A hit expansion of 3-benzamidopyrazine-2-carboxamide: Toward inhibitors of prolyl-tRNA synthetase with antimycobacterial activity.

This study presents an exploration of the chemical space around derivatives of 3-benzamidopyrazine-2-carboxamides, previously identified as potent antimycobacterial compounds with predicted binding to mycobacterial prolyl-transfer RNA synthetase. New urea derivatives (Series-1) were generally inactive, probably due to their preference for cis-trans conformation (confirmed by density functional theory calculations and experimentally by nuclear overhauser effect spectroscopy NMR). Series-2 (3-benzamidopyrazine-2-carboxamides with disubstituted benzene ring) demonstrated that substituents larger than fluorine are not tolerated in the ortho position of the benzene ring. This series brought two new compounds (21: R = 2-F, 4-Cl and 22: R = 2-F, 4-Br) with in vitro activity against Mycobacterium tuberculosis H37Rv as well as multidrug-resistant clinical isolates, with minimum inhibitory concentration ranging from 6.25 to 25 µg/mL. The lactone-type derivatives 4H-pyrazino[2,3-d][1,3]oxazin-4-ones (Series-3) were inactive, but solvent stability studies of compound 29 indicated that they might be developed to usable lactone prodrugs of inhibitors of mycobacterial aspartate decarboxylase (PanD).

Synthesis and Characterization of New Triazole-Bispidinone Scaffolds and Their Metal Complexes for Catalytic Applications.

Bispidines are a family of ligands that plays a pivotal role in various areas of coordination chemistry, with applications in medicinal chemistry, molecular catalysis, coordination polymers synthesis, and molecular magnetism. In the present work, triazole moieties were introduced using the CuAAC click-reaction, with the aim of expanding the number of coordination sites on the bispidine core. The 1,2,3-triazole rings were thus synthesized on propargyl-derived bispidines after reaction with different alkyl azides. The new class of triazole-bispidines was characterized, and their chelation capabilities were evaluated with different metals through NMR titration, ESI-MS spectrometry, and single-crystal X-ray diffraction (SC-XRD). Finally, the suitability of these molecules as metal ligands for the catalytic Henry reaction was demonstrated with copper and zinc.

Elagolix Sodium Salt and Its Synthetic Intermediates: A Spectroscopic, Crystallographic, and Conformational Study.

Elagolix sodium salt is the first marketed orally active non-peptide gonadotropin-releasing hormone receptor antagonist (GnRHR-ant) for the management of hormone dependent diseases, such as endometriosis and uterine fibroids. Despite its presence on the market since 2018, a thorough NMR analysis of this drug, together with its synthetic intermediates, is still lacking. Hence, with the aim of filling this literature gap, we here performed a detailed NMR investigation, which allowed the complete assignment of the 1H, 13C, and 15N NMR signals. These data allowed, with the support of the conformational analysis, the determination of the stereochemical profile of the two atropisomers, detectable in solution. Moreover, these latter were also detected by means of cellulose-based chiral HPLC, starting from a sample prepared through an implemented synthetic procedure with respect to the reported ones. Overall, these results contribute to further understanding of the topic of atropisomerism in drug discovery and could be applied in the design of safe and stable analogs, endowed with improved target selectivity.

Substituent-Guided Cluster Nuclearity for Tetranuclear Iron(III) Compounds with Flat {Fe4(µ3-O)2} Butterfly Core.

