https://staff.blog.ui.ac.id/hsuryadi/files/2012/02/ROS_RNS.pdf

Free radicals and antioxidants in normal physiological functions and human disease

Lipid peroxidation can be described generally as a process under which oxidants such as free radicals attack lipids containing carbon-carbon double bond(s), especially polyunsaturated fatty acids (PUFAs). Over the last four decades, an extensive body of literature regarding lipid peroxidation has shown its important role in cell biology and human health. Since the early 1970s, the total published research articles on the topic of lipid peroxidation was 98 (1970–1974) and has been increasing at almost 135-fold, by up to 13165 in last 4 years (2010–2013). New discoveries about the involvement in cellular physiology and pathology, as well as the control of lipid peroxidation, continue to emerge every day. Given the enormity of this field, this review focuses on biochemical concepts of lipid peroxidation, production, metabolism, and signaling mechanisms of two main omega-6 fatty acids lipid peroxidation products: malondialdehyde (MDA) and, in particular, 4-hydroxy-2-nonenal (4-HNE), summarizing not only its physiological and protective function as signaling molecule stimulating gene expression and cell survival, but also its cytotoxic role inhibiting gene expression and promoting cell death. Finally, overviews of in vivo mammalian model systems used to study the lipid peroxidation process, and common pathological processes linked to MDA and 4-HNE are shown.

/pdf/lipid-peroxidation-production-metabolism-and-signaling-234bwmyps5.pdf

Lipid peroxidation: production, metabolism, and signaling mechanisms of malondialdehyde and 4-hydroxy-2-nonenal.

Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect several million individuals worldwide. Crohn's disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study's infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi'omics Database ( http://ibdmdb.org ), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases.

/pdf/multi-omics-of-the-gut-microbial-ecosystem-in-inflammatory-233td423ej.pdf

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.

Oxidative stress basically defines a condition in which prooxidant-antioxidant balance in the cell is disturbed; cellular biomolecules undergo severe oxidative damage, ultimately compromising cells viability. In recent years, a number of studies have shown that oxidative stress could cause cellular apoptosis via both the mitochondria-dependent and mitochondria-independent pathways. Since these pathways are directly related to the survival or death of various cell types in normal as well as pathophysiological situations, a clear picture of these pathways for various active molecules in their biological functions would help designing novel therapeutic strategy. This review highlights the basic mechanisms of ROS production and their sites of formation; detail mechanism of both mitochondria-dependent and mitochondria-independent pathways of apoptosis as well as their regulation by ROS. Emphasis has been given on the redox-sensitive ASK1 signalosome and its downstream JNK pathway. This review also describes the involvement of oxidative stress under various environmental toxin- and drug-induced organ pathophysiology and diabetes-mediated apoptosis. We believe that this review would provide useful information about the most recent progress in understanding the mechanism of oxidative stress-mediated regulation of apoptotic pathways. It will also help to figure out the complex cross-talks between these pathways and their modulations by oxidative stress. The literature will also shed a light on the blind alleys of this field to be explored. Finally, readers would know about the ROS-regulated and apoptosis-mediated organ pathophysiology which might help to find their probable remedies in future.

Oxidative stress: the mitochondria-dependent and mitochondria-independent pathways of apoptosis

Since its discovery in 2002, the copper-catalyzed azide-alkyne cycloaddition (CuAAC)[1] reaction—the most widely recognized example of click chemistry[2]—has been rapidly embraced for applications in myriad fields.[3] The attractiveness of this procedure (and its copper-free strained-alkyne variant[4]) stems from the selective reactivity of azides and alkynes only with each other. Because of the fragile nature and low concentrations at which biomolecules are often manipulated, bioconjugation presents significant challenges for any ligation methodology. Several different CuAAC procedures have been reported to address specific cases involving peptides, proteins, polynucleotides, and fixed cells, often with excellent results,[5] but also occasionally with somewhat less satisfying outcomes.[6] We describe here a generally applicable procedure that solves the most vexing click bioconjugation problems in our laboratory, and therefore should be of use in many other situations.

The CuAAC reaction requires the copper catalyst, usually prepared with an appropriate chelating ligand,[7] to be maintained in the CuI oxidation state. Several years ago we developed a system featuring a sulfonated bathophenanthroline ligand,[8] which was optimized into a useful bioconjugation protocol.[9] A significant drawback was the catalyst’s acute oxygen sensitivity, requiring air-free techniques which can be difficult to execute when an inert-atmosphere glove box is unavailable or when sensitive biomolecules are used in small volumes of aqueous solution. We also introduced an electrochemical method to generate and protect catalytically active CuI–ligand species for CuAAC bioconjugation and synthetic coupling reactions with miminal effort to exclude air.[10] Under these conditions, no hydrogen peroxide was produced in the oxygen-scrubbing process, resulting in protein conjugates that were uncontaminated with oxidative byproducts. However, this solution is also practical only for the specialist with access to the proper equipment. Other protocols have employed copper(I) sources such as CuBr for labeling fixed cells[11] and synthesizing glycoproteins.[12] In these cases, the instability of CuI in air imposes a requirement for large excesses of Cu (greater than 4 mm) and ligand for efficient reactions, which raises concerns about protein damage or precipitation, plus the presence of residual metal after purification.

