Biological Pathway: Reactome:R-HSA-8941413
Events associated with phagocytolytic activity of PMN cells related metabolites
find 21 related metabolites which is associated with the biological pathway Events associated with phagocytolytic activity of PMN cells
this pathway object is a organism specific pathway, which is related to taxonomy Homo sapiens (human).
When neutrophils engulf bacteria they enclose them in small vacuoles (phagosomes) into which superoxide is released by activated NADPH oxidase (NOX2) on the internalized neutrophil membrane. The directional nature of NOX2 activity creates a charge imbalance that must be counteracted to prevent depolarization of the membrane and the shutdown of activity (Winterbourn CC et al. 2016). Also, protons are produced in the cytosol and consumed in the external compartment (for example, the phagosome) through the dismutation of superoxide. Both situations are largely overcome by a balancing flow of protons transported by voltage-gated proton channels, primarily VSOP/HV1, which are activated in parallel with the oxidase (Demaurex N & El Chemaly A 2010; El Chemaly A et al. 2010; Petheo GL et al. 2010; Kovacs I et al. 2014; Henderson LM et al. 1987, 1988). The pH of the phagosome is regulated by these activities. In contrast to the phagosomes of macrophages, in which pH drops following particle ingestion, neutrophil phagosomes remain alkaline during the period that the oxidase is active. Until recently, their pH has been accepted to lie between 7.5 and 8. However, in a 2015 study using a probe that is more sensitive at higher pH, an average pH closer to 9 was measured in individual phagosomes (Levine AP et al. 2015).
The superoxide dismutates to hydrogen peroxide, which is used by myeloperoxidase (MPO) to generate other oxidants, including the highly microbicidal species such as hypochlorous acid (Winterbourn CC et al. 2013, 2016).
N-Acetylmuramate
This compound belongs to the family of N-acyl-alpha-hexosamines. These are carbohydrate derivatives containing a hexose moeity in which the oxygen atom is replaced by an n-acyl group. KEIO_ID A191
Water
Water is a chemical substance that is essential to all known forms of life. It appears colorless to the naked eye in small quantities, though it is actually slightly blue in color. It covers 71\\% of Earths surface. Current estimates suggest that there are 1.4 billion cubic kilometers (330 million m3) of it available on Earth, and it exists in many forms. It appears mostly in the oceans (saltwater) and polar ice caps, but it is also present as clouds, rain water, rivers, freshwater aquifers, lakes, and sea ice. Water in these bodies perpetually moves through a cycle of evaporation, precipitation, and runoff to the sea. Clean water is essential to human life. In many parts of the world, it is in short supply. From a biological standpoint, water has many distinct properties that are critical for the proliferation of life that set it apart from other substances. It carries out this role by allowing organic compounds to react in ways that ultimately allow replication. All known forms of life depend on water. Water is vital both as a solvent in which many of the bodys solutes dissolve and as an essential part of many metabolic processes within the body. Metabolism is the sum total of anabolism and catabolism. In anabolism, water is removed from molecules (through energy requiring enzymatic chemical reactions) in order to grow larger molecules (e.g. starches, triglycerides and proteins for storage of fuels and information). In catabolism, water is used to break bonds in order to generate smaller molecules (e.g. glucose, fatty acids and amino acids to be