Synthesis, characterization, and biological study of new synthetic opioid hemorphin-4 peptides containing sterically restricted nonnatural amino acids.

Some new hemorphin-4 analogs with structures of Xxx-Pro-Trp-Thr-NH2 and Tyr-Yyy-Trp-Thr-NH2, where Xxx is 2-amino-3-(4-hydroxy-2,6-dimethylphenyl)propanoic acid or 2-amino-3-(4-dibenzylamino-2,6-dimethylphenyl)propanoic acid, and Yyy is (2S,4S)-4-amino-pyrrolidine-2-carboxylic acid, were synthesized and characterized by electrochemical and spectral analyses. In vivo anticonvulsant and antinociceptive activities of peptide derivatives were studied after intracerebroventricular injection in mice. The therapeutic effects of the modified peptides on seizures and pain in mice were evaluated to provide valuable insights into the potential applications of the novel compounds. Electrochemical characterization showed that the compounds behave as weak protolytes and that they are in a soluble, stable molecular form at physiological pH values. The antioxidant activity of the peptides was evaluated with voltammetric analyses, which were confirmed by applying the 2,2-Diphenyl-1-picrylhydrazyl method. The compounds showed satisfactory results regarding their structural stability, reaching the desired centers for the manifestation of biological activity without hydrolysis processes at 37°C and physiological pH. Dm-H4 and H4-P1 exhibited 100% and 83% potency to suppress the psychomotor seizures in the 6-Hz test compared to 67% activity of H4. Notably, only the H4-P1 had efficacy in blocking the tonic component in the maximal electroshock test with a potency comparable to H4. All investigated peptides containing unnatural conformationally restricted amino acids showed antinociceptive effects. The analogs Db-H4 and H4-P1 showed the most pronounced and long-lasting effect in both experimental models of pain induced by thermal and chemical stimuli. Dm-H4 produced a dose-dependent thermal antinociception and H4-P2 inhibited only formalin-induced pain behavior.

Aggregation induced nucleic acids recognition by homodimeric asymmetric monomethyne cyanine fluorochromes in mesenchymal stem cells.

In the light of recent retrovirus pandemics, the issue of discovering new and diverse RNA-specific fluorochromes for research and diagnostics became of acute importance. The great majority of nucleic acid-specific probes either do not stain RNA or cannot distinguish between DNA and RNA. The versatility of polymethine dyes makes them suitable as stains for visualization, analysis, and detection of nucleic acids, proteins, and other biomolecules. We synthesized the asymmetric dicationic homodimeric monomethine cyanine dyes 1,1'-(1,3-phenylenebis(methylene))bis(4-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)pyridin-1-ium) bromide (Т1) and 1,1'-(1,3-phenylenebis(methylene))bis(4-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)quinolin-1-ium) bromide (M1) and tested their binding specificity, spectral characteristics, membrane penetration in living and fixed cells, cellular toxicity, and stability of fluorescent emission. Mesenchymal cells have diverse phenotypes and extensive proliferation and differentiation properties. We found dyes T1 and M1 to show high photochemical stability in living mesenchymal stem cells from apical papilla (SCAP) with a strong fluorescent signal when bound to nucleic acids. We found M1 to perform better than control fluorochrome (Hoechst 33342) for in vivo DNA visualization. T1, on the other hand, stains granular cellular structures resembling ribosomes in living cells and after permeabilization of the nuclear membrane stains the nucleoli and not the chromatin in the nucleus. This makes T1 suitable for the visualization of structures rich in RNA in living and fixed cells.

Dioxepine-Peri-Annulated PMIs-Synthesis and Spectral and Sensing Properties.

New perylene monoimide (PMI) derivatives bearing a seven-membered heterocycle and 1,8-diaminosarcophagine (DiAmSar) or N,N-dimethylaminoethyl chelator fragments were synthesized, and their spectroscopic properties in the absence and presence of metal cations were determined to evaluate their potential applications as PET optical sensors for such analytes. DFT and TDDFT calculations were employed to rationalize the observed effects.