The most convenient CuAAC procedure involves the use of an in situ reducing agent. Sodium ascorbate is the reductant of choice for CuAAC reactions in organic and materials synthesis, but is avoided in bioconjugation with a few exceptions.[13] Copper and sodium ascorbate have been shown to be detrimental to biological[14] and synthetic[15] polymers due to copper-mediated generation of reactive oxygen species.[16] Moreover, dehydroascorbate and other ascorbate byproducts can react with lysine amine and arginine guanidine groups, leading to covalent modification and potential aggregation of proteins.[6a,17] We hoped that solutions to these problems would allow ascorbate to be used in fast and efficient CuAAC reactions using micromolar concentration of copper in the presence of atmospheric oxygen. This has now been achieved, allowing demanding reactions to be performed with biomolecules of all types by the nonspecialist.

For purposes of catalyst optimization and reaction screening, the fluorogenic coumarin azide 1 developed by Wang et al. has proven to be invaluable (Scheme 1).[18] The progress of cycloaddition reactions between mid-micromolar concentrations of azide and alkyne in aqueous buffers was followed by the increase in fluorescence at 470 nm upon formation of the triazole 2.



Scheme 1

Top: Reaction used for screening CuAAC catalysts and conditions. Below: Accelerating ligand 3 and additive 4 used in these studies. DMSO=dimethylsulfoxide.

/pdf/analysis-and-optimization-of-copper-catalyzed-azide-alkyne-2jcgy89zji.pdf

Analysis and Optimization of Copper-Catalyzed Azide–Alkyne Cycloaddition for Bioconjugation

Aldehydes are organic compounds that are widespread in nature. They can be formed endogenously by lipid peroxidation (LPO), carbohydrate or metabolism ascorbate autoxidation, amine oxidases, cytochrome P-450s, or myeloperoxidase-catalyzed metabolic activation. This review compares the reactivity of many aldehydes towards biomolecules particularly macromolecules. Furthermore, it includes not only aldehydes of environmental or occupational concerns but also dietary aldehydes and aldehydes formed endogenously by intermediary metabolism. Drugs that are aldehydes or form reactive aldehyde metabolites that cause side-effect toxicity are also included. The effects of these aldehydes on biological function, their contribution to human diseases, and the role of nucleic acid and protein carbonylation/oxidation in mutagenicity and cytotoxicity mechanisms, respectively, as well as carbonyl signal transduction and gene expression, are reviewed. Aldehyde metabolic activation and detoxication by metabolizing enzymes are also reviewed, as well as the toxicological and anticancer therapeutic effects of metabolizing enzyme inhibitors. The human health risks from clinical and animal research studies are reviewed, including aldehydes as haptens in allergenic hypersensitivity diseases, respiratory allergies, and idiosyncratic drug toxicity; the potential carcinogenic risks of the carbonyl body burden; and the toxic effects of aldehydes in liver disease, embryo toxicity/teratogenicity, diabetes/hypertension, sclerosing peritonitis, cerebral ischemia/neurodegenerative diseases, and other aging-associated diseases.

Aldehyde sources, metabolism, molecular toxicity mechanisms, and possible effects on human health.

Mitochondrial function and toxicity: role of the B vitamin family on mitochondrial energy metabolism.

Mitochondrial function and toxicity: Role of B vitamins on the one-carbon transfer pathways

The biology of the mitochondrial electron transport chain is summarized. Our approach to the mechanism of uncouplers, inhibitors, and toxins is based on electron transfer (ET) and reactive oxygen species (ROS). Extensive supporting evidence, which is broadly applicable, is cited. ROS can be generated either endogenously or exogenously. Generally, the reactive entities arise via redox cycling by ET functionalities, such as, quinones (or precursors), metal compounds, imines (or iminiums), and aromatic nitro compounds (or reduced metabolites). In most cases, the ET functions are formed metabolically. The toxic substances belong to many categories, e.g., medicinals, industrial chemicals, abused drugs, and pesticides. Structure-activity relationships are presented from the ET-ROS perspective, and also quantitatively. Evidence for the theoretical framework is provided by the protective effect of antioxidants. Among other topics addressed are proton flux, membrane pores, and apoptosis. There is support for the thesis that mitochondrial insult may contribute to illnesses and aging.

Nandita Shangari

Papers

Aldehyde sources, metabolism, molecular toxicity mechanisms, and possible effects on human health.

Mitochondrial function and toxicity: role of the B vitamin family on mitochondrial energy metabolism.

Mitochondrial function and toxicity: Role of B vitamins on the one-carbon transfer pathways

Mechanism of mitochondrial uncouplers, inhibitors, and toxins: focus on electron transfer, free radicals, and structure-activity relationships.

The cytotoxic mechanism of glyoxal involves oxidative stress.