One-Step Synthesis of Functionalized Pyrazolo[3,4-b]pyridines via Ring Opening of the Pyrrolinium Ion.

Herein, we report a highly regioselective one-pot synthesis of pyrazolo[3,4-b]pyridines via the reaction of 3-arylidene-1-pyrrolines with aminopyrazoles. The reaction proceeds through the sequential nucleophilic addition/electrophilic substitution/C-N bond cleavage and provides easy access to pyrazolo[3,4-b]pyridine derivatives featuring a primary amino group. Moreover, the reaction can be terminated at the electrophilic substitution stage, thus providing convenient entry to the hardly accessible pyrazolopyrrolopyridine scaffold.

Extent of N-Terminus Folding of Semenogelin 1 Cleavage Product Determines Tendency to Amyloid Formation.

It is known that four peptide fragments of predominant protein in human semen Semenogelin 1 (SEM1) (SEM1(86-107), SEM1(68-107), SEM1(49-107) and SEM1(45-107)) are involved in fertilization and amyloid formation processes. In this work, the structure and dynamic behavior of SEM1(45-107) and SEM1(49-107) peptides and their N-domains were described. According to ThT fluorescence spectroscopy data, it was shown that the amyloid formation of SEM1(45-107) starts immediately after purification, which is not observed for SEM1(49-107). Seeing that the peptide amino acid sequence of SEM1(45-107) differs from SEM1(49-107) only by the presence of four additional amino acid residues in the N domain, these domains of both peptides were obtained via solid-phase synthesis and the difference in their dynamics and structure was investigated. SEM1(45-67) and SEM1(49-67) showed no principal difference in dynamic behavior in water solution. Furthermore, we obtained mostly disordered structures of SEM1(45-67) and SEM1(49-67). However, SEM1(45-67) contains a helix (E58-K60) and helix-like (S49-Q51) fragments. These helical fragments may rearrange into ß-strands during amyloid formation process. Thus, the difference in full-length peptides' (SEM1(45-107) and SEM1(49-107)) amyloid-forming behavior may be explained by the presence of a structured helix at the SEM1(45-107) N-terminus, which contributes to an increased rate of amyloid formation.

Dithiophosphate-Induced Redox Conversions of Reduced and Oxidized Glutathione.

Phosphorus species are potent modulators of physicochemical and bioactive properties of peptide compounds. O,O-diorganyl dithiophoshoric acids (DTP) form bioactive salts with nitrogen-containing biomolecules; however, their potential as a peptide modifier is poorly known. We synthesized amphiphilic ammonium salts of O,O-dimenthyl DTP with glutathione, a vital tripeptide with antioxidant, protective and regulatory functions. DTP moiety imparted radical scavenging activity to oxidized glutathione (GSSG), modulated the activity of reduced glutathione (GSH) and profoundly improved adsorption and electrooxidation of both glutathione salts on graphene oxide modified electrode. According to NMR spectroscopy and GC-MS, the dithiophosphates persisted against immediate dissociation in an aqueous solution accompanied by hydrolysis of DTP moiety into phosphoric acid, menthol and hydrogen sulfide as well as in situ thiol-disulfide conversions in peptide moieties due to the oxidation of GSH and reduction of GSSG. The thiol content available in dissolved GSH dithiophosphate was more stable during air oxidation compared with free GSH. GSH and the dithiophosphates, unlike DTP, caused a thiol-dependent reduction of MTS tetrazolium salt. The results for the first time suggest O,O-dimenthyl DTP as a redox modifier for glutathione, which releases hydrogen sulfide and induces biorelevant redox conversions of thiol/disulfide groups.

La(III), Ce(III), Gd(III), and Eu(III) Complexation with Tris(hydroxymethyl)aminomethane in Aqueous Solution.

Lanthanides such as cerium(III), europium(III), and gadolinium(III) are widely used for designing fluorescent probes or magnetic resonance imaging contrasting agents for biological systems. The synthesis and study of lanthanide complexes in buffer solutions imitating biological fluids are often complicated because of a lack of data on the lanthanide interactions with buffer solution components. Therefore, Ln(III) [where Ln(III) = La(III), Ce(III), Gd(III), Eu(III)] complexation with a widely used buffer agent, tris(hydroxymethyl)aminomethane (Tris), in aqueous solution is studied using potentiometry, spectrofluorimetry, and 139La NMR spectroscopy. The stoichiometric composition of complexes is determined using mass spectrometry. The thermodynamic stability constants of Ln(III)-Tris complexes are calculated from potentiometric and spectral data; the difficulties in the study of these systems, reliability, and accuracy of the obtained constants are discussed. The possible structures of free Tris and its complexes with lanthanides(III) are optimized on the density functional theory/PBE0 level; the peculiarities of metal-ligand bonds were studied by Quantum Theory Atoms in Molecules analysis.