Synthesis of Novel 1-Oxo-2,3,4-trisubstituted Tetrahydroisoquinoline Derivatives, Bearing Other Heterocyclic Moieties and Comparative Preliminary Study of Anti-Coronavirus Activity of Selected Compounds.

A series of novel 1-oxo-2,3,4-trisubstituted tetrahydroisoquinoline (THIQ) derivatives bearing other heterocyclic moieties in their structure were synthesized based on the reaction between homophthalic anhydride and imines. Initial studies were carried out to establish the anti-coronavirus activity of some of the newly obtained THIQ-derivatives against two strains of human coronavirus-229E and OC-43. Their antiviral activity was compared with that of their close analogues, piperidinones and thiomorpholinones, previously synthesized in our group, with aim to expand the range of the tested representative sample and to obtain valuable preliminary information about biological properties of a wider variety of compounds.

Asymmetric Monomethine Cyanine Dyes with Hydrophobic Functionalities for Fluorescent Intercalator Displacement Assay.

A new green procedure has been applied for the synthesis and purification of asymmetric monomethine cyanine dyes. The photophysical properties of the newly synthesized compounds have been examined by combined application of spectroscopic and theoretical methods. The structural characteristics of the molecules and dimer formation were characterized by quantum chemical computation and juxtaposed to the aggregachromism in UV/Vis spectra. The applicability of the dyes as fluorogenic nucleic acid probes has been proven by fluorescence titration, and their binding constants have been calculated. The mode of ligand-dsDNA/RNA interaction was rationalized by means of CD spectroscopy, molecular docking analysis, and fluorescent intercalator displacement experiments.

Mini-Review on Structure-Reactivity Relationship for Aromatic Molecules: Recent Advances.

Recent advances in quantifying nucleophilic reactivities in chemical reactions and intermolecular interactions of aromatic molecules are reviewed. This survey covers experimental (IR frequency shifts induced by hydrogen bonding) and theoretical (modeling of potential energy surfaces, atomic charges, molecular electrostatic potential) approaches in characterizing chemical reactivity. Recent advances in software developments assisting the evaluation of the reactive sites for electrophilic aromatic substitution are briefly discussed.

A DFT/PCM Study on the Affinity of Salinomycin to Bind Monovalent Metal Cations.

The affinity of the polyether ionophore salinomycin to bind IA/IB metal ions was accessed using the Gibbs free energy of the competition reaction between SalNa (taken as a reference) and its rival ions: [M+-solution] + [SalNa] → [SalM] + [Na+-solution] (M = Li, K, Rb, Cs, Cu, Ag, Au). The DFT/PCM computations revealed that the ionic radius, charge density and accepting ability of the competing metal cations, as well as the dielectric properties of the solvent, have an influence upon the selectivity of salinomycin. The optimized structures of the monovalent metal complexes demonstrate the flexibility of the ionophore, allowing the coordination of one or two water ligands in SalM-W1 and SalM-W2, respectively. The metal cations are responsible for the inner coordination sphere geometry, with coordination numbers spread between 2 (Au+), 4 (Li+ and Cu+), 5/6 (Na+, K+, Ag+), 6/7 (Rb+) and 7/8 (Cs+). The metals' affinity to salinomycin in low-polarity media follows the order of Li+ > Cu+ > Na+ > K+ > Au+ > Ag+ > Rb+ > Cs+, whereas some derangement takes place in high-dielectric environment: Li+ ≥ Na+ > K+ > Cu+ > Au+ > Ag+ > Rb+ > Cs+.

Ca2+/Sr2+ Selectivity in Calcium-Sensing Receptor (CaSR): Implications for Strontium's Anti-Osteoporosis Effect.

