Nα-Aroyl-N-Aryl-Phenylalanine Amides: A Promising Class of Antimycobacterial Agents Targeting the RNA Polymerase.

Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains the leading cause of death from a bacterium in the world. The global prevalence of clinically relevant infections with opportunistically pathogenic non-tuberculous mycobacteria (NTM) has also been on the rise. Pharmacological treatment of both TB and NTM infections usually requires prolonged regimens of drug combinations, and is often challenging because of developed or inherent resistance to common antibiotic drugs. Medicinal chemistry efforts are thus needed to improve treatment options and therapeutic outcomes. Nα-aroyl-N-aryl-phenylalanine amides (AAPs) have been identified as potent antimycobacterial agents that target the RNA polymerase with a low probability of cross resistance to rifamycins, the clinically most important class of antibiotics known to inhibit the bacterial RNA polymerase. In this review, we describe recent developments in the field of AAPs, including synthesis, structural characterization, in vitro microbiological profiling, structure-activity relationships, physicochemical properties, pharmacokinetics and early cytotoxicity assessment.

Racemization-free synthesis of Nα-2-thiophenoyl-phenylalanine-2-morpholinoanilide enantiomers and their antimycobacterial activity.

Nα-2-thiophenoyl-D-phenylalanine-2-morpholinoanilide (MMV688845, IUPAC: N-(1-((2-morpholinophenyl)amino)-1-oxo-3-phenylpropan-2-yl)thiophene-2-carboxamide) from the Pathogen Box® library (Medicines for Malaria Ventures, MMV) is a promising lead compound for antimycobacterial drug development. Two straightforward synthetic routes to the title compound starting from phenylalanine or its Boc-protected derivative are reported. Employing Boc-phenylalanine as starting material and the T3P® and PyBOP® amide coupling reagents enables racemization-free synthesis, avoiding the need for subsequent separation of the enantiomers. The crystal structure of the racemic counterpart gives insight into the molecular structure and hydrogen bonding interactions in the solid state. The R-enantiomer of the title compound (derived from D-phenylalanine) exhibits activity against non-pathogenic and pathogenic mycobacterial strains, whereas the S-enantiomer is inactive. Neither of the enantiomers and the racemate of the title compound shows cytotoxicity against various mammalian cells.

Synthesis, structural characterization and antimycobacterial evaluation of several halogenated non-nitro benzothiazinones.

8-Nitro-1,3-benzothiazin-4-ones (BTZs), with BTZ043 and PBTZ169 as the most advanced compounds, represent a new class of potent antitubercular agents, which irreversibly inhibit decaprenylphosphoryl-ß-d-ribose-2'-epimerase (DprE1), an enzyme crucial for cell wall synthesis in the pathogen Mycobacterium tuberculosis. Synthesis, structural characterization and in vitro testing against Mycobacterium aurum DSM 43999 and M. tuberculosis H37Rv of halogenated 2-(4-ethoxycarbonylpiperazin-1-yl)-1,3-benzothiazin-4-ones lacking a nitro group are reported. X-ray crystallography reveals that the structure of the BTZ scaffold can significantly deviate from planarity. In contrast to recent reports, the results of the present study indicate that further investigation of halogenated non-nitro BTZs for antitubercular activity is less than a promising approach.

Atom-Precise Organometallic Zinc Clusters.

The bottom-up synthesis of organometallic zinc clusters is described. The cation {[Zn10](Cp*)6 Me}(+) (1) is obtained by reacting [Zn2 Cp*2] with [FeCp2][BAr4 (F)] in the presence of ZnMe2. In the presence of suitable ligands, the high reactivity of 1 enables the controlled abstraction of single Zn units, providing access to the lower-nuclearity clusters {[Zn9 ](Cp*)6} (2) and {[Zn8 ](Cp*)5 ((t) BuNC)3}(+) (3). According to DFT calculations, 1 and 2 can be described as closed-shell species that are electron-deficient in terms of the Wade-Mingos rules because the apical ZnCp* units that constitute the cluster cage do not have three, but only one, frontier orbitals available for cluster bonding. Zinc behaves flexibly in building the skeletal metal-metal bonds, sometimes providing one major frontier orbital (like Group 11 metals) and sometimes providing three frontier orbitals (like Group 13 elements).

Dizinc cation [Zn2](2+) trapped in a homoleptic metalloid coordination environment stabilized by dispersion forces: [Zn2(GaCp*)6][BAr4(F)]2.