used for fuels for energy use or other purposes). Water is thus essential and central to these metabolic processes. Water is also central to photosynthesis and respiration. Photosynthetic cells use the suns energy to split off waters hydrogen from oxygen. Hydrogen is combined with CO2 (absorbed from air or water) to form glucose and release oxygen. All living cells use such fuels and oxidize the hydrogen and carbon to capture the suns energy and reform water and CO2 in the process (cellular respiration). Water is also central to acid-base neutrality and enzyme function. An acid, a hydrogen ion (H+, that is, a proton) donor, can be neutralized by a base, a proton acceptor such as hydroxide ion (OH-) to form water. Water is considered to be neutral, with a pH (the negative log of the hydrogen ion concentration) of 7. Acids have pH values less than 7 while bases have values greater than 7. Stomach acid (HCl) is useful to digestion. However, its corrosive effect on the esophagus during reflux can temporarily be neutralized by ingestion of a base such as aluminum hydroxide to produce the neutral molecules water and the salt aluminum chloride. Human biochemistry that involves enzymes usually performs optimally around a biologically neutral pH of 7.4. (Wikipedia). Water, also known as purified water or dihydrogen oxide, is a member of the class of compounds known as homogeneous other non-metal compounds. Homogeneous other non-metal compounds are inorganic non-metallic compounds in which the largest atom belongs to the class of other nonmetals. Water can be found in a number of food items such as caraway, oxheart cabbage, alaska wild rhubarb, and japanese walnut, which makes water a potential biomarker for the consumption of these food products. Water can be found primarily in most biofluids, including ascites Fluid, blood, cerebrospinal fluid (CSF), and lymph, as well as throughout all human tissues. Water exists in all living species, ranging from bacteria to humans. In humans, water is involved in several metabolic pathways, some of which include cardiolipin biosynthesis CL(20:4(5Z,8Z,11Z,14Z)/18:0/20:4(5Z,8Z,11Z,14Z)/18:2(9Z,12Z)), cardiolipin biosynthesis cl(i-13:0/i-15:0/i-20:0/i-24:0), cardiolipin biosynthesis CL(18:0/18:0/20:4(5Z,8Z,11Z,14Z)/22:5(7Z,10Z,13Z,16Z,19Z)), and cardiolipin biosynthesis cl(a-13:0/i-18:0/i-13:0/i-19:0). Water is also involved in several metabolic disorders, some of which include de novo triacylglycerol biosynthesis tg(i-21:0/i-13:0/21:0), de novo triacylglycerol biosynthesis tg(22:0/20:0/i-20:0), de novo triacylglycerol biosynthesis tg(a-21:0/i-20:0/i-14:0), and de novo triacylglycerol biosynthesis tg(i-21:0/a-17:0/i-12:0). Water is a drug which is used for diluting or dissolving drugs for intravenous, intramuscular or subcutaneous injection, according to instructions of the manufacturer of the drug to be administered [fda label]. Water plays an important role in the world economy. Approximately 70\\% of the freshwater used by humans goes to agriculture. Fishing in salt and fresh water bodies is a major source of food for many parts of the world. Much of long-distance trade of commodities (such as oil and natural gas) and manufactured products is transported by boats through seas, rivers, lakes, and canals. Large quantities of water, ice, and steam are used for cooling and heating, in industry and homes. Water is an excellent solvent for a wide variety of chemical substances; as such it is widely used in industrial processes, and in cooking and washing. Water is also central to many sports and other forms of entertainment, such as swimming, pleasure boating, boat racing, surfing, sport fishing, and diving .