The extracellular calcium-sensing receptor (CaSR) controls vital bone cell functions such as cell growth, differentiation and apoptosis. The binding of the native agonist (Ca2+) to CaSR activates the receptor, which undergoes structural changes that trigger a cascade of events along the cellular signaling pathways. Strontium (in the form of soluble salts) has been found to also be a CaSR agonist. The activation of the receptor by Sr2+ is considered to be the major mechanism through which strontium exerts its anti-osteoporosis effect, mostly in postmenopausal women. Strontium-activated CaSR initiates a series of signal transduction events resulting in both osteoclast apoptosis and osteoblast differentiation, thus strengthening the bone tissue. The intimate mechanism of Sr2+ activation of CaSR is still enigmatic. Herewith, by employing a combination of density functional theory (DFT) calculations and polarizable continuum model (PCM) computations, we have found that the Ca2+ binding sites 1, 3, and 4 in the activated CaSR, although possessing a different number and type of protein ligands, overall structure and charge state, are all selective for Ca2+ over Sr2+. The three binding sites, regardless of their structural differences, exhibit almost equal metal selectivity if they are flexible and have no geometrical constraints on the incoming Sr2+. In contrast to Ca2+ and Sr2+, Mg2+ constructs, when allowed to fully relax during the optimization process, adopt their stringent six-coordinated octahedral structure at the expense of detaching a one-backbone carbonyl ligand and shifting it to the second coordination layer of the metal. The binding of Mg2+ and Sr2+ to a rigid/inflexible calcium-designed binding pocket requires an additional energy penalty for the binding ion; however, the price for doing so (to be paid by Sr2+) is much less than that of Mg2+. The results obtained delineate the key factors controlling the competition between metal cations for the receptor and shed light on some aspects of strontium's therapeutic effects.

Synthesis, Photophysical Characterization, and Sensor Activity of New 1,8-Naphthalimide Derivatives.

Three new 1,8-naphthalimide derivatives M1-M3 with different substituents at the C-4 position have been synthesized and characterized. Their photophysical properties have been investigated in organic solvents of different polarity, and their fluorescence intensity was found to depend strongly on both the polarity of the solvents and the type of substituent at C-4. For compounds M1 and M2 having a tertiary amino group linked via an ethylene bridge to the chromophore system, high quantum yield was observed only in non-polar media, whereas for compound M3, the quantum efficiency did not depend on the medium polarity. The effect of different metal ions (Ag+, Ba2+, Cu2+, Co2+, Mg2+, Pb2+, Sr2+, Fe3+, and Sn2+) on the fluorescence emission of compounds M1 and M2 was investigated. A significant enhancement has been observed in the presence of Ag+, Pb2+, Sn2+, Co2+, Fe3+, as this effect is expressed more preferably in the case of M2. Both compounds have shown significant pH dependence, as the fluorescence intensity was low in alkaline medium and has been enhanced more than 20-fold in acidic medium. The metal ions and pH do not affect the fluorescence intensity of M3. Density-functional theory (DFT) and Time-dependent density-functional theory (TDDFT) quantum chemical calculations are employed in deciphering the intimate mechanism of sensor mechanism. The functional properties of M1 and M2 were compared with polyamidoamine (PAMAM) dendrimers of different generations modified with 1,8-naphthalimide.

Factors governing the competition between group IA and IB cations for monensin A: a DFT/PCM study.

The affinity of monensin A to bind monovalent metal cations was evaluated by means of density functional theory (DFT) combined with polarizable continuum model (PCM) computations. The effect of various factors on complex formation between the monensinate A anion and group IA and IB metal ions was assessed. Competition between Na+ taken as a reference and monovalent metal cations was estimated using the Gibbs free energy for substituting the ligand-bound Na+ with its rival ions in the process [M+-solution] + [Mon-Na+] → [Mon-M+] + [Na+-solution] (M+ = Li+, K+, Rb+, Cs+, Cu+, Ag+ and Au+). The calculations revealed that the decrease in size of the cations accompanied by an increase of their accepting ability enhances the metal selectivity towards ligand donor atoms. In the gas-phase the affinity of monensinate A decreases in the order Cu+ > Li+ > Na+ > Au+ > Ag+ > K+ > Rb+ > Cs+. The complex formation can be manipulated by changing the solvent used. The polyether ionophore selectively binds Na+ ions in polar solvents but could become Li+ or Cu+-selective in low-polarity solvents.