Structure and function of the N-terminal domain of the yeast telomerase reverse transcriptase.

The elongation of single-stranded DNA repeats at the 3'-ends of chromosomes by telomerase is a key process in maintaining genome integrity in eukaryotes. Abnormal activation of telomerase leads to uncontrolled cell division, whereas its down-regulation is attributed to ageing and several pathologies related to early cell death. Telomerase function is based on the dynamic interactions of its catalytic subunit (TERT) with nucleic acids-telomerase RNA, telomeric DNA and the DNA/RNA heteroduplex. Here, we present the crystallographic and NMR structures of the N-terminal (TEN) domain of TERT from the thermotolerant yeast Hansenula polymorpha and demonstrate the structural conservation of the core motif in evolutionarily divergent organisms. We identify the TEN residues that are involved in interactions with the telomerase RNA and in the recognition of the 'fork' at the distal end of the DNA product/RNA template heteroduplex. We propose that the TEN domain assists telomerase biological function and is involved in restricting the size of the heteroduplex during telomere repeat synthesis.

Solution structure of the N-terminal domain of the Staphylococcus aureus hibernation promoting factor.

Staphylococcus aureus hibernation promoting factor (SaHPF) is a 22,2 kDa protein which plays a crucial role in 100S Staphylococcus aureus ribosome formation during stress. SaHPF consists of N-terminal domain (NTD) that prevents proteins synthesis by binding to the 30S subunit at the P- and A-sites, connected through a flexible linker with a C-terminal domain (CTD) that keeps ribosomes in 100S form via homodimerization. Recently obtained 100S ribosome structure of S. aureus by cryo-EM shown that SaHPF-NTD bound to the ribosome active sites, however due to the absence of SaHPF-NTD structure it was modeled by homology with the E. coli hibernation factors HPF and YfiA. In present paper we have determined the solution structure of SaHPF-NTD by high-resolution NMR spectroscopy which allows us to increase structural knowledge about HPF structure from S. aureus.

Effect of triphenylphosphonium moiety on spatial structure and biointeractions of stereochemical variants of YRFK motif.

Chemical modification of therapeutic peptides is an important approach to improving their physicochemical and pharmacokinetic properties. The triphenylphosphonium (TPP) cation has proved to be a powerful modifier; however, its effects on peptide structure and activity remain uncharacterized. In this study, cytoprotective tetrapeptides based on the YRFK opioid motif with L- or D-Arg residues were linked to (triphenylphosphonio)carboxylic acids with ethylene and pentylene spacers (TPP-3 and TPP-6 groups, respectively). The three-dimensional structure of the oligopeptides was analyzed by NMR spectroscopy, computational methods and circular dichroism (CD). A more compact and bent structure with segregated aromatic groups was revealed for the D-arginine-containing tetrapeptide and its TPP-6 derivative. The TPP moiety caused structure-organizing effect on the tetrapeptides, resulting in transition from random coil to ß-sheet structures, and decreased the peptide backbone flexibility up to ten times. The TPP-3-modified oligopeptide with the lowest RMSD value (ca. 0.05 Å) was characterized by intrapeptide hydrophobic interactions between the TPP and side groups of Tyr and Phe residues accompanied by strong CD induction. The TPP-6-modified oligopeptides showed enhanced ability to form intermolecular associates and disturb liposomal membranes. The relationship between the spatial structure of the oligopeptides and some of their biologically relevant interactions were additionally revealed and are discussed.

Mechanistic Basis for the Binding of RGD- and AGDV-Peptides to the Platelet Integrin αIIbß3.