Hydrogen peroxide
Hydrogen peroxide (H2O2) is a very pale blue liquid that appears colourless in a dilute solution. H2O2 is slightly more viscous than water and is a weak acid. H2O2 is unstable and slowly decomposes in the presence of light. It has strong oxidizing properties and is, therefore, a powerful bleaching agent that is mostly used for bleaching paper. H2O2 has also found use as a disinfectant and as an oxidizer. H2O2 in the form of carbamide peroxide is widely used for tooth whitening (bleaching), both in professionally- and in self-administered products. H2O2 is a well-documented component of living cells and is a normal metabolite of oxygen in the aerobic metabolism of cells and tissues. A total of 31 human cellular H2O2 generating enzymes has been identified so far (PMID: 25843657). H2O2 plays important roles in host defence and oxidative biosynthetic reactions. At high levels (>100 nM) H2O2 is toxic to most cells due to its ability to non-specifically oxidize proteins, membranes and DNA, leading to general cellular damage and dysfunction. However, at low levels (<10 nM), H2O2 functions as a signalling agent, particularly in higher organisms. In plants, H2O2 plays a role in signalling to cause cell shape changes such as stomatal closure and root growth. As a messenger molecule in vertebrates, H2O2 diffuses through cells and tissues to initiate cell shape changes, to drive vascular remodelling, and to activate cell proliferation and recruitment of immune cells. H2O2 also plays a role in redox sensing, signalling, and redox regulation (PMID: 28110218). This is normally done through molecular redox “switches” such as thiol-containing proteins. The production and decomposition of H2O2 are tightly regulated (PMID: 17434122). In humans, H2O2 can be generated in response to various stimuli, including cytokines and growth factors. H2O2 is degraded by several enzymes including catalase and superoxide dismutase (SOD), both of which play important roles in keeping the amount of H2O2 in the body below toxic levels. H2O2 also appears to play a role in vitiligo. Vitiligo is a skin pigment disorder leading to patchy skin colour, especially among dark-skinned individuals. Patients with vitiligo have low catalase levels in their skin, leading to higher levels of H2O2. High levels of H2O2 damage the epidermal melanocytes, leading to a loss of pigment (PMID: 10393521). Accumulating evidence suggests that hydrogen peroxide H2O2 plays an important role in cancer development. Experimental data have shown that cancer cells produce high amounts of H2O2. An increase in the cellular levels of H2O2 has been linked to several key alterations in cancer, including DNA changes, cell proliferation, apoptosis resistance, metastasis, angiogenesis and hypoxia-inducible factor 1 (HIF-1) activation (PMID: 17150302, 17335854, 16677071, 16607324, 16514169). H2O2 is found in most cells, tissues, and biofluids. H2O2 levels in the urine can be significantly increased with the consumption of coffee and other polyphenolic-containing beverages (wine, tea) (PMID: 12419961). In particular, roasted coffee has high levels of 1,2,4-benzenetriol which can, on its own, lead to the production of H2O2. Normal levels of urinary H2O2 in non-coffee drinkers or fasted subjects are between 0.5-3 uM/mM creatinine whereas, for those who drink coffee, the levels are between 3-10 uM/mM creatinine (PMID: 12419961). It is thought that H2O2 in urine could act as an antibacterial agent and that H2O2 is involved in the regulation of glomerular function (PMID: 10766414). A - Alimentary tract and metabolism > A01 - Stomatological preparations > A01A - Stomatological preparations > A01AB - Antiinfectives and antiseptics for local oral treatment D - Dermatologicals > D08 - Antiseptics and disinfectants > D08A - Antiseptics and disinfectants S - Sensory organs > S02 - Otologicals > S02A - Antiinfectives > S02AA - Antiinfectives It is used in foods as a bleaching agent, antimicrobial agent and oxidising agent C254 - Anti-Infective Agent > C28394 - Topical Anti-Infective Agent D009676 - Noxae > D016877 - Oxidants > D010545 - Peroxides D000890 - Anti-Infective Agents
Chloride ion
Under standard conditions, chlorine exists as a diatomic molecule. Chlorine is a highly toxic, pale yellow-green gas that has a specific strong smell. In nature, chlorine is most abundant as a chloride ion. Physiologically, it exists as an ion in the body. The chloride ion is an essential anion that the body needs for many critical functions. It also helps keep the bodys acid-base balance. The amount of chloride in the blood is carefully controlled by the kidneys. Chloride ions have important physiological roles. For instance, in the central nervous system, the inhibitory action of glycine and some of the action of GABA relies on the entry of Cl- into specific neurons. Also, the chloride-bicarbonate exchanger biological transport protein relies on the chloride ion to increase the bloods capacity of carbon dioxide, in the form of the bicarbonate ion. Chloride-transporting proteins (CLC) play fundamental roles in many tissues in the plasma membrane as well as in intracellular membranes. CLC proteins form a gene family that comprises nine members in mammals, at least four of which are involved in human genetic diseases. GABA(A) receptors are pentameric complexes that function as ligand-gated chloride ion channels. WNK kinases are a family of serine-threonine kinases that have been shown to play an essential role in the regulation of electrolyte homeostasis, and they are found in diverse epithelia throughout the body that are involved in chloride ion flux. Cystic fibrosis (CF) is caused by alterations in the CF transmembrane conductance regulator (CFTCR) gene that result in deranged sodium and chloride ion transport channels. (PMID: 17539703, 17729441, 17562499, 15300163) (For a complete review see Evans, Richard B. Chlorine: state of the art. Lung (2005), 183(3), 151-167. PMID: 16078037). The chloride ion is formed when the element chlorine picks up one electron to form the Cl- anion. The chloride ion is one of the most common anions in nature and is necessary to most forms of life. It is an essential electrolyte responsible for maintaining acid/base balance and regulating fluid in and out of cells. [Wikipedia]. Chloride is found in many foods, some of which are jute, grapefruit, lentils, and lime.
