Effect of Indole-Containing Pyrazino[2,1-b]quinazoline-3,6-diones in the Virulence of Resistant Bacteria

Drug resistance is rising to alarming levels, constituting one of the major threats to global health. The overexpression of efflux pumps and the formation of biofilms constitute two of the most common resistance mechanisms, favoring the virulence of bacteria. Therefore, the research and development of effective antimicrobial agents that can also counteract resistance mechanisms are extremely important. Pyrazino[2,1-b]quinazoline-3,6-diones, from marine and terrestrial organisms and simpler synthetic analogues, were recently disclosed by us as having relevant antimicrobial properties. In this study, using a multi-step approach, it was possible to synthesize new pyrazino[2,1-b]quinazoline-3,6-diones focusing on compounds with fluorine substituents since, to the best of our knowledge, the synthesis of fluorinated fumiquinazoline derivatives had not been attempted before. The new synthesized derivatives were screened for antibacterial activity and, along with previously synthetized pyrazino[2,1-b]quinazoline-3,6-diones, were characterized for their antibiofilm and efflux-pump-inhibiting effects against representative bacterial species and relevant resistant clinical strains. Several compounds showed relevant antibacterial activity against the tested Gram-positive bacterial species with MIC values in the range of 12.5-77 μM. Furthermore, some derivatives showed promising results as antibiofilm agents in a crystal violet assay. The results of the ethidium bromide accumulation assay suggested that some compounds could potentially inhibit bacterial efflux pumps.

Damage of amino acids by aliphatic peroxyl radicals: a kinetic and computational study

Absolute second-order rate coefficients for the reaction of the N- and C-protected amino acids tyrosine (Tyr), tryptophan (Trp), methionine (Met) and proline (Pro) with triethylamine-derived aliphatic peroxyl radical TEAOO˙, which was used as a model for lipid peroxyl radicals, were determined using laser flash photolysis. For Ac-Tyr-OMe a rate coefficient of 1.4 × 10⁴ M^-1 s^-1 was obtained, whereas the reactions with Ac-Trp-OMe and Ac-Met-OMe were slower by a factor of 4 and 6, respectively. For the reaction with Ac-Pro-OMe only an upper value of 10³ M^-1 s^-1 could be determined, suggesting that Pro residues are not effective traps for lipid peroxyl radicals. Density functional theory (DFT) calculations revealed that the reactions proceed via radical hydrogen atom transfer (HAT) from the Cα position, indicating that the rate is determined by the exothermicity of the reaction. In the case of Ac-Tyr-OMe, HAT from the phenolic OH group is the kinetically preferred pathway, which shuts down when hydrogen bonding with an amine occurs. In an alkaline environment, where the phenolic OH group is deprotonated, the reaction is predicted to occur preferably at Cβ, likely through a proton-coupled electron transfer (PCET) mechanism.

Oxidative Damage of Aliphatic Amino Acid Residues by the Environmental Pollutant NO3·: Impact of Water on the Reactivity

The rate of oxidative damage of aliphatic amino acids and dipeptides by the environmental pollutant nitrate radical (NO₃^·) in an aqueous acidic environment was studied by laser flash photolysis. The reactivity dropped by a factor of about four for amino acid residues with secondary amide bonds and by a factor of up to nearly 20 for amino acid residues with tertiary amide bonds, compared with that in acetonitrile. According to density functional theory studies, the lower reactivity is due to protonation of the amide moiety, whereas in neutral water, hydrogen bonding with the amide should have little impact on the absolute reaction rate compared with that in acetonitrile. This finding can be rationalized by the high reactivity and broad reaction pattern of NO₃^·. Although hydrogen bonding involving the amide group raises the energies associated with some electron transfer processes, alternative low-energy pathways remain available so that the overall reaction rate is barely affected. The undiminished high reactivity of NO₃^· toward aliphatic amino acid residues in a neutral aqueous environment highlights the health-damaging potential of exposure to the combined air pollutants nitrogen dioxide (NO₂^·) and ozone (O₃).