Electric field influence on the helical structure of peptides: insights from DFT/PCM computations.

The secondary structure of proteins is of prime importance to their proper functioning and protein misfolding may cause serious disorders in the human body. Here, the electric field influence on the conformational stability of model alpha helical peptides is studied by employing density functional theory calculations combined with continuum dielectric method computations. Our results show that the basic parameters of the electric field - its strength and directionality - are determinative for the alpha helix stability. An electric field strength of 0.005 a.u. (2.5 V nm-1) applied along the X coordinate axis (the long axis of the helix) in the direction of the µx component of the molecular dipole moment does affect the peptide conformation, destroys the helix, and leads to the formation of a cyclic-peptide-like structure. Interestingly, the process of denaturation can be reversible when the electric field is switched-off. The reversibility of the process of the electric field induced disruption of the peptide secondary structure suggests a possible mechanism for the healing of misfolded proteins.

Atomic Charges in Describing Properties of Aromatic Molecules.

The performance of four frequently employed population analysis methods is assessed by comparisons with experimentally derived properties of monosubstituted benzene derivatives. The analysis is based on the expected dependence between site reactivities and electron densities at the respective ring carbon atoms. The correspondence between charges obtained from Mulliken, NPA, Hirshfeld, and QTAIM approaches and the σ0m and σ0p aromatic substituent constants is examined. The series of molecules investigated includes benzene and 18 monosubstituted derivatives. The atomic charges are derived using the B3LYP, ωB97X-D density functional, and MP2 MO methods combined with the 6-311++G(3df,2pd) basis set. A quantitative correspondence between Hirshfeld charges and σ0 constants is established. Application of Møller-Plesset second-order perturbation theory (MP2) wave functions appears to be essential in obtaining a more realistic electron density distribution. NPA and QTAIM charges provide in most cases a satisfactory description of the substituent effects. The net transfer of charges between substituents and the aromatic ring is assessed.

Competition between abiogenic Al3+ and native Mg2+, Fe2+ and Zn2+ ions in protein binding sites: implications for aluminum toxicity.

Abiogenic aluminum has been implicated in some health disorders in humans. Protein binding sites containing essential metals (mostly magnesium) have been detected as targets for the "alien" Al3+. However, the acute toxicity of aluminum is very low. Although a substantial body of information has been accumulated on the biochemistry of aluminum, the underlying mechanisms of its toxicity are still not fully understood. Several outstanding questions remain unanswered: (1) Why is the toxicity of aluminum, unlike that of other "alien" metal cations, relatively low? (2) Apart from Mg2+ active centers in proteins, how vulnerable are other essential metal binding sites to Al3+ attack? (3) Generally, what factors do govern the competition between 'alien" Al3+ and cognate divalent metal cations in metalloproteins under physiologically relevant conditions? Here, we endeavor to answer these questions by studying the thermodynamic outcome of the competition between Al3+ and a series of biogenic metal cations, such as Mg2+, Fe2+ and Zn2+, in model protein binding sites of various structures, compositions, solvent exposure and charge states. Density functional theory calculations were employed in combination with polarizable continuum model computations. For the first time, the presence of different Al3+ soluble species at physiological pH was properly modeled in accordance with experimental observations. The results suggest that a combination of concentration and physicochemical factors renders the Al3+ → M2+ (M = Mg, Fe, Zn) substitution and subsequent metalloenzyme inhibition a low-occurrence event at ambient pH: the more active aluminum species, [Al(H2O)6]3+, presents in very minute quantities at physiological conditions, while the more abundant soluble aluminum hydrate, {[Al(OH-)4](H2O)2}-, appears to be thermodynamically incapable of substituting for the native cation.

