Tailored Peptide Phenyl Esters Block ClpXP Proteolysis by an Unusual Breakdown into a Heptamer–Hexamer Assembly

The proteolytic complex ClpXP is fundamental to bacterial homeostasis and pathogenesis. Because of its conformational flexibility, the development of potent ClpXP inhibitors is challenging, and novel tools to decipher its intricate regulation are urgently needed. Herein, we present amino acid based phenyl esters as molecular probes to study the activity and oligomerization of the ClpXP complex of S. aureus. Systematic screening of (R)‐ and (S)‐amino acids led to compounds showing potent inhibition, as well as stimulation of ClpXP‐mediated proteolysis. Substoichiometric binding of probes arrested ClpXP in an unprecedented heptamer–hexamer assembly, in which the two heptameric ClpP rings are dissociated from each other. At the same time, the affinity between ClpX and ClpP increased, leading to inhibition of both enzymes. This conformational arrest is beneficial for the consolidated shutdown of ClpXP, as well as for the study of the oligomeric state during its catalytic cycle.     

Reversible Inhibitors Arrest ClpP in a Defined Conformational State that Can Be Revoked by ClpX Association

Caseinolytic protease P (ClpP) is an important regulator of Staphylococcus aureus pathogenesis. A high‐throughput screening for inhibitors of ClpP peptidase activity led to the identification of the first non‐covalent binder for this enzyme class. Co‐crystallization of the small molecule with S. aureus ClpP revealed a novel binding mode: Because of the rotation of the conserved residue proline 125, ClpP is locked in a defined conformational state, which results in distortion of the catalytic triad and inhibition of the peptidase activity. Based on these structural insights, the molecule was optimized by rational design and virtual screening, resulting in derivatives exceeding the potency of previous ClpP inhibitors. Strikingly, the conformational lock is overturned by binding of ClpX, an associated chaperone that enables proteolysis by substrate unfolding in the ClpXP complex. Thus, regulation of inhibitor binding by associated chaperones is an unexpected mechanism important for ClpP drug development.     

Characterization of a specificity factor for an AAA+ ATPase: assembly of SspB dimers with ssrA-tagged proteins and the ClpX hexamer

SspB, a specificity factor for the ATP-dependent ClpXP protease, stimulates proteolysis of protein substrates bearing the ssrA degradation tag. The SspB protein is shown here to form a stable homodimer with two independent binding sites for ssrA-tagged proteins or peptides. SspB by itself binds to ClpX and stimulates the ATPase activity of this enzyme. In the presence of ATPgammaS, a ternary complex of SspB, GFP-ssrA, and the ClpX ATPase was sufficiently stable to isolate by gel-filtration or ion-exchange chromatography. This complex consists of one SspB dimer, two molecules of GFP-ssrA, and one ClpX hexamer. SspB dimers do not commit bound substrates to ClpXP degradation but increase the affinity and cooperativity of binding of ssrA-tagged substrates to ClpX, facilitating enhanced degradation at low substrate concentrations.     

Gas‐phase intramolecular hydroxyl‐amino exchange of protonated arginine and verified by the synthetic intermediate compound

A new fragmentation process was proposed to interpret the characteristic product ion at m/z 130 of protonated arginine. The α‐amino group was dissociated from protonated arginine and then combined with the (M + H‐NH₃) fragment to form an ion‐neutral complex which further generated a hydroxyl‐amino exchange intermediate compound through an ion‐molecule reaction. This intermediate compound was synthesized from argininamide through a diazo reaction, and then the reaction mixture was analyzed using liquid chromatography combined with mass spectrometry (LC‐MS). The collision‐induced dissociation experiments under the same conditions revealed that this intermediate compound produced the characteristic product ion at m/z 130 as well as protonated arginine, and in addition, density functional theory calculations were performed to confirm simultaneous loss of NH₃ and CO from this intermediate to give the m/z 130 ion.     