Oxidative damage of proline residues by nitrate radicals (NO3˙): a kinetic and product study

Tertiary amides, such as in N-acylated proline or N-methyl glycine residues, react rapidly with nitrate radicals (NO₃˙) with absolute rate coefficients in the range of 4-7 × 10⁸ M^-1 s^-1 in acetonitrile. The major pathway proceeds through oxidative electron transfer (ET) at nitrogen, whereas hydrogen abstraction is only a minor contributor under these conditions. However, steric hindrance at the amide, for example by alkyl side chains at the α-carbon, lowers the rate coefficient by up to 75%, indicating that NO₃˙-induced oxidation of amide bonds proceeds through initial formation of a charge transfer complex. Furthermore, the rate of oxidative damage of proline and N-methyl glycine is significantly influenced by its position in a peptide. Thus, neighbouring peptide bonds, particularly in the N-direction, reduce the electron density at the tertiary amide, which slows down the rate of ET by up to one order of magnitude. The results from these model studies suggest that the susceptibility of proline residues in peptides to radical-induced oxidative damage should be considerably reduced, compared with the single amino acid.

Oxidative Damage in Aliphatic Amino Acids and Di- and Tripeptides by the Environmental Free Radical Oxidant NO3•: The Role of the Amide Bond Revealed by Kinetic and Computational Studies

Kinetic and computational data reveal a complex behavior of the important environmental free radical oxidant NO₃^• in its reactions with aliphatic amino acids and di- and tripeptides, suggesting that attack at the amide N-H bond in the peptide backbone is a highly viable pathway, which proceeds through a proton-coupled electron transfer (PCET) mechanism with a rate coefficient of about 1 × 10⁶ M^-1 s^-1 in acetonitrile. Similar rate coefficients were determined for hydrogen abstraction from the α-carbon and from tertiary C-H bonds in the side chain. The obtained rate coefficients for the reaction of NO₃^• with aliphatic di- and tripeptides suggest that attack occurs at all of these sites in each individual amino acid residue, which makes aliphatic peptide sequences highly vulnerable to NO₃^•-induced oxidative damage. No evidence for amide neighboring group effects, which have previously been found to facilitate radical-induced side-chain damage in phenylalanine, was found for the reaction of NO₃^• with side chains in aliphatic peptides.

A hierarchical modelling approach to assess multi pollutant effects in time-series studies

When assessing the short-term effect of air pollution on health outcomes, it is common practice to consider one pollutant at a time, due to their high correlation. Multi pollutant methods have been recently proposed, mainly consisting of collapsing the different pollutants into air quality indexes or clustering the pollutants and then evaluating the effect of each cluster on the health outcome. A major drawback of such approaches is that it is not possible to evaluate the health impact of each pollutant. In this paper we propose the use of the Bayesian hierarchical framework to deal with multi pollutant concentrations in a two-component model: a pollutant model is specified to estimate the ‘true’ concentration values for each pollutant and then such concentration is linked to the health outcomes in a time-series perspective. Through a simulation study we evaluate the model performance and we apply the modelling framework to investigate the effect of six pollutants on cardiovascular mortality in Greater London in 2011-2012.

Air pollutants and asthma patient visits: Indication of source influence

BACKGROUND

Sources of air pollutants are significant factors for adverse health effect. Few current studies explored the linking of sources influence and ambient pollutants to asthma patient visits in Shanghai, China.

OBJECTIVES

This study explored the associations between short-term exposures to ambient pollutants and asthma morbidity with terrestrial and marine source influence in Shanghai.

METHODS

Generalized additive model (GAM) was used to explore the association of daily patient visits and ambient pollutants. These analyses were calculated in R statistical software in mgcv package. PSCF modeling was used to locate potential source areas contributing to the concentrations of pollutants.

RESULTS

We found that per IQR of PM_2.5, PM₁₀, NO₂, SO₂, O₃ and CO in terrestrial source were associated with an increase of 6.63% (95% CI: -0.27% to 14%), 6.48% (95% CI: 0.06% to 13.3%), 1.68% (95% CI: -2.68% to 6.24%), 2.81% (95% CI: -1.42% to 7.22%), -0.60% (95% CI: -5.94% to 5.04%) and 16.6% (95% CI: 8.68% to 25.2%), respectively in asthma patient visits. Per IQR of PM_2.5, PM₁₀, NO₂, SO₂, O₃ and CO in marine source were associated with an increase of 5.34% (95% CI: 0.42% to 10.5%), 3.84% (95% CI: 0.08% to 7.74%), 3.21% (95% CI: -0.92% to 7.52%), 2.58% (95% CI: -1.02% to 6.30%), 1.42% (95% CI: -3.10% to 6.15%) and 8.81% (95% CI: 2.56% to 15.4%). The PSCF show all of the pollutants except O₃ mainly come from terrestrial during observation. We also found that all of the pollutants except NO₂ displayed the highest effect in the spring for relative risk of asthma morbidity.

