A persulfide analogue of the nitrosothiol SNAP: formation, characterization and reactivity

The proposal of the post-translational modification "S-sulfhydration" as a major pathway for H2 S-induced signaling has recently shed light on persulfides. However, the study of these species is hampered by their instability under biologically relevant conditions; this requires generating them in situ immediately prior to use. The current methods to prepare persulfides in aqueous solution suffer from several drawbacks. In particular, their formation requires (or generates) hydrogen sulfide, thus resulting in difficulties in distinguishing polysulfide reactivity from that of H2 S. Here we report the H2 S-free formation, characterization, and some biologically relevant reactions of a water-soluble persulfide analogue of the nitrosothiol SNAP, a widely used nitric oxide donor.

New fluorescent zinc complexes: towards specific sensors for hydrogen sulfide in solution

Two new fluorescent zinc complexes 1 and 2 have been synthesized by reaction of the complex Tp(Ph,Me)Zn(OH) with 7-hydroxy-4-methylcoumarin (MUH) or 7-mercapto-4-methylcoumarin (MUSH). While the alcoholato derivative Tp(Ph,Me)Zn(MU) 1 is not efficient for sensing hydrogen sulfide, the thiolato complex Tp(Ph,Me)Zn(MUS) 2 is a colorimetric "turn-on" and fluorescence "turn-off" sensor which shows high selectivity for hydrogen sulfide in the presence of additional thiols like cysteine or glutathione.

Metabolism of polychlorinated phenols by Pseudomonas cepacia AC1100: determination of the first two steps and specific inhibitory effect of methimazole

Resting cells of 2,4,5-trichlorophenoxyacetic acid-grown Pseudomonas cepacia AC1100 metabolize both dichlorophenols, such as 2,4-dichlorophenol, 2,6-dichlorophenol, 3,4-dichlorophenol, and 3,5-dichlorophenol, and more highly substituted phenols, such as 2,4,6-trichlorophenol and pentachlorophenol, to the corresponding chlorohydroquinones. The first hydroxylation occurs in the para position of the phenol regardless of whether this position is replaced by a chlorine substituent. The first evidence leading to the characterization of para-hydroxylase as a flavin-containing enzyme is provided by the inhibitory effect of methimazole, an alternate substrate for this monooxygenase, on the degradative ability of the strain. In a second step, with tetrachlorohydroquinone, trichlorohydroxyquinone was isolated and completely characterized. Trichlorohydroxyquinone was also obtained from tetrachloroquinone. Incubation of the cells in the presence of an external source of NADPH prevents the further degradation of tetrachlorohydroquinone, suggesting that the quinone derived from the two-electron oxidation of the hydroquinone is more likely the substrate for the second hydroxylation.

Discovery and Refinement of a New Structural Class of Potent Peptide Deformylase Inhibitors

New classes of antibiotics are urgently needed to counter increasing levels of pathogen resistance. Peptide deformylase (PDF) was originally selected as a specific bacterial target, but a human homologue, the inhibition of which causes cell death, was recently discovered. We developed a dual-screening strategy for selecting highly effective compounds with low inhibition effect against human PDF. We selected a new scaffold in vitro that discriminated between human and bacterial PDFs. Analyses of structure-activity relationships identified potent antibiotics such as 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide (6b) with the same mode of action in vivo as previously identified PDF inhibitors but without the apoptotic effects of these inhibitors in human cells.

Highly efficient control of iron-containing nitrile hydratases by stoichiometric amounts of nitric oxide and light

The reaction of two iron-containing nitrile hydratases (NHase) with NO has been studied: NHase from Rhodococcus sp. R312, which is probably similar to the photosensitive N771 NHase, and the new NHase from Comamonas testosteroni NI1 whose aminoacid sequence is quite different from those of BR312 and N771 NHases. Both enzymes are equally inactivated after addition of stoichiometric amounts of NO added as an anaerobic solution or produced in situ under physiological conditions by a rat brain NO-synthase. Both enzymes are reactivated by photoirradiation, and two cycles of NO inactivation/photoactivation can be performed without significant loss of activity. Both iron-containing NHases have a high affinity for NO, similar to that of methemoglobin.

Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis

For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally “zipped up” by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A “movie” that reconstructs this entire process can be further extrapolated to catalysis.

The notion of induced fit when a protein binds its ligand—like a glove adapting to the shape of a hand—is a central concept of structural biochemistry introduced over 50 years ago. A detailed molecular demonstration of this phenomenon has eluded biochemists, however, largely due to the difficulty of capturing the steps of this very transient process: the “conformational change.” In this study, we were able to see this process by using X-ray diffraction to determine more than 10 distinct structures adopted by a single enzyme when it binds a ligand. To do this, we took advantage of the “slow, tight-binding” of a potent inhibitor to its specific target enzyme to trap intermediates in the binding process, which allowed us to monitor the action of an enzyme in real-time at atomic resolution. We showed the kinetics of the conformational change from an initial open state, including the encounter complex, to the final closed state of the enzyme. From these data and other biochemical and biophysical analyses, we make a coherent causal reconstruction of the sequence of events leading to inhibition of the enzyme's activity. We also generated a movie that reconstructs the sequence of events during the encounter. Our data provide new insights into how enzymes achieve a catalytically competent conformation in which the reactive groups are brought into close proximity, resulting in catalysis.

Clean oxidation of thiolates to sulfinates in a four-coordinate CoIII complex with a mixed carboxamido N–thiolato S donor set: relevance to nitrile hydratase

A new [Co(N2(SO2)2)(CNtBu)2](Et4N) complex 6 was prepared from N,N'-(3-mercapto-3-methyl-butyryl)-o-phenylenediamine and completely characterized. While the starting square planar complex [Co(N2S2)](Et4N) 4 was destroyed by dioxirane, the Co ligated thiolates of the six-coordinate intermediate [Co(N2S2)(CNtBu)2](Et4N) complex 5 was readily oxidized to sulfinates with a stoichiometric amount of this oxidant. The resulting complex 6 crystallizes with an octahedral structure. The SO bonds of the SO2 groups are almost equivalent (approximately 1.483 and approximately 1.453 A). The isonitrile is linearly bonded to the cobalt with a Co-C-N angle of 177.5 degrees and a very short C-N(tBu) distance of 1.13 A, which has a triple bond character. As expected for six-coordinate CoIII complexes, 5 and 6 are diamagnetic in agreement with their 1H and 13C NMR spectra. The SO2 IR bands are located at 1210 cm(-1) (v(as)SO2) and 1070 cm(-1) (v(s)SO2), while the CN vibration of the isonitrile is observed at 2170 cm(-1) in 5 and 2210 cm(-1) in 6. Very recently, it has been reported in the literature that oxidation of the coordinated thiolates was required for activity of both Fe and Co nitrile hydratases. Complex 6, with two oxidized thiolates trans to two deprotonated carboxamido nitrogens, is the first to have an in-plane closely related to that of the Co-NHase active site.

Toward model complexes of Co-containing nitrile hydratases: synthesis, complete characterization and reactivity toward ligands such as CN- and NO of the first square planar CoIII complex with two different carboxamido nitrogens and two thiolato sulfur donors

A [CoIII(N2S2)]NEt4 complex, with two carboxamido nitrogens and two alkylthiolato sulfurs, was prepared from N,N'-(2-thioacetylisobutyryl)-2-aminobenzylamine, and characterized. It crystallizes with a distorted square planar structure including two short Co-N bonds (approximately 1.882 A) and two short Co-S bonds (approximately 2.134 A). The ligand defines an 11-atom chelate, which may be Co ligands in the mean plane of Co-containing nitrile hydratase. The CoIII oxidation state, reversibly reduced at -1.13 V (vs. SCE) and irreversibly oxidized at +1.29 V (vs. SCE) in DMF, is stable over a 2 V potential range. From the temperature dependence of its magnetic susceptibility, cobalt(III) was found to be in an S = 1 triplet ground state, in agreement with the broad resonances observed in its 1H-NMR spectrum. Preliminary spectral studies showed that this complex does not interact with imidazole, H2O or HO-, but binds two CN anions or two NO molecules. The IR spectrum of the dinitrosyl complex exhibits two NO stretches at 1765 and 1820 cm(-1), in the range previously observed for dinitrosylated complexes derived from cobalt(I). This result suggests that, similarly to Fe NHases, Co NHases might readily bind NO.

