Pyrrolidine/Azepane Ring Expansion via Intramolecular Ullmann-Type Annulation/Rearrangement Cascade: Synthesis of Highly Functionalized 1H-Benzazepines.

5-Arylpyrrolidine-2-carboxylates with an ortho-halogen substituent at 5-aryl and an electron-withdrawing group at the C4 position of the pyrrolidine ring were transformed into 1H-benzo[b]azepine-2-carboxylates under Cu(I) promotion and microwave activation. Reaction promoter copper(I) thiophene-2-carboxylate has been generated in situ in the reaction's environment from Cu2O and thiophene-2-carboxylic acid. Functionalized 1H-benzo[b]azepine-2-carboxylates were obtained in racemic and optically active forms in 67-89% yields. Subsequent stereoselective 1,3-dipolar cycloaddition and an Ullmann-type annulation/rearrangement cascade (UARC) ensure a synthetic route to oligomeric optically active benzazepine species with a well-defined 3D-structure.

Oligopeptide Sortase Inhibitor Modulates Staphylococcus aureus Cell Adhesion and Biofilm Formation.

Prevention of bacterial adhesion is one of the most important antivirulence strategies for meeting the global challenge posed by antimicrobial resistance. We aimed to investigate the influence of a peptidic S. aureus sortase A inhibitor on bacterial adhesion to eukaryotic cells and biofilm formation as a potential method for reducing S. aureus virulence. The pentapeptide LPRDA was synthesized and characterized as a pure individual organic compound. Incubation of MSSA and MRSA strains with LPRDA induced a subsequent reduction in staphylococcal adhesion to Vero cells and biofilm formation, as visualized by microscopic and spectrophotometric methods, respectively. LPRDA did not have a cytotoxic effect on eukaryotic or bacterial cells. The pentapeptide LPRDA deserves further investigation using in vitro and in vivo models of Gram-positive bacteriemia as a potential antibacterial agent with an antiadhesive mechanism of action.

Theoretical Studies of Leu-Pro-Arg-Asp-Ala Pentapeptide (LPRDA) Binding to Sortase A of Staphylococcus aureus.

Sortase A (SrtA) of Staphylococcus aureus is a well-defined molecular target to combat the virulence of these clinically important bacteria. However up to now no efficient drugs or even clinical candidates are known, hence the search for such drugs is still relevant and necessary. SrtA is a complex target, so many straight-forward techniques for modeling using the structure-based drug design (SBDD) fail to produce the results they used to bring for other, simpler, targets. In this work we conduct theoretical studies of the binding/activity of Leu-Pro-Arg-Asp-Ala (LPRDA) polypeptide, which was recently shown to possess antivirulence activity against S. aureus. Our investigation was aimed at establishing a framework for the estimation of the key interactions and subsequent modification of LPRDA, targeted at non-peptide molecules, with better drug-like properties than the original polypeptide. Firstly, the available PDB structures are critically analyzed and the criteria to evaluate the quality of the ligand-SrtA complex geometry are proposed. Secondly, the docking protocol was investigated to establish its applicability to the LPRDA-SrtA complex prediction. Thirdly, the molecular dynamics studies were carried out to refine the geometries and estimate the stability of the complexes, predicted by docking. The main finding is that the previously reported partially chaotic movement of the ß6/ß7 and ß7/ß8 loops of SrtA (being the intrinsically disordered parts related to the SrtA binding site) is exaggerated when SrtA is complexed with LPRDA, which in turn reveals all the signs of the flexible and structurally disordered molecule. As a result, a wealth of plausible LPRDA-SrtA complex conformations are hard to distinguish using simple modeling means, such as docking. The use of more elaborate modeling approaches may help to model the system reliably but at the cost of computational efficiency.

Selection of Promising Novel Fragment Sized S. aureus SrtA Noncovalent Inhibitors Based on QSAR and Docking Modeling Studies.

Sortase A (SrtA) of Staphylococcus aureus has been identified as a promising target to a new type of antivirulent drugs, and therefore, the design of lead molecules with a low nanomolar range of activity and suitable drug-like properties is important. In this work, we aimed at identifying new fragment-sized starting points to design new noncovalent S. aureus SrtA inhibitors by making use of the dedicated molecular motif, 5-arylpyrrolidine-2-carboxylate, which has been previously shown to be significant for covalent binding SrtA inhibitors. To this end, an in silico approach combining QSAR and molecular docking studies was used. The known SrtA inhibitors from the ChEMBL database with diverse scaffolds were first employed to derive descriptors and interpret their significance and correlation to activity. Then, the classification and regression QSAR models were built, which were used for rough ranking of the virtual library of the synthetically feasible compounds containing the dedicated motif. Additionally, the virtual library compounds were docked into the "activated" model of SrtA (PDB:2KID). The consensus ranking of the virtual library resulted in the most promising structures, which will be subject to further synthesis and experimental testing in order to establish new fragment-like molecules for further development into antivirulent drugs.