Binding of soluble fibrinogen to the activated conformation of the integrin αIIbß3 is required for platelet aggregation and is mediated exclusively by the C-terminal AGDV-containing dodecapeptide (γC-12) sequence of the fibrinogen γ chain. However, peptides containing the Arg-Gly-Asp (RGD) sequences located in two places in the fibrinogen Aα chain inhibit soluble fibrinogen binding to αIIbß3 and make substantial contributions to αIIbß3 binding when fibrinogen is immobilized and when it is converted to fibrin. Here, we employed optical trap-based nanomechanical measurements and computational molecular modeling to determine the kinetics, energetics, and structural details of cyclic RGDFK (cRGDFK) and γC-12 binding to αIIbß3. Docking analysis revealed that NMR-determined solution structures of cRGDFK and γC-12 bind to both the open and closed αIIbß3 conformers at the interface between the αIIb ß-propeller domain and the ß3 ßI domain. The nanomechanical measurements revealed that cRGDFK binds to αIIbß3 at least as tightly as γC-12. A subsequent analysis of molecular force profiles and the number of peptide-αIIbß3 binding contacts revealed that both peptides form stable bimolecular complexes with αIIbß3 that dissociate in the 60-120 pN range. The Gibbs free energy profiles of the αIIbß3-peptide complexes revealed that the overall stability of the αIIbß3-cRGDFK complex was comparable with that of the αIIbß3-γC-12 complex. Thus, these results provide a mechanistic explanation for previous observations that RGD- and AGDV-containing peptides are both potent inhibitors of the αIIbß3-fibrinogen interactions and are consistent with the observation that RGD motifs, in addition to AGDV, support interaction of αIIbß3 with immobilized fibrinogen and fibrin.

Oligomerization of the antimicrobial peptide Protegrin-5 in a membrane-mimicking environment. Structural studies by high-resolution NMR spectroscopy.

Protegrin pore formation is believed to occur in a stepwise fashion that begins with a nonspecific peptide interaction with the negatively charged bacterial cell walls via hydrophobic and positively charged amphipathic surfaces. There are five known nature protegrins (PG1-PG5), and early studies of PG-1 (PDB ID:1PG1) shown that it could form antiparallel dimer in membrane mimicking environment which could be a first step for further oligomeric membrane pore formation. Later, we solved PG-2 (PDB ID:2MUH) and PG-3 (PDB ID:2MZ6) structures in the same environment and for PG-3 observed a strong dαα NOE effects between residues R18 and F12, V14, and V16. These "inconsistent" with monomer structure NOEs appears due to formation of an additional antiparallel ß-sheet between two monomers. It was also suggested that there is a possible association of protegrins dimers to form octameric or decameric ß-barrels in an oligomer state. In order to investigate a more detailed oligomerization process of protegrins, in the present article we report the monomer (PDB ID: 2NC7) and octamer pore structures of the protegrin-5 (PG-5) in the presence of DPC micelles studied by solution NMR spectroscopy. In contrast to PG-1, PG-2, and PG-3 studies, for PG-5 we observed not only dimer NOEs but also several additional NOEs between side chains, which allows us to calculate an octamer pore structure of PG-5 that was in good agreement with previous AFM and PMF data.

Stereoselective PCO/POC-Rearrangement of P-C-Cage Phosphorane in the Reaction of 4,5-Dimethyl-2-(2-oxo-1,2-diphenyl)ethoxy-1,3,2-dioxaphospholane with Hexafluoroacetone.

Interaction of 4,5-dimethyl-2-(2-oxo-1,2-diphenyl)ethoxy-1,3,2-dioxaphospholane, bearing a carboxyl group in the γ-position with respect to the phosphorus atom and obtained from d,l-butanediol, with hexafluoroacetone (CCl4, -40 °C) leads to the simultaneous formation of regio- and stereoisomeric cage-like phosphoranes with phosphorus-carbon and phosphorus-oxygen bonds with a high stereoselectivity (>95%), whose structure was determined by 1D and 2D NMR spectroscopy and XRD. When stored as a solution in dichloromethane for one month, the PCO-isomer rearranges into the thermodynamically more stable POC-isomer of the cage-like phosphorane. Mild hydrolysis of the PCO/POC-isomers proceeds with a high chemoselectivity and leads to the formation of P(IV)-dioxaphospholane derivatives. Acidic hydrolysis of the POC-isomer leads to the formation of an oxirane derivative with an unexpectedly high stereoselectivity (>95%). DFT calculations (using the PBE functional) allowed us to obtain structures and energies of the initial phospholane, reaction products (PCO/POC-isomers), and an intermediate P(V)-oxaphosphirane.

Synthesis of a new quaternary phosphonium salt: NMR study of the conformational structure and dynamics.

A novel phosphonium salt based on pyridoxine was synthesized. Conformational analysis of the compound in solution was performed using dynamic NMR experiments and calculations. The obtained results revealed some differences in the conformational transitions and the energy parameters of the conformational exchange of the studied compound in comparison to previously reported data for other phosphorus-containing pyridoxine derivatives. It was shown that increasing the substituent at the C-11 carbon leads to greater differences in the populations of stable states and the corresponding equilibrium energies. Copyright © 2015 John Wiley & Sons, Ltd.

Dynamic NMR study of dinitrophenyl derivatives of seven-membered cyclic ketals of pyridoxine.