Specific glutamic acid residues in targeted proteins induce exaggerated retardations in Phos‐tag SDS‐PAGE migration

We describe two unique proteins, Escherichia coli ClpX and human histone H2A, that show extremely retarded migrations relative to their molecular weights in Phos‐tag SDS‐PAGE, despite being nonphosphorylated. Although ClpX separated into multiple migration bands in Phos‐tag gels, the separation was not due to phosphorylation. The N‐terminal 47–61 region of ClpX was responsible for producing multiple phosphorylation‐independent structural variants, even under denaturing conditions, and some of these variants were detected as highly up‐shifted bands. By systematic Ala‐scanning mutation analysis in the N‐47–61 region, we concluded that the Glu‐51 or Glu‐54 residue was responsible for the appearance of exaggerated mobility‐shifting bands. Histone H2A showed a much slower migration in Phos‐tag gels in comparison with other major histones having similar molecular weights, and we found that the Glu‐62 or Glu‐65 residue caused the retarded migration. In addition, Phos‐tag SDS‐PAGE permitted us to detect a shift in the mobility of the phosphorylated form of histone H2A from that of the nonphosphorylated one. This is the first report showing that exaggerated retardation in the migration of a certain protein in Phos‐tag SDS‐PAGE is induced by interactions between the Phos‐tag molecule and the carboxylate group of a specific Glu residue on the target.     

Synergistic Photobactericidal Activity Based on Ultraviolet‐A Irradiation and Ferulic Acid Derivatives

Ultraviolet‐A (UV‐A)‐mediated bactericidal activity was enhanced by combined treatment with trans‐ferulic acid (trans‐FA, compound 1 ) or its derivatives. Derivative compounds 4 and 10 contain a phenyl group or an l ‐tyrosine HCl tert‐butyl ester, respectively, linked to the carboxyl group of trans‐FA. Of the three compounds, 10 exhibited the highest synergistic activity in a photobactericidal assay based on treating Escherichia coli with a derivative compound and UV‐A irradiation (wavelength 350–385 nm). Inactivation of viable cells at a 4.9 J cm^?2 UV‐A fluence increased from 1.90 to 5.19 logs in the presence of 10 (100 μm ); a 4.95‐log inactivation was achieved with 10 (5 μm ) and a 7.4 J cm^?2 UV‐A fluence. Addition of antioxidants significantly suppressed photosynergistic bactericidal activity, suggesting that reactive oxygen species (ROS) are involved in the combined bactericidal mechanism. Flow cytometry revealed that combined treatment with UV‐A and compound 10 , which showed the highest photobactericidal activity, generates an excess of oxidative radicals in bacterial cells. The bactericidal activity of compound 10 may be due to electrostatic interaction between the molecule's cationic moiety and the cell surface, followed by amplification of ROS generation in the cells.     

Synthesis and Antimicrobial Activity of Novel Azolopyrimidines and Pyrido‐Triazolo‐Pyrimidinones Incorporating Pyrazole Moiety

A new series of azolopyrimidine derivatives incorporating pyrazole moiety were synthesized by reaction of 1‐(pyrazol‐3‐yl)‐2‐propenone with a number of heterocyclic amines in the presence of a catalytic amount of acetic acid. The mechanism of formation of the products was also discussed, and the structure assigned was elucidated based on both elemental and spectral analyses data. In addition, 7‐(pyrazolyl)‐2‐thioxo‐5‐phenyl‐1,3‐dihydropyrido[2,3‐d ]pyrimidin‐4‐one was used as starting material for preparation of a new series of pyridotriazolopyrimidines via its reaction with a variety of hydrazonoyl chlorides in dioxane using triethylamines as catalyst. The assigned structure for these products was also proved via elemental analysis and spectroscopic techniques (IR, ¹H NMR, and Mass). Moreover, the antimicrobial activity of some selected examples of the new products was evaluated, and the results obtained revealed high activity of compound 20a against the Gram positive bacteria Staphylococcus aureus and the Gram negative bacteria Klebsiella pneumonie . All the tested compounds have no antifungal activity.     