The tetranuclear iron(III) compounds [Fe4(µ3-O)2(µ-LZ)4] (1-3) were obtained by reaction of FeCl3 with the shortened salen-type N2O2 tetradentate Schiff bases N,N'-bis(salicylidene)-o-Z-phenylmethanediamine H2LZ (Z = NO2, Cl and OMe, respectively), where the one-carbon bridge between the two iminic nitrogen donor atoms guide preferentially to the formation of oligonuclear species, and the ortho position of the substituent Z on the central phenyl ring selectively drives towards Fe4 bis-oxido clusters. All compounds show a flat almost-symmetric butterfly-like conformation of the {Fe4(µ3-O)2} core, surrounded by the four Schiff base ligands, as depicted by both the X-ray molecular structures of 1 and 2 and the optimized geometries of all derivatives as obtained by UM06/6-311G(d) DFT calculations. The strength of the antiferromagnetic exchange coupling constants between the iron(III) ions varies among the three derivatives, despite their magnetic cores remain structurally almost unvaried, as well as the coordination of the metal ions, with a distorted octahedral environment for the two-body iron ions, Feb, and a pentacoordination with trigonal bipyramidal geometry for the two-wing iron ions, Few. The different magnetic behavior within the series of examined compounds may be ascribed to the influence of the electronic features of Z on the electron density distribution (EDD) of the central {Fe4(µ3-O)2} core, substantiated by a Quantum Theory of Atoms In Molecules (QTAIM) topological analysis of the EDD, as obtained by UM06 calculations 1-3.

Synthesis and Conformational Analysis of Hydantoin-Based Universal Peptidomimetics.

The synthesis of a collection of enantiomerically pure, systematically substituted hydantoins as structural privileged universal mimetic scaffolds is presented. It relies on a chemoselective condensation/cyclization domino process between isocyanates of quaternary or unsubstituted α-amino esters and N-alkyl aspartic acid diesters followed by standard hydrolysis/coupling reactions with amines, using liquid-liquid acid/base extraction protocols for the purification of the intermediates. Besides the nature of the α carbon on the isocyanate moiety, either a quaternary carbon or a more flexible methylene group, conformational studies in silico (molecular modeling), in solution (NMR, circular dichroism (CD), Fourier transform infrared (FTIR)), and in solid state (X-ray) showed that the presented hydantoin-based peptidomimetics are able to project their substituents in positions superimposable to the side chains of common protein secondary structures such as α-helix and ß-turn, being the open α-helix conformation slightly favorable according to molecular modeling, while the closed ß-turn conformation preferred in solution and in solid state.

Role of the Solvent in the Reactivity of Bis-4-imidazoline-2-selone Derivatives toward I2: An Experimental and Theoretical Approach.

The reactivity of 1,1'-bis(3-methyl-4-imidazolin-2-selone)methane (L1) and 1,2-bis(3-methyl-4-imidazolin-2-selone)ethane (L2) toward I2 has been explored in MeCN under different experimental conditions and compared with that in CH2Cl2. The compounds [L1'](I)2 (I), [L1I]n(I)n (II), [L1(µ-Se)](I)2·1/2H2O (III), [L1I](I3)·2I2 (IV), and [L2](I)2·MeCN (V) were obtained and characterized. X-ray diffraction analyses point out an ionic nature for these compounds, which is presumably favored by the polarity of the solvent used. In particular, [L1I]n(I)n (II) represents the first example of an iodonium complex of imidazoline-2-selone derivatives, while [L1(µ-Se)](I)2·1/2H2O (III) represents a unique example of a dicationic [RSeSeSeR] triselane. Density functional theory calculations have allowed us to better understand the nature of the obtained compounds and to justify their formations in polarizing reaction conditions rather than in low polar solvents.

Photoactivated Nanoscale Temperature Gradient Detection Using X-ray Absorption Spectroscopy as a Direct Nanothermometry Method.

Nanoparticle-mediated thermal treatments have demonstrated high efficacy and versatility as a local anticancer strategy beyond traditional global hyperthermia. Nanoparticles act as heating generators that can trigger therapeutic responses at both the cell and tissue level. In some cases, treatment happens in the absence of a global temperature rise, damaging the tumor cells even more selectively than other nanotherapeutic strategies. The precise determination of the local temperature in the vicinity of such nanoheaters then stands at the heart of thermal approaches to better adjust the therapeutic thermal onset and reduce potential toxicity-related aspects. Herein, we describe an experimental procedure by X-ray absorption spectroscopy, which directly and accurately infers the local temperature of gold-based nanoparticles, single and hybrid nanocrystals, upon laser photoexcitation, revealing significant nanothermal gradients. Such nanothermometric methodology based on the temperature-dependency of atomic parameters of nanoparticles can be extended to any nanosystem upon remote hyperthermal conditions.