Interplay of Pyrrolidine Units with Homo/Hetero Chirality and CF3-Aryl Substituents on Secondary Structures of ß-Proline Tripeptides in Solution.

All possible variants of ß-proline functionalized tripeptides consisting of homo/hetero chiral monomeric all-cis 5-arylpyrrolidine-2,4-dicarboxylate units were synthesized for the first time by a nonpeptidic coupling method based on 1,3-dipolar cycloaddition chemistry of azomethine ylides. Secondary structures of ß-proline tripeptides in solution were determined using the NMR spectroscopy data. o-(Trifluoromethyl)phenyl substituent contributes to stereoselectivity of 1,3-dipolar cycloaddition and structural features of ß-proline tripeptides. A ß-proline CF3-tripeptide with alternating absolute chirality between adjacent pyrrolidine units mimics natural PPII helix secondary structure.

Chemoselectivity issues of the asymmetric interaction between cyclohexanone, ß-nitrostyrene, and benzoic acid under 5-aryl prolinate's organocatalysis.

4-l-menthyloxycarbonyl 5-aryl prolinates were studied as organocatalysts of a novel three-component reaction of cyclohexanone, benzoic acid, and ß-nitrostyrene. The presence of ortho-halogen atom in 5-aryl fragment of the catalyst is favored for driving the formation of chiral 7a-hydroxyoctahydro-2H-indol-2-one scaffold. 5-(o-Chlorophenyl) prolinate selectively afforded 3-phenyl-7a-hydroxyoctahydro-2H-indol-2-one with ee 63%, whereas 5-phenyl prolinate led to conjugation of ß-nitrostyrene to cyclohexanone (the Michael adduct). Plausible chlorine effect is accounted for the specific interaction of the 5-aryl prolinate enamine intermediate with ß-nitrostyrene in the transition state.

Crystal structure of 4-[(1R,2S,5R)-2-isopropyl-5-methyl-cyclo-hex-yl] 2-methyl (2S,4S,5R)-1-[(2S,3R,5R)-5-meth-oxy-carbonyl-2-(2-methyl-phen-yl)pyrrolidine-3-carbon-yl]-5-(2-methyl-phen-yl)pyrrolidine-2,4-di-carboxyl-ate.

The title compound, C38H50N2O7, represents a chiral ß-proline dipeptide. Corresponding stereogenic centres of constituting pyrrolidine units have opposite absolute configurations. The central amide fragment is planar within 0.1 Šand adopts a Z configuration along the N-CO bond. In the crystal, the hydrogen atoms of the methyl-ene groups form several short inter-molecular C-H⋯O contacts with the carbonyl oxygen atoms of an adjacent mol-ecule. The only active amino hydrogen atom is not involved in hydrogen bonding.

Theoretical and NMR Conformational Studies of ß-Proline Oligopeptides With Alternating Chirality of Pyrrolidine Units.

Synthetic ß-peptides are potential functional mimetics of native α-proteins. A recently developed, novel, synthetic approach provides an effective route to the broad group of ß-proline oligomers with alternating patterns of stereogenic centers. Conformation of the pyrrolidine ring, Z/E isomerism of ß-peptide bonds, and hindered rotation of the neighboring monomers determine the spatial structure of this group of ß-proline oligopeptides. Preferences in their structural organization and corresponding thermodynamic properties are determined by NMR spectroscopy, restrained molecular dynamics and quantum mechanics. The studied ß-proline oligopeptides exist in dimethyl sulfoxide solution in a limited number of conformers, with compatible energy of formation and different spatial organization. In the ß-proline tetrapeptide with alternating chirality of composing pyrrolidine units, one of three peptide bonds may exist in an E configuration. For the alternating ß-proline pentapeptide, the presence of an E configuration for at least of one ß-peptide bond is mandatory. In this case, three peptide bonds synchronously change their configurations. Larger polypeptides may only exist in the presence of several E configurations of ß-peptide bonds forming a wave-like extended structure.

Enantiomerically pure ß-dipeptide derivative induces anticancer activity against human hormone-refractory prostate cancer through both PI3K/Akt-dependent and -independent pathways.