The synthesis and characterization of the cationic mixed metal Ga/Zn cluster [Zn2(GaCp*)6](2+) (1) is presented. The reaction of [Zn2Cp*2] with [Ga2Cp*][BAr4(F)] leads to the formation of the novel complex being the first example of a [Zn2](2+) core exclusively ligated by metalloid group-13 organyl-ligands. Compound 1 exhibits two different coordination modes: In the solid state, two of the six GaCp* ligands occupy bridging positions, whereas VT (1)H NMR indicates the coexistence of a second isomer in solution featuring six terminal GaCp* ligands. Quantum chemical calculations have been carried out to assign the gallium and zinc positions; the bonding situation in 1 is characterized and the importance of dispersion forces is discussed.

The σ-aromatic clusters [Zn3]⁺ and [Zn2Cu]: embryonic brass.

The triangular clusters [Zn3Cp*3](+) and [Zn2CuCp*3] were obtained by addition of the in situ generated, electrophilic, and isolobal species [ZnCp*](+) and [CuCp*] to Carmona's compound, [Cp*Zn-ZnCp*], without splitting the ZnZn bond. The choice of non-coordinating fluoroaromatic solvents was crucial. The bonding situations of the all-hydrocarbon-ligand-protected clusters were investigated by quantum chemical calculations revealing a high degree of σ-aromaticity similar to the triatomic hydrogen ion [H3](+). The new species serve as molecular building units of Cu(n)Zn(m) nanobrass clusters as indicated by LIFDI mass spectrometry.

The intermetalloid cluster [(Cp*AlCu)6H4], embedding a Cu6 core inside an octahedral Al6 shell: molecular models of Hume-Rothery nanophases.

Defined molecular models for the surface chemistry of Hume-Rothery nanophases related to catalysis are very rare. The Al-Cu intermetalloid cluster [(Cp*AlCu)6H4] was selectively obtained from the clean reaction of [(Cp*Al)4] and [(Ph3PCuH)6]. The stronger affinity of Cp*Al towards Cu sweeps the phosphine ligands from the copper hydride precursor and furnishes an octahedral Al6 cage to encapsulate the Cu6 core. The resulting hydrido cluster M12H4 reacts with benzonitrile to give the stoichiometric hydrometalation product [(Cp*AlCu)6H3(N=CHPh)].

3-[(Benzo-1,3-dioxol-5-yl)amino]-4-methoxycyclobut-3-ene-1,2-dione: polymorphism and twinning of a precursor to an antimycobacterial squaramide.

The title compound, 3-[(benzo-1,3-dioxol-5-yl)amino]-4-methoxycyclobut-3-ene-1,2-dione, C12H9NO5 (3), is a precursor to an antimycobacterial squaramide. Block-shaped crystals of a monoclinic form (3-I, space group P21/c, Z = 8, Z' = 2) and needle-shaped crystals of a triclinic form (3-II, space group P-1, Z = 4, Z' = 2) were found to crystallize concomitantly. In both crystal forms, R22(10) dimers assemble through N-H...O=C hydrogen bonds. These dimers are formed from crystallographically unique molecules in 3-I, but exhibit crystallographic Ci symmetry in 3-II. Twinning by pseudomerohedry was encountered in the crystals of 3-II. The conformations of 3 in the solid forms 3-I and 3-II are different from one another but are similar for the unique molecules in each polymorph. Density functional theory (DFT) calculations on the free molecule of 3 indicate that a nearly planar conformation is preferred.

Comparing the crystal structures and spectroscopic properties of a p-hydroxy styrylquinolinium dye with those of its p-dimethylamino analogue.

Two previously synthesized styrylquinolinium dyes, namely (E)-1-butyl-4-(4-(dimethylamino)styryl)quinolinium iodide (D36) and (E)-1-butyl-4-(4-hydroxystyryl)quinolinium iodide (D34), were compared in terms of their properties by single-crystal X-ray diffraction (XRD), Hirshfeld surface analysis, Fourier transform Raman (FT-Raman), Fourier transform infrared (FT-IR), fluorescence, and ultraviolet-visible (UV-Vis) spectroscopy, and 1H- and 13C-NMR methods. Both dyes D36 and D34 crystallized in the triclinic and monoclinic systems in the centrosymmetric space groups P-1 and P21/n, respectively. The unit cell of D36 contains two molecules of the dye, participating in weak intermolecular interactions, whereas that of D34 contains four formula units. The phenolic hydroxy group of D34 participates in the formation of a hydrogen bond with the iodide anion. The 4-styrylquinolinium moieties of the cationic dye molecules are nearly planar. The dihedral angle between the mean planes through the ten-membered quinolinium system and the benzene ring is 7.5° in D36 and 5.9(1)° in D34. The structural parameters planarity and bond length alternation (BLA) are discussed, which are important for the evaluation of the first hyperpolarizability ß at the molecular level, even in a centrosymmetric crystal. The UV-visible spectra of the dyes in 14 solvents of different polarities were investigated. The reversible solvatochromic behavior of the dyes is demonstrated experimentally and compared with known "binuclear dyes" by evaluating the Rezende model. Dye D36 does not fluoresce, and D34 has a very low emission in the solvents tested.