Selective Formation, Reactivity, Redox and Magnetic Properties of MnIII and FeIII Dinuclear Complexes with Shortened Salen-Type Schiff Base Ligands.

The reactivity of the shortened salen-type ligands H3salmp, H2salmen and H2sal(p-X)ben with variable para-substituent on the central aromatic ring (X = tBu, Me, H, F, Cl, CF3, NO2) towards the trivalent metal ions manganese(III) and iron(III) is presented. The selective formation of the dinuclear complexes [M2(µ-salmp)2], M = Mn (1a), Fe (2a), [M2(µ-salmen)2(µ-OR)2)], R = Et, Me, H and M = Mn (3a-c) or Fe (4a-c), and (M2(µ-sal[p-X]ben)2(µ-OMe)2), X = tBu, Me, H, F, Cl, CF3, NO2 and M = Mn (5a-g) or Fe (6a-g), could be identified by reaction of the Schiff bases with metal salts and the base NEt3, and their characterization through elemental analysis, infrared spectroscopy, mass spectrometry and single-crystal X-ray diffraction of 2a·2AcOEt, 2a·2CH3CN and 3c·2DMF was performed. In the case of iron(III) and H3salmp, when using NaOH as a base instead of NEt3, the dinuclear complexes [Fe2(µ-salmp)(µ-OR)(salim)2], R = Me, H (2b,c) could be isolated and spectroscopically characterized, including the crystal structure of 2b·1.5H2O, which showed that rupture of one salmp3- to two coordinated salim- ligands and release of one salH molecule occurred. The same hydrolytic tendency could be identified with sal(p-X)ben ligands in the case of iron(III) also by using NEt3 or upon standing in solution, while manganese(III) did not promote such a C-N bond breakage. Cyclic voltammetry studies were performed for 3b, 4b, 5a and 6a, revealing that the iron(III) complexes can be irreversibly reduced to the mixed-valence FeIIFeIII and FeII2 dinuclear species, while the manganese(III) derivatives can be reversibly oxidized to either the mixed-valence MnIIIMnIV or to the MnIV2 dinuclear species. The super-exchange interaction between the metal centers, mediated by the bridging ligands, resulted in being antiferromagnetic (AFM) for the selected dinuclear compounds 3b, 4b, 5a, 5e,5f, 6a and 6e. The coupling constants J (-2JS1·S2 formalism) had values around -13 cm-1 for manganese(III) compounds, among the largest AFM coupling constants reported so far for dinuclear MnIII2 derivatives, while values between -3 and -10 cm-1 were obtained for iron(III) compounds.

Tuneable solvent adsorption and exchange by 1D bispidine-based Mn(II) coordination polymers via ligand design.

Here we report novel bispidine-based coordination polymers (CPs) 2·TCM, 3·TCM, 3·NB, 5·TCM and 5·TCM·NB, of compostition [Mn(Cl)2(L2)2·(TCM)2], [Mn(Cl)2(L3)2·(TCM)5], [Mn(Cl)2(L3)2·(NB)8], [Mn(Cl)2(L5)2·(TCM)4], [Mn(Cl)2(L5)2·(TCM)2·(NB)2], respectively (NB = nitrobenzene; TCM = chloroform). They were obtained starting from novel bispidine ligands L2 (dimethyl 7-isopropyl-3-methyl-9-oxo-2,4-di(pyridin-4-yl)-3,7-diazabicyclo[3.3.1]nonane-1,5-dicarboxylate), L3 (dimethyl 7-(cyclohexylmethyl)-3-methyl-9-oxo-2,4-di(pyridin-4-yl)-3,7-diazabicyclo[3.3.1]nonane-1,5-dicarboxylate) and L5 (dimethyl 7-(4-(dimethylamino)benzyl)-3-methyl-9-oxo-2,4-di(pyridin-4-yl)-3,7-diazabicyclo[3.3.1]nonane-1,5-dicarboxylate), The novel CPs were characterized by single crystal X-ray diffraction (SC-XRD), powder X-ray diffraction (PXRD) and thermal analyses (TGA). We describe their structural and dynamic properties in terms of solvent exchange and adsorption processes, and we outline the general trends observed on the basis of a total of 16 X-ray structures (4 new) and 21 microcrystalline powder phases (10 new), which have been obtained so far for CPs by coordination of ligands L1-L5, having different substitution at the N7 position. This large set of CPs comprises monosolvated, bisolvated and desolvated species, and it shows a good demonstration of how small differences in the functionalization of the organic ligand can have a strong impact on the resulting structural and dynamic properties of this class of 1D CPs.