The use of peptides that target cancer cells and induce anticancer activities through various mechanisms is developing as a potential anticancer strategy. KUD983, an enantiomerically pure ß-dipeptide derivative, displays potent activity against hormone-refractory prostate cancer (HRPC) PC-3 and DU145 cells with submicromolar IC50. KUD983 induced G1 arrest of the cell cycle and subsequent apoptosis associated with down-regulation of several related proteins including cyclin D1, cyclin E and Cdk4, and the de-phosphorylation of RB. The levels of nuclear and total c-Myc protein, which could increase the expression of both cyclin D1 and cyclin E, were profoundly inhibited by KUD983. Furthermore, it inhibited PI3K/Akt and mTOR/p70S6K/4E-BP1 pathways, the key signaling in multiple cellular functions. The transient transfection of constitutively active myristylated Akt (myr-Akt) cDNA significantly rescued KUD983-induced caspase activation but did not blunt the inhibition of mTOR/p70S6K/4E-BP1 signaling cascade suggesting the presence of both Akt-dependent and -independent pathways. Moreover, KUD983-induced effect was enhanced with the down-regulation of anti-apoptotic Bcl-2 members (e.g., Bcl-2, and Mcl-1) and IAP family members (e.g., survivin). Notably, KUD983 induced autophagic cell death using confocal microscopic examination, tracking the level of conversion of LC3-I to LC3-II and flow cytometric detection of acidic vesicular organelles-positive cells. In conclusion, the data suggest that KUD983 is an anticancer ß-dipeptide against HRPCs through the inhibition of cell proliferation and induction of apoptotic and autophagic cell death. The suppression of signaling pathways regulated by c-Myc, PI3K/Akt and mTOR/p70S6K/4E-BP1 and the collaboration with down-regulation of Mcl-1 and survivin may explain KUD983-induced anti-HRPC mechanism.

Control of Azomethine Cycloaddition Stereochemistry by CF3 Group: Structural Diversity of Fluorinated ß-Proline Dimers.

ß-Proline-functionalized dimers consisting of homochiral monomeric units were synthesized by a non-peptidic coupling method for the first time. The applied synthetic methodology is based on 1,3-dipolar cycloaddition chemistry of azomethine ylides and provides absolute control over the ß-proline backbone stereogenic centers. An o-(trifluoromethyl)phenyl substituent contributes to appropriate stabilization of the definite acrylamide chiral cis conformation and to achieve the dipole reactivity that is not observed for aryl groups lacking strong electronegative character.

Menthols as Chiral Auxiliaries for Asymmetric Cycloadditive Oligomerization: Syntheses and Studies of ß-Proline Hexamers.

To produce a novel class of structurally ordered poly-ß-prolines, an emergent method for synthesizing chiral ß-peptide molecular frameworks was developed based on 1,3-dipolar cycloaddition chemistry of azomethine ylides. Functionalized short ß-peptides with up to six monomeric residues were efficiently synthesized in homochiral forms using a cycloadditive oligomerization approach. X-ray, NMR, and CD structural analyses of the novel ß-peptides revealed secondary structure features that were generated primarily by Z/E-ß-peptide bond isomerism. Anticancer in cellulo activity of the new ß-peptides toward hormone-refractory prostate cancer cells was observed and was dependent on the absolute configuration of the stereogenic centers and the chain length of the ß-proline oligomers.

KUD773, a phenylthiazole derivative, displays anticancer activity in human hormone-refractory prostate cancers through inhibition of tubulin polymerization and anti-Aurora A activity.

BACKGROUND: Hormone-refractory prostate cancer (HRPC), which is resistant to hormone therapy, is a major obstacle in clinical treatment. An approach to inhibit HRPC growth and ultimately to kill cancers is highly demanded. RESULTS: KUD773 induced the anti-proliferative effect and subsequent apoptosis in PC-3 and DU-145 (two HRPC cell lines); whereas, it showed less active in normal prostate cells. Further examination showed that KUD773 inhibited tubulin polymerization and induced an increase of mitotic phosphoproteins and polo-like kinase 1 (PLK1) phosphorylation, indicating a mitotic arrest of the cell cycle through an anti-tubulin action. The kinase assay demonstrated that KUD773 inhibited Aurora A activity. KUD773 induced an increase of Cdk1 phosphorylation at Thr(161) (a stimulatory phosphorylation site) and a decrease of phosphorylation at Tyr(15) (an inhibitory phosphorylation site), suggesting the activation of Cdk1. The data were substantiated by an up-regulation of cyclin B1 (a Cdk1 partner). Furthermore, KUD773 induced the phosphorylation and subsequent down-regulation of Bcl-2 and activation of caspase cascades. CONCLUSIONS: The data suggest that KUD773 induces apoptotic signaling in a sequential manner. It inhibits tubulin polymerization associated with an anti-Aurora A activity, leading to Cdk1 activation and mitotic arrest of the cell cycle that in turn induces Bcl-2 degradation and a subsequent caspase activation in HRPCs.