Synthesis and in†vitro Metabolic Stability of Sterically Shielded Antimycobacterial Phenylalanine Amides.

Nα-aroyl-N-aryl-phenylalanine amides (AAPs) are RNA polymerase inhibitors with activity against Mycobacterium tuberculosis and non-tuberculous mycobacteria. We observed that AAPs rapidly degrade in microsomal suspensions, suggesting that avoiding hepatic metabolism is critical for their effectiveness in vivo. As both amide bonds are potential metabolic weak points of the molecule, we synthesized 16 novel AAP analogs in which the amide bonds are shielded by methyl or fluoro substituents in close proximity. Some derivatives show improved microsomal stability, while being plasma-stable and non-cytotoxic. In parallel with the metabolic stability studies, the antimycobacterial activity of the AAPs against Mycobacterium tuberculosis, Mycobacterium abscessus, Mycobacterium avium and Mycobacterium intracellulare was determined. The stability data are discussed in relation to the antimycobacterial activity of the panel of compounds and reveal that the concept of steric shielding of the anilide groups by a fluoro substituent has the potential to improve the stability and bioavailability of AAPs.

The organozinc rich compounds [Cp*M(ZnR)5] (M = Fe, Ru; R = Cp*, Me, Cl, Br).

Organozinc (ZnR with R = Cp*, Me, Cl, Br) ligated transition metal (M) half-sandwich compounds of general formula [Cp*M(ZnR)5] (M = Fe, Ru) are presented in this work. The new compounds were obtained by treatment of various GaCp* ligated precursors with suitable amounts of ZnMe2 to exchange Ga against Zn. This exchange follows a strict Ga:Zn ratio of 1:2. Accordingly, a Ga/Zn mixed compound [{Cp*Ru(GaCp*)(ZnCp*)(ZnCl)2}2] can be obtained if the amount of ZnMe2 is reduced so that one GaCp* remains coordinated to the transition metal. All new compounds were characterized by elemental analysis, (1)H and (13)C NMR spectroscopy as well as by single crystal X-ray diffraction techniques, if applicable. The coordination polyhedra of [Cp*M(ZnR)5] can be derived from the pseudo homoleptic parent compound [Ru(ZnCp*)4(ZnMe)6], as emphasized by continuous shape measures analysis (CShM). Computational investigations at the density functional theory (DFT) level of theory were performed, revealing no significant attractive interaction of the zinc atoms and therefore these compounds are best described as classical complexes, rather than cluster compounds. The Ru-L bond strength follow the order Cp* > ZnCl > ZnMe > ZnCp*.

Clusters [Ma(GaCp*)b(CNR)c] (M = Ni, Pd, Pt): synthesis, structure, and Ga/Zn exchange reactions.

Reactions of homoleptic isonitrile ligated complexes or clusters of d(10)-metals with the potent carbenoid donor ligand GaCp* are presented (Cp* = pentamethylcyclopentadienyl). Treatment of [Ni4(CNt-Bu)7], [{M(CNR)2}3] (M = Pd, Pt) and [Pd(CNR)2Me2] (R = t-Bu, Ph) with suitable amounts of GaCp* lead to the formation of the heteroleptic, tri- and tetranuclear clusters [Ni4(CNt-Bu)7(GaCp*)3] (1), [{M(CNt-Bu)}3(GaCp*)4] (M = Pd: 2a, Pt: 2b), and [{Pd(CNR)}4(GaCp*)4] (R = t-Bu: 3a, Ph: 3b). The reactions involve isonitrile substitution reactions, GaCp* addition reactions, and cluster formation reactions. The new compounds were investigated for their ability to undergo Ga/Zn exchange reactions when treated with ZnMe2. The novel tetranuclear Zn-rich clusters [Ni4GaZn7(Cp*)2Me7(CNt-Bu)6] (4) and [{Pd(CNR)}4(ZnCp*)4(ZnMe)4] (R = t-Bu: 5a, Ph: 5b) were obtained and isolated. The electronic situation and geometrical arrangement of atoms of all compounds will be presented and discussed. All new compounds are characterized by solution (1)H, (13)C NMR and IR spectroscopy, elemental analysis (EA), liquid injection field desorption ionization mass spectrometry (LIFDI-MS) as well as single crystal X-ray crystallography.