Local Structure and Magnetism of Fe2O3 Maghemite Nanocrystals: The Role of Crystal Dimension.

Here we report on the impact of reducing the crystalline size on the structural and magnetic properties of γ-Fe2O3 maghemite nanoparticles. A set of polycrystalline specimens with crystallite size ranging from ~2 to ~50 nm was obtained combining microwave plasma synthesis and commercial samples. Crystallite size was derived by electron microscopy and synchrotron powder diffraction, which was used also to investigate the crystallographic structure. The local atomic structure was inquired combining pair distribution function (PDF) and X-ray absorption spectroscopy (XAS). PDF revealed that reducing the crystal dimension induces the depletion of the amount of Fe tetrahedral sites. XAS confirmed significant bond distance expansion and a loose Fe-Fe connectivity between octahedral and tetrahedral sites. Molecular dynamics revealed important surface effects, whose implementation in PDF reproduces the first shells of experimental curves. The structural disorder affects the magnetic properties more and more with decreasing the nanoparticle size. In particular, the saturation magnetization reduces, revealing a spin canting effect. Moreover, a large effective magnetic anisotropy is measured at low temperature together with an exchange bias effect, a behavior that we related to the existence of a highly disordered glassy magnetic phase.

Synthesis, Characterization and Biological Activity of Novel Cu(II) Complexes of 6-Methyl-2-Oxo-1,2-Dihydroquinoline-3-Carbaldehyde-4n-Substituted Thiosemicarbazones.

Three new 6-methyl-2-oxo-1,2-dihydroquinoline-3-carbaldehyde-thiosemicarbazones-N-4-substituted pro-ligands and their Cu(II) complexes (1, -NH2; 2, -NHMe; 3, -NHEt) have been prepared and characterized. In both the X-ray structures of 1 and 3, two crystallographically independent complex molecules were found that differ either in the nature of weakly metal-binding species (water in 1a and nitrate in 1b) or in the co-ligand (water in 3a and methanol in 3b). Electron Paramagnetic Resonance (EPR) measurements carried out on complexes 1 and 3 confirmed the presence of such different species in the solution. The electrochemical behavior of the pro-ligands and of the complexes was investigated, as well as their biological activity. Complexes 2 and 3 exhibited a high cytotoxicity against human tumor cells and 3D spheroids derived from solid tumors, related to the high cellular uptake. Complexes 2 and 3 also showed a high selectivity towards cancerous cell lines with respect to non-cancerous cell lines and were able to circumvent cisplatin resistance. Via the Transmission Electron Microscopy (TEM) imaging technique, preliminary insights into the biological activity of copper complexes were obtained.

Combined structural and theoretical investigation on differently substituted bispidine ligands: predicting the properties of their corresponding coordination polymers.