New antibiotic molecules: bypassing the membrane barrier of gram negative bacteria increases the activity of peptide deformylase inhibitors

Background

Multi-drug resistant (MDR) bacteria have become a major concern in hospitals worldwide and urgently require the development of new antibacterial molecules. Peptide deformylase is an intracellular target now well-recognized for the design of new antibiotics. The bacterial susceptibility to such a cytoplasmic target primarily depends on the capacity of the compound to reach and accumulate in the cytosol.

Methodology/Principal Findings

To determine the respective involvement of penetration (influx) and pumping out (efflux) mechanisms to peptide deformylase inhibitors (PDF-I) activity, the potency of various series was determined using various genetic contexts (efflux overproducers or efflux-deleted strains) and membrane permeabilizers. Depending on the structure of the tested molecules, two behaviors could be observed: (i) for actinonin the first PDF-I characterized, the AcrAB efflux system was the main parameter involved in the bacterial susceptibility, and (ii), for the lastest PDF-Is such as the derivatives of 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide, the penetration through the membrane was a important limiting step.

Conclusions/Significance

Our results clearly show that the bacterial membrane plays a key role in modulating the antibacterial activity of PDF-Is. The bacterial susceptibility for these new antibacterial molecules can be improved by two unrelated ways in MDR strains: by collapsing the Acr efflux activity or by increasing the uptake rate through the bacterial membrane. The efficiency of the second method is associated with the nature of the compound.

Oxygenation of thiolates to S-bonded sulfinate in an iron(iii) complex related to nitrile hydratase

Air oxidation of the iron(III) complex derived from (2-mercaptoisobutyryl)-4,5-dichloro-O-phenylenediamine in the presence of Et4NCN afforded the corresponding disulfinato species. With two carboxamido nitrogens trans to two S-bonded sulfinates, this complex mimics the disulfinate inactive form of Fe-NHase.

Chaperone-assisted expression, purification, and characterization of recombinant nitrile hydratase NI1 from Comamonas testosteroni

Nitrile hydratases (NHases) are industrially important iron- and cobalt-containing enzymes that are used in the large-scale synthesis of acrylamide. Heterologous expression of NHases has been complicated by the fact that other proteins (activators or metallochaperones) appear to be required to produce NHases in their catalytically active form. We report a novel heterologous system for the expression of catalytically active iron-containing NI1 NHase in Escherichia coli, involving coexpression with the E. coli GroES and GroEL chaperones. The purified recombinant enzyme was found to be highly similar to the enzyme purified from Comamonas testosteroni according to its spectroscopic features, catalytic properties with various substrates, and post-translational modifications. In addition, we report a rapid and convenient spectrophotometric method to monitor the activity of NI1 NHase during purification.

Microspectrofluorimetry to dissect the permeation of ceftazidime in Gram-negative bacteria