A Glutathione Activatable Ion Channel Induces Apoptosis in Cancer Cells by Depleting Intracellular Glutathione Levels

Cancer cells use elevated glutathione (GSH) levels as an inner line of defense to evade apoptosis and develop drug resistance. In this study, we describe a novel 2,4‐nitrobenzenesulfonyl (DNS) protected 2‐hydroxyisophthalamide system that exploits GSH for its activation into free 2‐hydroxyisophthalamide forming supramolecular M⁺/Cl^? channels. Better permeation of the DNS protected compound into MCF‐7 cells compared to the free 2‐hydroxyisophthalamide and GSH‐activatable ion transport resulted in higher cytotoxicity, which was associated with increased oxidative stress that further reduced the intracellular GSH levels and altered mitochondrial membrane permeability leading to the induction of the intrinsic apoptosis pathway. The GSH‐activatable transport‐mediated cell death was further validated in rat insulinoma cells (INS‐1E); wherein the intracellular GSH levels showed a direct correlation to the resulting cytotoxicity. Lastly, the active compound was found to restrict the growth and proliferation of 3D spheroids of MCF‐7 cells with efficiency similar to that of the anticancer drug doxorubicin.     

Theoretical Study of the Substituent Effects on the Nonlinear Optical Properties of a Room‐Temperature‐Stable Organic Electride

Excess‐electron compounds can be considered as novel candidates for nonlinear optical (NLO) materials because of their large static first hyperpolarizabilities (β₀). A room‐temperature‐stable, excess‐electron compound, that is, the organic electride Na@(TriPip222), was successfully synthesized by the Dye group (J. Am. Chem. Soc. 2005 , 127, 12416). In this work, the β₀ of this electride was first evaluated to be 1.13×10⁶ au, which revealed its potential as a high‐performance NLO material. In particular, the substituent effects of different substituents on the structure, electride character, and NLO response of this electride were systemically studied for the first time by density functional theory calculations. The results revealed that the β₀ of Na@(TriPip222) could be further increased to 8.30×10⁶ au by introducing a fluoro substituent, whereas its NLO response completely disappeared if one nitryl group was introduced because the nitro‐group substitution deprived the material of its electride identity. Moreover, herein the dependence of the NLO properties on the number of substituents and their relative positions was also detected in multifluoro‐substituted Na@(TriPip222) compounds.     

Manganese(II) Coordination Polymer with μ1,1‐Azido Bridge: Synthesis,Crystal Structure,and Magnetic Properties

The manganese(II) coordination polymer [Mn(2‐Meimi)₂(μ_1,1‐N₃)₂]_n · nH₂O ( 1 ) (Meimi = 2‐methyl‐imidazole) with μ_1,1‐N₃ (end‐on, EO) bridge was synthesized by hydrothermal reaction of MnCl₂, NaN₃, and Meimi. It was characterized by elemental analysis, IR spectroscopy, powder XRD, and magnetic measurements. Single crystal X‐ray analysis revealed that compound 1 features a one‐dimensional (1D) catenated structure and the 1D chains are further connected by strong intermolecular hydrogen bonds to a 3D supramolecular framework. Variable‐temperature magnetic susceptibility measurements revealed that compound 1 displays dominant ferromagnetic interactions through the μ_1,1‐N₃ (end‐on, EO) bridging mode.     

Synthesis and Cytotoxicity in Vitro of N‐Aryl‐4‐(tert‐butyl)‐5‐(1H‐1,2,4‐triazol‐1‐yl)thiazol‐2‐amine

A series of novel N‐aryl‐4‐(tert‐butyl)‐5‐(1H‐1,2,4‐triazol‐1‐yl)thiazol‐2‐amines synthesized in a green way. H₂O₂‐NaBr Brominating circulatory system was used in the synthesis of the key intermediate in a mild condition. All of the target compounds were confirmed by ¹H NMR and elemental analysis and tested for their cytotoxicity against two different human cancer cell lines. The cytotoxicity assay revealed that some of the title compounds showed moderate to strong cytotoxic activities. Compound 2i was the most potent compound with the IC₅₀ values of 9 μM against Hela cells and 15 μM against Bel–7402 cells, respectively.     