Pyridine-based bispidine ligands L1-L7, which differ in the substituent at the N7 position of the bispidine scaffold, have been studied by single crystal X-ray diffraction and density functional theory (DFT) calculations, also including solid-state algorithms. Qualitative description of the packing interactions and quantitative data on the stability of each ligand in the solid-state have been employed to draw reasonable predictions on the ligand potential for the formation of linear 1D coordination polymers (CPs) with Mn(ii)Cl2 and on their resulting dynamic properties, in terms of adsorption and solvent exchange capabilities. The basic assumption lies in the fact that volume and polarizability of the ligands would similarly affect packing energies in both molecular solids and CP materials. The results here obtained confirm the data previously reported on CPs (those made from L4 are less dynamic than the ones with L1), but they also allow the prediction that CPs made with L2 and L5 should be more dynamic than expected, while CPs with L6 and L7 should not form altogether. This latter prediction was derived from the analysis of the steric and electronic factors of the ligand substituents on the N7 position and it is further substantiated by the obtainment of a 2 : 1 molecular complex, and not a CP, by crystallization of L6 with MnCl2.

Drugs/lamellae interface influences the inner structure of double-loaded liposomes for inhaled anti-TB therapy: An in-depth small-angle neutron scattering investigation.

With the aim of developing new drug carriers for inhalation therapy, we report here an in depth investigation of the structure of multilamellar liposomes loaded with two well-established anti-tubercular (anti-TB) drugs, isoniazid (INH) and rifampicin (RIF), by means of small-angle neutron-scattering (SANS) analysis. Unloaded, single drug-loaded and co-loaded liposomes were prepared using different amounts of drugs and characterized regarding size, encapsulation efficiency and drug release. Detailed information on relevant properties of the investigated host-guest structures, namely the steric bilayer thickness, particle dispersion, number of lamellae and drug localization was studied by SANS. Results showed that RIF-liposomes were less ordered than unloaded liposomes. INH induced a change in the inter-bilayer periodical spacing, while RIF-INH co-loading stabilized the multilamellar liposome architecture, as confirmed by the increment of the drug loading capacity. These findings could be useful for the understanding of in vitro and in vivo behavior of these systems and for the design of new drug carriers, intended for inhaled therapy.

Intriguing C-HCu interactions in bis-(phenanthroline)Cu(i) redox mediators for dye-sensitized solar cells.

We have synthesized and characterized a series of bis-(phenanthroline)Cu(i) complexes of interest as redox mediators for dye-sensitized solar cells. This study led to the discovery of intriguing anagostic interactions between the hydrogen atom and the copper center as evidenced by X-ray diffraction studies on a single crystal. Remarkably, an anagostic interaction was found between a H atom of a methyl group and a copper site.

Novel coumarins and related copper complexes with biological activity: DNA binding, molecular docking and in vitro antiproliferative activity.

Coumarins show biological activity and are widely exploited for their therapeutic effects. Although a great number of coumarins substituted by heterocyclic moieties have been prepared, few studies have been carried out on coumarins containing pyridine heterocycle, which is known to modulate their physiological activities. We prepared and characterized three novel 3-(pyridin-2-yl)coumarins and their corresponding copper(II) complexes. We extended our investigations also to three known similar coumarins, since no data about their biochemical activity was previously been reported. The antiproliferative activity of the studied compounds was tested against human derived tumor cell lines and one human normal cell line. The DNA binding constants were determined and docking studies with DNA carried out. Selected Quantitative Structure-Activity Relationship (QSAR) descriptors were calculated in order to relate a set of structural and topological descriptors of the studied compounds to their DNA interaction and cytotoxic activity.

Spectroscopic, Structural, and Computational Characterization of Three Bispidinone Derivatives, as Ligands for Enantioselective Metal Catalyzed Reactions.

Three chiral derivatives of the alkaloid sparteine (bispidines), characterized by the 3,7-diazabicyclo[3.3.1]nonane moiety, were designed as efficient ligands in a number of enantioselective reactions due to their metal coordination properties. A full evaluation of the 3D properties of the compounds was carried out, as the geometrical features of the bicyclic framework are strictly related to the efficiency of the ligands in the asymmetric catalysis. The selected molecules have different molecular complexity for investigating the effects of different chiral groups on the bicycle conformation. We report here a thorough analysis of their molecular arrangement, by NMR spectroscopy, single crystal X-ray crystallography, and computational techniques, which put in evidence their conformational preferences and the parameters needed for the design of more efficient ligands in asymmetric synthetic routes. The results confirmed the high molecular flexibility of the compounds, and indicated how to achieve a control of the chair-chair/boat-chair conformational ratio, by adjusting the relative size of the substituents on the piperidine nitrogens.