Two pyridoxine derivatives containing a dinitrophenyl moiety were investigated by (1)H NMR spectroscopy. Conformational dynamics in solution were studied for each compound using dynamic NMR experiments. It was shown that both compounds studied are involved into two conformational exchange processes. The first process is a transformation of the seven-membered cycle conformation between the enantiomeric P-twist and M-twist forms, and the second is a rotation of the dinitrophenyl fragment of the molecules around the C-O bond. Energy barriers of both conformational transitions were determined.

Use of a combination of the RDC method and NOESY NMR spectroscopy to determine the structure of Alzheimer's amyloid Aß10-35 peptide in solution and in SDS micelles.

The spatial structure of Alzheimer's amyloid Aß10-35-NH2 peptide in aqueous solution at pH 7.3 and in SDS micelles was investigated by use of a combination of the residual dipolar coupling method and two-dimensional NMR spectroscopy (TOCSY, NOESY). At pH 7.3 Aß10-35-NH2 adopts a compact random-coil conformation whereas in SDS micellar solutions two helical regions (residues 13-23 and 30-35) of Aß10-35-NH2 were observed. By use of experimental data, the structure of "peptide-micelle" complex was determined; it was found that Aß10-35-NH2 peptide binds to the micelle surface at two regions (residues 17-20 and 29-35).

Binding of Different Cyclosporin Variants to Micelles Evidenced by NMR and MD Simulations.

Peptides play a critical role in the life of organisms, performing completely different functions. The biological activity of some peptides, such as cyclosporins, can be determined by the degree of membrane permeability. Thus, it becomes important to study how the molecule interacts with lipid bilayers. Cyclosporins C, E, H and L were characterised molecular dynamics simulation; NMR spectroscopy studies were also carried out for cyclosporins C and E. The comparison of one- and two-dimensional spectra revealed certain similarities between spatial structures of the studied cyclosporin variants. Upon dissolving in water containing DPC micelles, which serve as model membranes, subtle changes in the NMR spectra appear, but in a different way for different cyclosporins. In order to understand whether observed changes are related to any structural modifications, simulation of the interaction of the peptide with the phospholipid micelle was performed. The onset of the interaction was observed, when the peptide is trapped to the surface of the micelle. Simulations of this kind are also of interest in the light of the well-known membrane permeability of cyclosporin, which is important for its biological action.

Silicas with Polyoxyethylene Branches for Modification of Membranes Based on Microporous Block Copolymers.

We have synthesized cubic and linear polysiloxanes containing polyoxyethylene branches (ASiP-Cu) using tetraethoxysilane, polyoxyethylene glycol, and copper chloride as precursors; the products are stable to self-condensation. The effect of copper chloride content on the chemical structure of ASiP-Cu has been established. A special study was aimed at defining the modifying effect of ASiP-Cu on the sorption characteristics of membranes based on microporous, optically transparent block copolymers (OBCs). These OBCs were produced using 2,4-toluene diisocyanate and block copolymers of ethylene and propylene oxides. The study demonstrated significantly increased sorption capacity of the modified polymers. On the basis of the modified microporous block copolymers and 1-(2-pyridylazo)-2-naphthol (PAN) analytical reagent, an analytical test system has been developed. Additionally, the modified OBCs have the benefit of high diffusion permeability for molecules of organic dyes and metal ions. It has been shown that the volume of voids and structural features of their internal cavities contribute to the complex formation reaction involving PAN and copper chloride.

Spatial structure of heptapeptide Aß(16-22) (beta-amyloid Aß(1-40) active fragment) in solution and in complex with a biological membrane model.

The spatial structure of an active fragment of beta-amyloid Aß(1-40) heptapeptide Aß(16-22) (Lys-Leu-Val-Phe-Phe-Ala-Glu) in aqueous buffer solution and in complex with sodium dodecyl sulfate micelles as a model membrane system was investigated by (1)H NMR spectroscopy and two-dimensional NMR (TOCSY, HSQC-HECADE (Heteronuclear Couplings from ASSCI-domain experiments with E.COSY-type crosspeaks), NOESY) spectroscopy. Complex formation was confirmed by the chemical shift changes of the heptapeptide's (1)H NMR spectra, as well as by the signs and values of the NOE effects in different environments. We compared the spatial structure of the heptapeptide in borate buffer solution and in complex with a model of the cell surface membrane.

Comparison of structural properties of cyclosporin A and its analogue alisporivir and their effects on mitochondrial bioenergetics and membrane behavior.