Molecular insight into the interaction mechanisms of amino‐2H‐imidazole derivatives with BACE1 protease: A QM/MM and QTAIM study

In this study, we described quantitatively the interactions between two new amino‐2H‐imidazole inhibitors ((R)‐1t and (S)‐1m) and BACE1 using a hybrid quantum mechanics‐molecular mechanical (QM/MM) method together with a quantum theory of atoms In Molecules (QTAIM) analysis. Our computational calculations revealed that the binding affinity of these compounds is mostly related to the amino‐2H‐imidazole core, which interact tightly with the aspartate dyad of the active site. The interactions were stronger when the inhibitors presented a bulky substituent with a hydrogen bond acceptor motif pointing toward Trp76, such as the 3,5‐dimethyl‐4‐methoxyphenyl group of compound (S)‐1m. Furthermore, the QTAIM analysis revealed that many hydrophobic interactions complement cooperatively the hydrogen bond which is not present when compound (R)‐1t is bound to the enzyme. The combined QM/MM‐QTAIM analysis allows identifying the interactions that account for the activity difference between compounds, even at a nanomolar range.     

Selective Photoreceptor Gene Knock‐out Reveals a Regulatory Role for the Growth Behavior of Pseudomonas syringae

The plant pathogen Pseudomonas syringae (Ps) is a well‐established model organism for bacterial infection of plants. The genome sequences of two pathovars, pv. syringae and pv. tomato, revealed one gene encoding a blue and two genes encoding red/far red light‐sensing photoreceptors. Continuing former molecular characterization of the photoreceptor proteins, we here report selective photoreceptor gene disruption for pv. tomato aiming at identification of potentially regulatory functions of these photoreceptors. Transformation of Ps cells with linear DNA constructs yielded interposon mutations of the corresponding genes. Cell growth studies of the generated photoreceptor knock‐out mutants revealed their role in light‐dependent regulation of cell growth and motility. Disruption of the blue‐light (BL) receptor gene caused a growth deregulation, in line with an observed increased virulence of this mutant (Moriconi et al., Plant J., 2013, 76, 322). Bacterial phytochrome‐1 (BphP1) deletion mutant caused unaltered cell growth, but a stronger swarming capacity. Inactivation of its ortholog, BphP2, however, caused reduced growth and remarkably altered dendritic swarming behavior. Combined knock‐out of both bacteriophytochromes reproduced the swarming pattern observed for the BphP2 mutant alone. A triple knock‐out mutant showed a growth rate between that of the BL (deregulation) and the phytochrome‐2 mutant (growth reduction).     

Asymmetric Synthesis and Antitumor Activity of Spiro‐Oxadiazole Derivatives from 1,4:3,6‐Dianhydro‐D‐fructose

A series of spiro‐oxadiazoles were synthesized from 1,4:3,6‐dianhydro‐D ‐fructose and hydrazides via a stereo‐ selective two‐step reaction sequence. The structures of newly synthesized compounds were established by spectral analysis. The absolute configuration of compound 2a was further confirmed by single crystal X‐ray analysis. All the synthesized compounds were screened for their in vitro antitumor activity, showing that these compounds have poor inhibitory activities against A549, MGC‐803 tumor cells.     

Antimicrobial Evaluation of New Quinoxaline Derivatives Synthesized by Selective Coupling with Alkyl Halides and Amino Acids Esters

Alkylation of quinoxaline scaffold 1 in the presence of K₂CO₃ preferred N‐alkylation than O‐alkylation. Quinoxaline hydrazide 6 was successfully coupled with various amino acids, esters, and amines via azide‐coupling method. New heterocyclic compounds containing quinoxaline linked to 1,3,4‐oxadiazolethione or pyrazole were obtained from cyclization of 6 with CS₂ and acetylacetone, respectively. A series of hydrazide Schiff's bases were formed from hydrazide 6 by condensation with a set of aldehydes and ketones. NMR spectroscopy and mass spectrometry were used for structure elucidation of new compounds. The antimicrobial activity of the synthesized compounds was investigated toward two wild‐type bacterial strains (Staphylococcus aureus and Escherichia coli ) and two fungal species (Alternaria brassicicola and Fusarium oxysporum ). Four compounds displayed a significant activity toward S. aureus . The ester 4 showed higher activity than the standard drugs, which make it a promising lead compound.     