A main challenge in chemotherapy is to determine the in cellulo parameters modulating the drug concentration required for therapeutic action. It is absolutely urgent to understand membrane permeation and intracellular concentration of antibiotics in clinical isolates: passing the membrane barrier to reach the threshold concentration inside the bacterial periplasm or cytoplasm is the pivotal step of antibacterial activity. Ceftazidime (CAZ) is a key molecule of the combination therapy for treating resistant bacteria. We designed and synthesized different fluorescent CAZ derivatives (CAZ*, CAZ**) to dissect the early step of translocation-accumulation across bacterial membrane. Their activities were determined on E. coli strains and on selected clinical isolates overexpressing ß-lactamases. The accumulation of CAZ* and CAZ** were determined by microspectrofluorimetry and epifluorimetry. The derivatives were properly translocated to the periplasmic space when we permeabilize the outer membrane barrier. The periplasmic location of CAZ** was related to a significant antibacterial activity and with the outer membrane permeability. This study demonstrated the correlation between periplasmic accumulation and antibiotic activity. We also validated the method for approaching ß-lactam permeation relative to membrane permeability and paved the way for an original matrix for determining "Structure Intracellular Accumulation Activity Relationship" for the development of new therapeutic candidates.

First Synthesis of a Binuclear [Mn(II)(bipy)-Fe(III)(porphyrin)] Complex: Spectroscopic Characterization and First Evidence of Reversible Formation of Manganese(III) as Manganese Peroxidase

A [(P)Fe(III)-Mn(II)] bimetallic complex, mimicking the active site of manganese peroxidase, has been synthesized. A modified highly fluorinated porphyrin, 5,10,15-tris(pentafluorophenyl)-20-(o-aminophenyl)porphyrin, has been used to introduce, through a short spacer linked to the amino function, a manganese auxiliary ligand, 6-aminomethyl-2,2'-bipyridine. Two successive metalations by FeCl(2) and MnCl(2) afforded the [(P)Fe(III)-Mn(II)] bimetallic complex that has been characterized by elemental analysis and FAB(+) mass spectrometry. X-band EPR spectroscopy and magnetic susceptibility measurements were in agreement with two high spin Fe(III) and Mn(II) centers without magnetic exchange interaction. Moreover, there is no higher intermolecular association through &mgr;-chloro bridging as observed by EPR with a simpler chloromanganese complex, Mn(bipy)(2)Cl(2), at high concentration. Addition of pentafluoroiodosobenzene in methanol at 0 degrees C led to the progressive and complete disappearance of the EPR Mn(II) signals, that were recovered after addition of a phenol. This result is consistent with Mn(III) formation. This production of Mn(III) requires the presence of the iron porphyrin and is proposed to occur through the intermediate formation of a Fe(IV) dimethoxide species which can be related to the oxidation of Mn(II) catalyzed by manganese peroxidase compound II.

Sulfheme formation during homocysteine S-oxygenation by catalase in cancers and neurodegenerative diseases

Accumulating evidence suggests that abnormal levels of homocysteine are associated with vascular dysfunctions, cancer cell proliferation and various neurodegenerative diseases. With respect to the latter, a perturbation of transition metal homeostasis and an inhibition of catalase bioactivity have been reported. Herein, we report on some of the molecular bases for the cellular toxicity of homocysteine and demonstrate that it induces the formation of sulfcatalase, an irreversible inactive state of the enzyme, without the intervention of hydrogen sulfide. Initially, homocysteine reacts with native catalase and/or redox-active transition metal ions to generate thiyl radicals that mediate compound II formation, a temporarily inactive state of the enzyme. Then, the ferryl centre of compound II intervenes into the unprecedented S-oxygenation of homocysteine to engender the corresponding sulfenic acid species that further participates into the prosthetic heme modification through the formation of an unusual Fe(II) sulfonium. In addition, our ex cellulo studies performed on cancer cells, models of neurodegenerative diseases and ulcerative colitis suggest the likelihood of this scenario in a subset of cancer cells, as well as in a cellular model of Parkinson's disease. Our findings expand the repertoire of heme modifications promoted by biological compounds and point out another deleterious trait of disturbed homocysteine levels that could participate in the aetiology of these diseases.

High levels of homocysteine in cells are linked to pathological states. Here, the authors report that homocysteine inactivates catalase by modifying the heme group, impairing cellular redox homeostasis, and show that this modification occurs in cancer cells and in a cellular model of Parkinson's disease.