Structural studies and anticancer activity of a novel class of ß-peptides.

Functionalized oligomeric organic compounds with well-defined ß-proline scaffold have been synthesized by a cycloadditive oligomerization approach in racemic and enantiopure forms. The structure of the novel ß-peptides was investigated by NMR spectroscopic and X-ray methods determining the conformational shapes of the ß-proline oligomers in solution and solid states. The main structural elements subject to conformational switches are ß-peptide bonds between 5-arylpyrrolidine-2-carboxylic acid units existing in Z/E configurations. The whole library of short ß-peptides and intermediate acrylamides has been tested on antiproliferative activity towards the hormone-refractory prostate cancer cell line PC-3 revealing several oligomeric compounds with low micromolar and submicromolar activities. Bromine-substituted dimeric and trimeric acrylamides induced caspase-dependent apoptosis of PC-3 cells through cell-cycle arrest and mitochondrial damage.

Pharmacological correction of stress-induced gastric ulceration by novel small-molecule agents with antioxidant profile.

This study was designed to determine novel small-molecule agents influencing the pathogenesis of gastric lesions induced by stress. To achieve this goal, four novel organic compounds containing structural fragments with known antioxidant activity were synthesized, characterized by physicochemical methods, and evaluated in vivo at water immersion restraint conditions. The levels of lipid peroxidation products and activities of antioxidative system enzymes were measured in gastric mucosa and correlated with the observed gastroprotective activity of the active compounds. Prophylactic single-dose 1 mg/kg treatment with (2-hydroxyphenyl)thioacetyl derivatives of L-lysine and L-proline efficiently decreases up to 86% stress-induced stomach ulceration in rats. Discovered small-molecule antiulcer agents modulate activities of gastric mucosa tissue superoxide dismutase, catalase, and xanthine oxidase in concerted directions. Gastroprotective effect of (2-hydroxyphenyl)thioacetyl derivatives of L-lysine and L-proline at least partially depends on the correction of gastric mucosa oxidative balance.

(1SR,3RS,3aSR,6aRS)-Methyl 5-methyl-4,6-dioxo-3-[2-(trifluoro-meth-yl)phen-yl]octa-hydro-pyrrolo-[3,4-c]pyrrole-1-carboxyl-ate.

In the title compound, C(16)H(15)F(3)N(2)O(4), the relative stereochemistry of the four stereogenic C atoms has been determined. The carb-oxy-methyl and 2-(trifluoro-meth-yl)-phenyl substituents of the pyrrolidine cycle have a cis mutual arrangement. The five-membered saturated aza-cycle adopts an envelope conformation with the N atom occupying the flap position. In the crystal, adjacent mol-ecules are combined in centrosymmetric dimers by two weak N-H⋯O hydrogen bonds.

2-(1H-Imidazol-1-yl)-4-[3-(trifluoro-meth-yl)phen-yl]-1,3-thia-zole.

The title compound, C(13)H(8)F(3)N(3)S, consists of three linked aromatic rings. The whole mol-ecule (except for the three F atoms) is planar to within 0.225 (2) Å. In the crystal, adjacent mol-ecules are linked into chains along the ac diagonal by weak C-H⋯N inter-actions.

syn-3-(4-Chloro-benz-yl)-1,5-dimethyl-3,7-diaza-bicyclo-[3.3.1]nonan-9-ol.

In the title compound, C(16)H(23)ClN(2)O, both six-membered rings adopt chair conformations, thus allowing the formation of an intra-molecular N-H⋯N hydrogen bond. In the crystal, adjacent mol-ecules are combined into chains running along the ac diagonal via O-H⋯N hydrogen bonds.

4-[(1RS,5RS,7SR)-5-Methyl-2,4-dioxo-3,6-diaza-bicyclo-[3.2.1]octan-7-yl]benzonitrile.

In the title compound, C(14)H(13)N(3)O(2), the relative stereochemistry of the three stereogenic C atoms has been determined. In the crystal, N-H⋯O hydrogen bonds link the mol-ecules into chains of inversion dimers running along the b axis.

2-[(1RS,3RS,3aRS,6aSR)-5-Benzyl-4,6-dioxo-3-phenyl-octa-hydro-pyrrolo-[3,4-c]pyrrol-1-yl]acetamide.

In the title compound, C(21)H(21)N(3)O(3), the relative stereochemistry of the four stereogenic C atoms has been determined. The dihedral angle between the phenyl rings is 77.63 (7)°. In the crystal, ribbons spread along the a axis are formed by N-H⋯O hydrogen bonds. C-H⋯π inter-actions also occur.