CONCLUSIONS

Ambient air pollutants that cause an increase in asthma patient visits, such as PM_2.5, PM₁₀, NO₂, SO₂ and CO are mainly produced from terrestrial sources, while O₃ is primarily from marine sources. The association of ambient pollutants and asthma patient visits is closely related with seasons, especially with spring. PM_2.5 and CO are major air pollutants increasing the relative risk of asthma patient visits in Shanghai.

Operational Experience of an Open-Access, Subscription-Based Mass Spectrometry and Proteomics Facility

This paper discusses the successful adoption of a subscription-based, open-access model of service delivery for a mass spectrometry and proteomics facility. In 2009, the Mass Spectrometry and Proteomics Facility at the University of Melbourne (Australia) moved away from the standard fee for service model of service provision. Instead, the facility adopted a subscription- or membership-based, open-access model of service delivery. For a low fixed yearly cost, users could directly operate the instrumentation but, more importantly, there were no limits on usage other than the necessity to share available instrument time with all other users. All necessary training from platform staff and many of the base reagents were also provided as part of the membership cost. These changes proved to be very successful in terms of financial outcomes for the facility, instrument access and usage, and overall research output. This article describes the systems put in place as well as the overall successes and challenges associated with the operation of a mass spectrometry/proteomics core in this manner. Graphical abstract ᅟ.

Oxidative Damage of Biomolecules by the Environmental Pollutants NO2• and NO3•

Air pollution is responsible for the premature death of about 7 million people every year. Ozone (O₃) and nitrogen dioxide (NO₂^•) are the key gaseous pollutants in the troposphere, which predominantly result from combustion processes. Their inhalation leads to reactions with constituents in the airway surface fluids (ASF) of the respiratory tract and/or lungs. ASF contain small molecular-weight antioxidants, which protect the underlying epithelial cells against oxidative damage. When this defense system is overwhelmed, proteins and lipids present on cell surfaces or within the ASF become vulnerable to attack. The resulting highly reactive protein and lipid oxidation products could subsequently damage the epithelial cells through secondary reactions, thereby causing inflammation. While reactions of NO₂^• with biological molecules are considered to proceed through radical pathways, the biological effect of O₃ is attributed to its high reactivity with π systems. Because O₃ and NO₂^• always coexist in the polluted ambient atmosphere, synergistic effects resulting from in situ formed strongly oxidizing nitrate radicals (NO₃^•) may also require consideration. For example, in vitro product studies revealed that phenylalanine, which is inert not only to oxidants produced through biochemical processes, but also to NO₂^• or O₃ in isolation, is damaged by NO₃^•. The reaction is initiated by oxidation of the aromatic ring and, depending on the availability of NO₂^•, leads to formation of nitrophenylalanine or β-nitrooxyphenylalanine, which could serve as marker for NO₃^•-induced oxidative damage in peptides. More easily oxidizable aromatic amino acids are directly attacked by NO₂^• and are converted to the same products independent of whether O₃ is also present. Remarkably, NO₂^•-induced oxidative damage in peptides occurs not only through the well-established radical oxidation of peptide side chains, but also through an unprecedented fragmentation/rearrangement of the peptide backbone. This process is initiated by a nonradical N-nitrosation of a peptide bond involving the dimer of NO₂^•, i.e., N₂O₄, and contracts the peptide chain in the N → C direction by expelling one amino acid residue with simultaneous fusion of the remaining molecular termini, thereby forming a new peptide bond. This peptide cleavage could potentially be highly relevant for peptide segments with "nonvulnerable" side chains closer to the terminus that are not tied up in complex secondary and tertiary structures and therefore accessible for environmental oxidants. Likewise, NO₂^• reacts with cholesterol at the C═C moiety through an ionic mechanism, which leads to formation of 6-nitrocholesterol in the presence of moisture. Contrary to common belief, this clearly shows that ionic chemistry, in particular nitrosation reactions by intermediately formed NO⁺, requires consideration when assessing NO₂^• toxicity. This conclusion is supported by recent work by Colussi et al. (Enami, S.; Hoffmann, M. R.; Colussi, A. J. Absorption of inhaled NO₂. J. Phys. Chem. B. 2009, 113, 7977-7981), who showed that anions in the airway surfaces fluids mediate NO₂^• absorption by catalyzing its hydrolytic disproportionation into NO₂^-/HNO₂ and NO₃^-. These findings could be the key to our understanding why NO₂^•, despite its low water solubility, has such pronounced biological effects in vivo.