Hyperconjugative effects in π-hydrogen bonding: Theory and experiment.

Density functional theory computations with the B3LYP/6-311++G(2df,2p) method and IR spectroscopy are employed in investigating the properties of twenty π-hydrogen bonded complexes between substituted phenols and hexamethylbenzene. All complexes possess T-shaped structures. The methyl hyperconjugative effects on interactions energies and OH stretching frequencies are estimated via comparisons with previously reported theoretical and experimental results for analogous phenol complexes with benzene. The theoretical computations provide excellent quantitative predictions of the OH stretching frequency shifts (ΔνOH ) resulting from the hydrogen bonding. The ΔνOH shifts in the hexamethylbenzene complexes are approximately twice as large as the corresponding shifts for the benzene complexes. Hirshfeld charges, electrostatic potential at nuclei values, and molecular electrostatic potential maps are employed in gaining insights into the mechanisms of methyl hyperconjugative effects on complex formation. © 2017 Wiley Periodicals, Inc.

Origin of the enantioselectivity in organocatalytic Michael additions of ß-ketoamides to α,ß-unsaturated carbonyls: a combined experimental, spectroscopic and theoretical study.

The organocatalytic enantioselective conjugate addition of secondary ß-ketoamides to α,ß-unsaturated carbonyl compounds is reported. Use of bifunctional Takemoto's thiourea catalyst allows enantiocontrol of the reaction leading either to simple Michael adducts or spirocyclic aminals in up to 99 % ee. The origin of the enantioselectivity has been rationalised based on combined DFT calculations and kinetic analysis. This study provides a deeper understanding of the reaction mechanism, which involves a predominant role of the secondary amide proton, and clarifies the complex interactions occurring between substrates and the catalyst.

Experimental and theoretical study on the absorption and fluorescence properties of substituted aryl hydrazones of 1,8-naphthalimide.

Absorption and fluorescence spectra in acetonitrile for a series of substituted aryl hydrazones of N-hexyl-1,8-naphthalimide are studied with the aim of potential application of the compounds for enzyme activity localization. The influence of the substituents on the spectral characteristics has been evaluated. The absorption and fluorescence energies of substituted aryl-1,8-naphthalimide hydrazones have been calculated with the PCM TDDFT formalism. The M06 and PBE0 functionals, combined with the 6-31+G(d) atomic basis set, have been found to accurately model the excited state properties of the present set of solvated fluorophores. Absorption and fluorescence spectral characteristics have been rationalized in terms of experimental and theoretical electronic indices in order to assess their predictive abilities for application in designing analogues with good emitting properties. An excellent linear dependence is established between the experimental fluorescence and Hammett σ(p)(+) substituent constants and on the other hand σ(p)(+) constants correlate with the theoretically calculated values for the electrostatic potential at nuclei (EPN). A model for predicting the fluorescence properties of substituted hydrazones by means of EPN is drawn, including the polysubstituted derivatives, where Hammett constants are not applicable.

Conformation of some biologically active aromatic ureas.

Experimental IR spectroscopic data for the N-H stretching mode frequencies for several types of tri-substituted ureas containing benzyl and/or phenyl substituents as well as theoretical results from B3LYP/6-31G(d,p) computations on selected compounds provide sufficient evidence to determine the conformational state of these molecules. Two types of N-H bands may be found the spectra: (a) A type band due to a classical trans conformation (trans I) of the CONH structure; (b) B type band arising from an alternative trans form (trans II), in which the N-H band is involved in a hydrogen bond like interaction with the aromatic ring at the neighbouring nitrogen atom (benzyl or phenyl substituents). The N-H band of trans ICONH structure is observed at frequencies higher than 3460 cm-1, the actual position depending on weather the non-substituted N-H group is linked to aryl or alkyl substituents. The N-H band of the trans II rotameric structure is observed at 3430-3420 cm-1.