Homoleptic gadolinium amidinates as precursors for MOCVD of oriented gadolinium nitride (GdN) thin films.

Five new homoleptic gadolinium tris-amidinate complexes are reported, which were synthesized via the salt-elimination reaction of GdCl(3) with 3 equiv of lithiated symmetric and asymmetric amidinates at ambient temperature. The Gd-tris-amidinates [Gd{(N(i)Pr)(2)CR}(3)] [R = Me (1), Et (2), (t)Bu (3), (n)Bu (4)] and [Gd{(NEt)(N(t)Bu)CMe}(3)] (5) are solids at room temperature and sublime at temperatures of about 125 °C (6 × 10(-2) mbar) with the exception of compound 4, which is a viscous liquid at room temperature. According to X-ray diffraction analysis of 3 and 5 as representative examples of the series, the complexes adopt a distorted octahedral structure in the solid state. Mass spectrometric (MS) data confirmed the monomeric structure in the gas phase, and high-resolution MS allowed the identification of characteristic fragments, such as [{(N(i)Pr)(2)CR}GdCH(3)](+) and [{(N(i)Pr)(2)CR}GdNH](+). The alkyl substitution patterns of the amidinate ligands clearly show an influence on the thermal properties, and specifically, the introduction of the asymmetric carbodiimide leads to a lowering of the onset of volatilization and decomposition. Compound 5, which is the first Gd complex with an asymmetric amidinate ligand system to be reported, was, therefore, tested for the MOCVD of GdN thin films. The as-deposited GdN films were capped with Cu in a subsequent MOCVD process to prevent postdeposition oxidation of the films. Cubic GdN on Si(100) substrates with a preferred orientation in the (200) direction were grown at 750 °C under an ammonia atmosphere and exhibited a columnar morphology and low levels of C or O impurities according to scanning electron microscopy, Rutherford backscattering, and nuclear reaction analysis.

(Hexafluorosilicato-κ(2)F,F')bis(1,10-phenanthroline-κ(2)N,N')zinc(II) methanol monosolvate.

The title compound, [Zn(SiF6)(C12H8N2)2]·CH3OH, contains a neutral heteroleptic tris-chelate Zn(II) complex, viz. [Zn(SiF6)(phen)2] (phen is 1,10-phenanthroline), exhibiting approximate molecular C2 point-group symmetry. The Zn(II) cation adopts a severely distorted octahedral coordination. As far as can be ascertained, the title complex represents the first structurally characterized example of a Zn(II) complex bearing a bidentate-bound hexafluorosilicate ligand. A density functional theory study of the isolated [Zn(SiF6)(phen)2] complex was undertaken to reveal the influence of crystal packing on the molecular structure of the complex. In the crystal structure, the methanol solvent molecule forms a hydrogen bond to one F atom of the hexafluorosilicate ligand. The hydrogen-bonded assemblies so formed are tightly packed in the crystal, as indicated by a high packing coefficient (74.1%).

catena-Poly[[(tetrahydrofuran-κO)potassium]-µ-(η5:η5)-2,3,4,5-tetramethyl-1-n-pentylcyclopentadienyl].

The title compound, [K(C14H23)(C4H8O)]n, comprises zigzag chains of alternating bridging 2,3,4,5-tetramethyl-1-n-pentylcyclopentadienyl ligands and potassium ions, with an ancillary tetrahydrofuran ligand in the coordination environment of potassium. The coordination polymer strands so formed extend by 21 screw symmetry in the b-axis direction. The chemically modified cyclopentadienyl ligand, with a tethered n-pentyl group, was synthesized from 2,3,4,5-tetramethylcyclopent-2-enone by a Grignard reaction.

Pyridin-4-ylmethanaminium perchlorate mono-hydrate.

Pyridin-4-ylmethanaminium perchlorate monohydrate (synonym: 4-picolyl-ammonium perchlorate monohydrate), C6H9N2 +·ClO4 -·H2O, crystallizes in the monoclinic system (space group P21/n) with the asymmetric unit comprising two formula units (Z' = 2). All mol-ecular entities are located on general positions. The two crystallographically distinct 4-picolyl-ammonium cations exhibit different conformations. The two unique perchlorate anions are non-disordered, showing an r.m.s. deviation of 0.011 Šfrom mol-ecular T d symmetry. The supra-molecular structure in the solid state features an intricate tri-periodic network of N-H⋯O, O-H⋯N and O-H⋯O hydrogen bonds.

