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.

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+.

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 results obtained suggest that the metal selectivity of monensin can be modulated by changing the solvents used.

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 σ⁰_m and σ⁰_p 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.

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

The switching of the electric field with a particular directionality could be used for the healing of misfolded proteins.

Hydroxamic acid derivatives as histone deacetylase inhibitors: a DFT study of their tautomerism and metal affinities/selectivities

Hydroxamic acids are regarded as potent inhibitors of histone deacetylases (HDAC), and can therefore be used to reduce malignancy growth and size in affected organisms. Although there is a substantial body of information on the structures, syntheses, and biological activities of HDAC inhibitors, several important questions regarding their physicochemical properties and metal affinities/selectivities remain answered. First, how do the conformation and ionization of the hydroxamic group depend on its chemical composition and the dielectric properties of the medium? Second, how do these factors affect the affinities and selectivities of HDAC inhibitors for essential biogenic metal cations? Third, what is the preferred deprotonation site of the hydroxamic moiety and its mode of binding to the metal cation? The present work addressed these questions by performing density functional calculations combined with polarizable continuum model computations. The geometry, deprotonation pattern, metal-binding mode, and metal affinity/selectivity of SAHA, a typical HDAC inhibitor, were examined, and key factors affecting its ligation properties were elucidated. Sulfur- and selenium-containing analogs of SAHA were also modeled for the first time, and their potential as efficient metal-binding entities (to Mg²⁺, Fe²⁺, and Zn²⁺ cations) was assessed. The present calculations shed light on the thermodynamics of the binding of HDAC inhibitors to metal ions, and suggest techniques for enhancing their metal-ligating properties.

Assembly of New Merocyanine Chromophores with a 1,8-Naphthalimide Core by a New Method for the Synthesis of the Methine Function

A new method for the synthesis of the monomethine group using nitro as a leaving group in an SN-Ar reaction is described. A series of novel merocyanine dyes has been synthesised and their photophysical properties have been elucidated. The longest wavelength absorption occurs in the range 519–619 nm and the molar absorptivities vary with the substituents and are in the range 1000–47700 L mol–1 cm–1. The dyes show high chemical and photostability. One example from the series has the ability to distinguish methanol from ethanol. The introduction of a quinoid fragment into the structure leads to a pronounced intramolecular charge transfer and hence a noticeable positive solvatochromism. The structures and electronic properties of the compounds have been studied by density functional theory (DFT) and time-dependent DFT.

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

The organocatalytic enantioselective conjugate addition of secondary β-ketoamides to α,β-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.

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.