performed to change the non-specific polyester interaction with proteins and cells, as well as to make possible the covalent attachment of low-molecular weight ligands and to control protein release. The effect of such modification on the film surface properties was studied. Parameters such as swelling, water contact angle, surface area, and binding capacity of low-molecular weight substances were evaluated and compared. The comparative study of adsorption of model protein (BSA) on the surface of non-modified and modified films was investigated and the protein release was evaluated. Cell viability on the surface of hydrogel-coated films was also tested. The developed approach could be applied for the modification of PLA-based scaffolds for tissue engineering and will be further studied for molecular-imprinting of biomolecules on the surface of polyester-based materials for control of biointeractions.

Supramolecular Au(I)-Cu(I) Complexes as New Luminescent Labels for Covalent Bioconjugation.

Two new supramolecular organometallic complexes, namely, [Au6Cu2(C2C6H4CHO)6(PPh2C6H4PPh2)3](PF6)2 and [Au6Cu2(C2C6H4NCS)6(PPh2C6H4PPh2)3](PF6)2, with highly reactive aldehyde and isothiocyanate groups have been synthesized and characterized using X-ray crystallography, ESI mass spectrometry, and NMR spectroscopy. The compounds obtained demonstrated bright emission in solution with the excited-state lifetime in microsecond domain both under single- and two-photon excitation. The luminescent complexes were found to be suitable for bioconjugation in aqueous media. In particular, they are able to form the covalent conjugates with proteins of different molecular size (soybean trypsin inhibitor, human serum albumin, rabbit anti-HSA antibodies). The conjugates demonstrated a high level of the phosphorescent emission from the covalently bound label, excellent solubility, and high stability in physiological media. The highest quantum yield, storage stability, and luminance were detected for bioconjugates formed by covalent attachment of the aldehyde-bearing supramolecular Au(I)-Cu(I) complex. The measured biological activity of one of the labeled model proteins clearly showed that introduced label did not prevent the biorecognition and specific protein-protein complex formation that was extremely important for the application of the conjugates in biomolecular detection and imaging.

Xylan degradation improved by a combination of monolithic columns bearing immobilized recombinant ß-xylosidase from Aspergillus awamori X-100 and Grindamyl H121 ß-xylanase.

Synergistic action of exo- and endohydrolazes is preferred for effective destruction of biopolymers. The main purpose of the present work was to develop an efficient tool for degradation of xylan. Macroporous lab-made monolithic columns and commercial CIM-Epoxy disk were used to immobilize the recombinant ß-xylosidase from Aspergillus awamori and Grindamyl ß-xylanase. The efficiency of xylan degradation using the low-loaded ß-xylosidase column appeared to be four times higher than for the in-solution process and about six times higher than for the high-loaded bioreactor. Disk bioreactor with the Grindamil ß-xylanase operated in a recirculation mode has shown noticeable advantages over the column design. Additionally, a system comprised of two immobilized enzyme reactors (IMERs) was tested to accelerate the biopolymer hydrolysis, yielding total xylan conversion into xylose within 20 min. Fast online monitoring HPLC procedure was developed where an analytical DEAE CIM disk was added to the two-enzyme system in a conjoint mode. A loss of activity of immobilized enzymes did not exceed 7% after 5 months of the bioreactor usage. We can therefore conclude that the bioreactors developed exhibit high efficiency and remarkable long-term stability.

Flow-through immobilized enzyme reactors based on monoliths: II. Kinetics study and application.

In the last decade, the application of monolithic materials has rapidly expanded to the realization of flow-through bioconversion processes. Up to these days, different classes of enzymes such as hydrolases, lyases, and oxidoreductases have been immobilized on organic, inorganic, or hybrid monolithic materials to prepare the effective flow-through enzymes reactors for application in proteomics, biotechnology, pharmaceutics, organic synthesis, and biosensoring. Current review describes the results of kinetic study and specialties of flow-through immobilized enzyme reactors based on the existing monolithic materials.

Flow-through immobilized enzyme reactors based on monoliths: I. Preparation of heterogeneous biocatalysts.

The application of monoliths for realization of solid-phase biocatalytic processes was dramatically extended since the beginning of new century. Different enzyme immobilization techniques regarding these modern stationary phases have been developed, adapted, and optimized within last decade. The choice of enzyme immobilization method depends on material nature and monolith manufacturing. The present review collected, analyzed, and discussed the accessible published data on existing approaches and specialties of preparation of flow-through enzyme reactors based on monoliths.

Macroporous methacrylate-based monoliths as platforms for DNA microarrays.

Macroporous monoliths with different surface functionalization (reactive groups) were utilized as platforms for DNA analysis in microarray format. The slides based on a copolymer glycidyl methacrylate-co-ethylene dimethacrylate (GMA-EDMA) have been chosen as well known and thoroughly studied standard. In particular, this material has been used at optimization of DNA microanalytical procedure. The concentration and pH of spotting solution, immobilization temperature and time, blocking agent and coupling reaction duration were selected as varied parameters. The efficiency of analysis performed on 3-D monolithic platforms was compared to that established for commercially available glass slides. As a practical example, a diagnostic test for detection of CFTR gene mutation was carried out. Additionally, the part of presented work was devoted to preparation of aptamer-based test-system that allowed successful and highly sensitive detection both of DNA and protein.