Crystallographic and spectroscopic study on a known orally active progestin.

6,17α-Dimethyl-4,6-pregnadiene-3,20-dione (medrogestone, 2) is for a long time known steroid endowed with progestational activity. In order to study its crystallographic and NMR spectroscopic properties with the aim to fill the literature gap, we prepared medrogestone following a traditional procedure. A careful NMR study allowed the complete assignment of the (1)H and (13)C NMR signals not only of medrogestone but also of its synthetic intermediates. The structural and stereochemical characterizations of medrogestone together with its precursor 17α-methyl-3-ethoxy-pregna-3,5-dien-20-one were described by means of X-ray analysis, allowing a deepened conformational investigation.

Dipeptide Nanotubes Containing Unnatural Fluorine-Substituted ß(2,3)-Diarylamino Acid and L-Alanine as Candidates for Biomedical Applications.

The synthesis and the structural characterization of dipeptides composed of unnatural fluorine-substituted ß(2,3)-diarylamino acid and L-alanine are reported. Depending on the stereochemistry of the ß amino acid, these dipeptides are able to self-assemble into proteolytic stable nanotubes. These architectures were able to enter the cell and locate in the cytoplasmic/perinuclear region and represent interesting candidates for biomedical applications.

Copper(II)-Catalyzed Alkoxyhalogenation of Alkynyl Ureas and Amides as a Route to Haloalkylidene-Substituted Heterocycles.

A highly effective synthesis of haloalkylidene-substituted heterocycles by copper(II)-catalyzed cyclization of alkynyl ureas and secondary amides has been developed. The reaction, which involves a catalytic amount of CuCl2 and a stoichiometric amount of N-halosuccinimide, occurs selectively through an alkoxyhalogenation process. Alternatively, alkoxychlorination and alkoxybromination reactions can be performed working solely with stoichiometric CuCl2 and CuBr2, respectively.

Zinc(II)-methimazole complexes: synthesis and reactivity.

The tetrahedral S-coordinated complex [Zn(MeImHS)4](ClO4)2, synthesised from the reaction of [Zn(ClO4)2] with methimazole (1-methyl-3H-imidazole-2-thione, MeImHS), reacts with triethylamine to yield the homoleptic complex [Zn(MeImS)2] (MeImS = anion methimazole). ESI-MS and MAS (13)C-NMR experiments supported MeImS acting as a (N,S)-chelating ligand. The DFT-optimised structure of [Zn(MeImS)2] is also reported and the main bond lengths compared to those of related Zn-methimazole complexes. The complex [Zn(MeImS)2] reacts under mild conditions with methyl iodide and separates the novel complex [Zn(MeImSMe)2I2] (MeImSMe = S-methylmethimazole). X-ray diffraction analysis of the complex shows a ZnI2N2 core, with the methyl thioethers uncoordinated to zinc. Conversely, the reaction of [Zn(MeImS)2] with hydroiodic acid led to the formation of the complex [Zn(MeImHS)2I2] having a ZnI2S2 core with the neutral methimazole units S-coordinating the metal centre. The Zn-coordinated methimazole can markedly modify the coordination environment when changing from its thione to thionate form and vice versa. The study of the interaction of the drug methimazole with the complex [Zn(MeIm)4](2+) (MeIm = 1-methylimidazole) - as a model for Zn-enzymes containing a N4 donor set from histidine residues - shows that methimazole displaces only one of the coordinated MeIm molecules; the formation constant of the mixed complex [Zn(MeIm)3(MeImHS)](2+) was determined.