Synthesis, structures, reactivity and medicinal chemistry of antitubercular benzothiazinones.

Tuberculosis is the leading bacterial killer worldwide. 8-Nitro-4H-benzo[e][1,3]thiazin-4-ones are a potent class of antitubercular agents with a new mechanism of action. BTZ043 and PBTZ169 (macozinone) have progressed to clinical studies. Herein, we give a comprehensive account of this important class of potential new drugs to treat tuberculosis. We present an overview of recent developments in the field of antitubercular benzothiazinones (BTZs) and summarize our own contributions. The review covers synthesis, structures and reactivity, mechanism of action, in vitro activity and structure activity relationships (SARs), physicochemical and pharmacokinetic properties as well as a brief summary of in vivo models and clinical studies. We address bioavailability issues and the challenge of the potentially toxic nitroaromatic moiety, including reactivity towards nucleophiles in vivo and highlight possible directions of further research into BTZs through chemical modification.

Crystal structure and anti-mycobacterial evaluation of 2-(cyclo-hexyl-meth-yl)-7-nitro-5-(tri-fluoro-meth-yl)benzo[d]iso-thia-zol-3(2H)-one.

The title compound, C15H15F3N2O3S, crystallizes in the monoclinic system, space group I2/a, with Z = 8. As expected, the nine-membered heterobicyclic system is virtually planar and the cyclo-hexyl group adopts a chair conformation. There is structural evidence for intra-molecular N-S⋯O chalcogen bonding between the benziso-thia-zolinone S atom and one O atom of the nitro group, approximately aligned along the extension of the covalent N-S bond [N-S⋯O = 162.7 (1)°]. In the crystal, the mol-ecules form centrosymmetric dimers through C-H⋯O weak hydrogen bonding between a C-H group of the electron-deficient benzene ring and the benzo-thia-zolinone carbonyl O atom with an R 2 2(10) motif. In contrast to the previously described N-acyl 7-nitro-5-(tri-fluoro-meth-yl)benzo[d]iso-thia-zol-3(2H)-ones, the title N-cyclo-hexyl-methyl analogue does not inhibit growth of Mycobacterium aurum and Mycobacterium smegmatis in vitro.

Methyl 1-[(6-meth-oxy-5-methyl-pyrimidin-4-yl)meth-yl]-1H-benzo[d]imidazole-7-carboxyl-ate: a combined X-ray and DFT study.

The title compound, C16H16N4O3, was obtained as a side product during the synthesis of the previously reported anti-tubercular agent N-(2-fluoro-eth-yl)-1-[(6-meth-oxy-5-methyl-pyrimidin-4-yl)meth-yl]-1H-benzo[d]imidazole-4-carboxamide and structurally characterized by X-ray crystallography and computational methods. In the crystal (space group P21/n, Z = 4), the title compound adopts a twisted conformation with a dihedral angle between the benzimidazole and pyrimidine mean planes of 84.11 (3)°. The carboxyl-ate group and the 5-methyl group on the pyrimidine ring exhibit partial disorder. The DFT-optimized mol-ecular structure resembles the structure of the minor component in the crystal.

Synthesis and Characterization of Phenylalanine Amides Active against Mycobacterium abscessus and Other Mycobacteria.

Nα-2-thiophenoyl-d-phenylalanine-2-morpholinoanilide [MMV688845, Pathogen Box; Medicines for Malaria Venture; IUPAC: (2R)-N-(1-((2-morpholinophenyl)amino)-1-oxo-3-phenylpropan-2-yl)thiophene-2-carboxamide)] is a hit compound, which shows activity against Mycobacterium abscessus (MIC90 6.25-12.5 µM) and other mycobacteria. This work describes derivatization of MMV688845 by introducing a thiomorpholine moiety and the preparation of the corresponding sulfones and sulfoxides. The molecular structures of three analogs are confirmed by X-ray crystallography. Conservation of the essential R configuration during synthesis is proven by chiral HPLC for an exemplary compound. All analogs were characterized in a MIC assay against M. abscessus, Mycobacterium intracellulare, Mycobacterium smegmatis, and Mycobacterium tuberculosis. The sulfone derivatives exhibit lower MIC90 values (M. abscessus: 0.78 µM), and the sulfoxides show higher aqueous solubility than the hit compound. The most potent derivatives possess bactericidal activity (99% inactivation of M. abscessus at 12.5 µM), while they are not cytotoxic against mammalian cell lines.