The paper considers the effect of the MPT pore inhibitor cyclosporin A (CsA) and its non-immunosuppressive analogue alisporivir (Ali) on the functioning of rat skeletal muscle mitochondria. We have shown that both agents at a standard in vitro concentration of 1 µM increase the calcium capacity of organelles and have no effect on the parameters of oxidative phosphorylation. However, an increase in their concentration to 5 µM leads to the suppression of oxygen consumption by mitochondria, which is more pronounced in the case of Ali. This effect is accompanied by a decrease in the membrane potential of organelles and, apparently, is based on the inhibition of electron transport along the mitochondrial respiratory chain due to limited mobility of coenzyme Q. We have noted that both agents do not affect the production of hydrogen peroxide by isolated mitochondria. NMR spectroscopy and molecular dynamics simulation did not reveal significant differences in the structure and backbone flexibility of CsA and Ali. Both agents decrease the overall fluidity of the membrane of DPPC liposomes, inducing an increase in laurdan generalized polarization parameter. A similar effect was also found in the case of mitochondrial membranes. We suggested that these effects of CsA and Ali, associated with their lipophilic nature and the ability to accumulate in the lipid phase of membranes, may cause a decrease in the efficiency of electron transport in the respiratory chain of mitochondria and suppression of the bioenergetics of these organelles.

Catalytic Etherification of ortho-Phosphoric Acid for the Synthesis of Polyurethane Ionomer Films.

The etherification reaction of ortho-phosphoric acid (OPA) with polyoxypropylene glycol in the presence of tertiary amines was studied. The reaction conditions promoting the catalytic activity of triethanolamine (TEOA) and triethylamine (TEA) in the low-temperature etherification of OPA were established. The catalytic activity of TEOA and TEA in the etherification reaction of phosphoric acid is explained by the hydrophobic-hydrophilic interactions of TEA with PPG, leading, as a result of collective interactions, to a specific orientation of polyoxypropylene chains around the tertiary amine. When using triethylamine, complete etherification of OPA occurs, accompanied by the formation of branched OPA ethers terminated by hydroxyl groups and even the formation of polyphosphate structures. When triethanolamine is used as a catalyst, incomplete etherification of OPA with polyoxypropylene glycol occurs and as a result, part of the phosphate anions remain unreacted in the composition of the resulting aminoethers of ortho-phosphoric acid (AEPA). In this case, the hydroxyl groups of triethanolamine are completely involved in the OPA etherification reaction, but the catalytic activity of the tertiary amine weakens due to a decrease in its availability in the branched structure of AEPA. The kinetics of the etherification reaction of OPA by polyoxypropylene glycol catalyzed by TEOA and TEA were studied. It was shown that triethanolamine occupies a central position in the AEPA structure. The physico-mechanical and thermomechanical properties of polyurethane ionomer films obtained on the basis of AEPA synthesized in a wide temperature range were studied.

Pervaporation Polyurethane Membranes Based on Hyperbranched Organoboron Polyols.

On the basis of aminoethers of boric acid (AEBA), polyurethane vapor-permeable and pervaporative membranes were obtained. AEBAs, the structure of which is modified by bulk adducts (EM) of diphenylol propane diglycidyl ether and ethanolamine, were studied. It turned out that AEBA exists in the form of clusters, and the use of EM as a result of partial destruction of associative interactions leads to a significant decrease in the size of AEBA-EM particles and their viscosity compared to unmodified AEBA. The introduction of EM into the composition of AEBA leads to a threefold increase in the vapor permeability of polyurethanes obtained on their basis. The observed effect is explained by the fact that a decrease in the size of clusters leads to loosening of their dense packing. Areas of clustering due to associative interactions of hydroxyl groups, together with the hydrophilic nature of polyoxyethylene glycol, create channels through which water molecules can penetrate. The increase in vapor permeability is accompanied by a multiple increase in the permeability coefficients in the pervaporative dehydration of isopropanol.

Design, Spectral Characteristics, Photostability, and Possibilities for Practical Application of BODIPY FL-Labeled Thioterpenoid.

This paper presents the design and a comparative analysis of the structural and solvation factors on the spectral and biological properties of the BODIPY biomarker with a thioterpene fragment. Covalent binding of the thioterpene moiety to the butanoic acid residue of meso-substituted BODIPY was carried out to find out the membranotropic effect of conjugate to erythrocytes, and to assess the possibilities of its practical application in bioimaging. The molecular structure of the conjugate was confirmed via X-ray, UV/vis-, NMR-, and MS-spectra. It was found that dye demonstrates high photostability and high fluorescence quantum yield (to ~100%) at 514-519 nm. In addition, the marker was shown to effectively penetrate the erythrocytes membrane in the absence of erythrotoxicity. The conjugation of BODIPY with thioterpenoid is an excellent way to increase affinity dyes to biostructures, including blood components.