Decomposition of N‐hydroxylated compounds during atmospheric pressure chemical ionization

N‐Hydroxylated polyamine derivatives were found to decompose during the ionization process of liquid chromatography‐atmospheric pressure chemical ionization‐mass spectrometry (LC‐APCI‐MS) experiments. The phenomenon was studied with a model compound, a synthetic N‐hydroxylated tetraamine derivative. It was found that reduction, oxidation and water elimination occurred during APCI to generate the corresponding amine, N‐oxide, and imine. The investigation further revealed that decomposition of hydroxylamines during APCI depends upon the concentration of the analyte and on the acidity of the solution introduced into the ionization source. The pH‐dependence of decomposition was utilized for the development of an MS method that allows for the unambiguous identification of N? OH functionalities. This method was applied for the study of natural products including polyamine toxins from the venom of the spider Agelenopsis aperta and mayfoline, a cyclic polyamine derivative of the shrub Maytenus buxifolia. Copyright © 2009 John Wiley & Sons, Ltd.     

Structure-Activity Relationship, Cytotoxicity and Mode of Action of 2-Ester-substituted 1,5-Benzothiazepines as Potent Antifungal Agents

Our studies examined the structural features responsible for the antifungal activity of 2-ethoxycarbonyl-1,5- benzothiazepine （7a）. Three series of 1,5-benzothiazepine derivatives were synthesized and screened for their antifungal activity. The results suggested that the ethoxycarbonyl group at the 2 position and the imine moiety on the seven-membered ring are essential for activity. The most potent of the synthesized analogues （7a, 7b） were further studied by evaluating their cytotoxicity and mode of action （for 7a）. The results showed that compounds 7a and 7b were relatively safe for BV2 cells, but compound 7a interfered with Cryptococcus neoformans cell wall integrity by increasing the chitinase activity. Therefore, compound 7a was considered safe as an antifungal agent for animal cells.     

Fluorescent Triazole Urea Activity‐Based Probes for the Single‐Cell Phenotypic Characterization of Staphylococcus aureus

Phenotypically distinct cellular (sub)populations are clinically relevant for the virulence and antibiotic resistance of a bacterial pathogen, but functionally different cells are usually indistinguishable from each other. Herein, we introduce fluorescent activity‐based probes as chemical tools for the single‐cell phenotypic characterization of enzyme activity levels in Staphylococcus aureus. We screened a 1,2,3‐triazole urea library to identify selective inhibitors of fluorophosphonate‐binding serine hydrolases and lipases in S. aureus and synthesized target‐selective activity‐based probes. Molecular imaging and activity‐based protein profiling studies with these probes revealed a dynamic network within this enzyme family involving compensatory regulation of specific family members and exposed single‐cell phenotypic heterogeneity. We propose the labeling of enzymatic activities by chemical probes as a generalizable method for the phenotyping of bacterial cells at the population and single‐cell level.     

Structure of the Complex between a Heparan Sulfate Octasaccharide and Mycobacterial Heparin‐Binding Hemagglutinin

Heparin‐binding hemagglutinin (HBHA) is a 199 amino acid virulence factor at the envelope of Mycobacterium tuberculosis that contributes to latent tuberculosis. The binding of HBHA to respiratory epithelial cells, which leads to extrapulmonary dissemination of the pathogen, is mediated by cell‐surface heparan sulfate (HS). We report the structural characterization of the HBHA/HS complex by NMR spectroscopy. To develop a model for the molecular recognition, the first chemically synthesized uniformly ¹³C‐ and ¹⁵N‐labeled HS octasaccharide and a uniformly ¹³C‐ and ¹⁵N‐labeled form of HBHA were prepared. Residues 180–195 at the C‐terminal region of HBHA show large chemical shift perturbation upon association with the octasaccharide. Molecular dynamics simulations conforming to the multidimensional NMR data revealed key electrostatic and even hydrophobic interactions between the binding partners that may aid in the development of agents targeting the binding event.