Atmospheric chemistry of bioaerosols: heterogeneous and multiphase reactions with atmospheric oxidants and other trace gases

Once airborne, biologically-derived aerosol particles are prone to reaction with various atmospheric oxidants such as OH, NO₃, and O₃.

Advances in analytical techniques and instrumentation have now established methods for detecting, quantifying, and identifying the chemical and microbial constituents of particulate matter in the atmosphere. For example, recent cryo-TEM studies of sea spray have identified whole bacteria and viruses ejected from ocean seawater into air. A focal point of this perspective is directed towards the reactivity of aerosol particles of biological origin with oxidants (OH, NO₃, and O₃) present in the atmosphere. Complementary information on the reactivity of aerosol particles is obtained from field investigations and laboratory studies. Laboratory studies of different types of biologically-derived particles offer important information related to their impacts on the local and global environment. These studies can also unravel a range of different chemistries and reactivity afforded by the complexity and diversity of the chemical make-up of these particles. Laboratory experiments as the ones reviewed herein can elucidate the chemistry of biological aerosols.

Oxidation of cholesterol and O-protected derivatives by the environmental pollutant NO2˙

Exposure of O-protected and free cholesterol to NO₂˙ leads to oxidation of the alkene moiety through non-radical pathways, demonstrating that ionic processes must be considered when assessing NO₂˙ toxicity.

What Are the Potential Sites of Protein Arylation by N-Acetyl-p-benzoquinone Imine (NAPQI)?

Acetaminophen (paracetamol, APAP) is a safe and widely used analgesic medication when taken at therapeutic doses. However, APAP can cause potentially fatal hepatotoxicity when taken in overdose or in patients with metabolic irregularities. The production of the electrophilic and putatively toxic compound N-acetyl-p-benzoquinone imine (NAPQI), which cannot be efficiently detoxicated at high doses, is implicated in APAP toxicity. Numerous studies have identified that excess NAPQI can form covalent linkages to the thiol side chains of cysteine residues in proteins; however, the reactivity of NAPQI toward other amino acid side chains is largely unexplored. Here, we report a survey of the reactivity of NAPQI toward 11 N-acetyl amino acid methyl esters and four peptides. (1)H NMR analysis reveals that NAPQI forms covalent bonds to the side-chain functional groups of cysteine, methionine, tyrosine, and tryptophan residues. Analogous reaction products were observed when NAPQI was reacted with synthetic model peptides GAIL-X-GAILR for X = Cys, Met, Tyr, and Trp. Tandem mass spectrometry peptide sequencing showed that the NAPQI modification sites are located on the "X" residue in each case. However, when APAP and the GAIL-X-GAILR peptide were incubated with rat liver microsomes that contain many metabolic enzymes, NAPQI formed by oxidative metabolism reacted with GAIL-C-GAILR exclusively. For the peptides where X = Met, Tyr, and Trp, competing reactions between NAPQI and alternative nucleophiles precluded arylation of the target peptide by NAPQI. Although Cys residues are favorably targeted under these conditions, these data suggest that NAPQI can, in principle, also damage proteins at Met, Tyr, and Trp residues.

Visible light photooxidation of nitrate: the dawn of a nocturnal radical

Highly oxidizing nitrate radicals (NO₃˙) are easily accessed from readily available nitrate salts by visible light photoredox catalysis using a purely organic dye as the catalyst and oxygen as the terminal oxidant.

A new method for peptide synthesis in the N→C direction: amide assembly through silver-promoted reaction of thioamides

The Ag(i)-promoted coupling of peptide-acids with thioamides generates peptide-imides, which was exploited in the synthesis of peptides in the N→C direction.