Hypochlorite
The hypochlorite ion is ClO-. A hypochlorite compound is a chemical compound containing this group. Hypochlorite is a strong oxidant. About 28\\% of oxygen consumed by phagocytes upon activation participates in its generation. Hypochlorite reacts with H2O2 producing singlet oxygen (1O2) - a strong initiator of Lipid peroxidation. O-sub 2, along with H2O2 can serve as the substrate for myeloperoxidase. When this takes place, Hypochlorite is formed. Hypochlorite is able to modify antioxidants incorporated into lipoproteins such as Alpha-tocopherol, Beta-carotene, lycopene, and ubiquinol-10. It is also able to modify a number of proteins which possess antioxidant functions such as ceruloplasmin, transferrin, superoxide dismutase, and catalase. Active myeloperoxidase is found at sites of atherosclerotic damage to the arterial vessel wall in humans. Lipid peroxidation is known to contribute to the development of pathological processes, among them atherosclerosis. The present hypothesis is that blood lipoproteins modified by Lipid peroxidation play a key role in the pathogenesis of this disease. One of the possible reasons for the appearance of oxidized blood lipoproteins in blood is the interaction of native blood lipoproteins with the reactive oxygen species generated by stimulated neutrophils, monocytes and other cells. The main reaction of Hypochlorite with unsaturated lipid is probably the generation of chlorohydrins. However, this reaction is not accompanied by generation of free radicals and Lipid peroxidation. This reaction is accompanied by the production of free radicals (but not singlet oxygen), probably alkoxyl radicals, which may play a role in the initiation of Hypochlorite-induced Lipid peroxidation. (PMID: 9260000, Biofactors. 1997;6(2):181-90.) [HMDB] The hypochlorite ion is ClO-. A hypochlorite compound is a chemical compound containing this group. Hypochlorite is a strong oxidant. About 28\\% of oxygen consumed by phagocytes upon activation participates in its generation. Hypochlorite reacts with H2O2 producing singlet oxygen (1O2) - a strong initiator of Lipid peroxidation. O-sub 2, along with H2O2 can serve as the substrate for myeloperoxidase. When this takes place, Hypochlorite is formed. Hypochlorite is able to modify antioxidants incorporated into lipoproteins such as Alpha-tocopherol, Beta-carotene, lycopene, and ubiquinol-10. It is also able to modify a number of proteins which possess antioxidant functions such as ceruloplasmin, transferrin, superoxide dismutase, and catalase. Active myeloperoxidase is found at sites of atherosclerotic damage to the arterial vessel wall in humans. Lipid peroxidation is known to contribute to the development of pathological processes, among them atherosclerosis. The present hypothesis is that blood lipoproteins modified by Lipid peroxidation play a key role in the pathogenesis of this disease. One of the possible reasons for the appearance of oxidized blood lipoproteins in blood is the interaction of native blood lipoproteins with the reactive oxygen species generated by stimulated neutrophils, monocytes and other cells. The main reaction of Hypochlorite with unsaturated lipid is probably the generation of chlorohydrins. However, this reaction is not accompanied by generation of free radicals and Lipid peroxidation. This reaction is accompanied by the production of free radicals (but not singlet oxygen), probably alkoxyl radicals, which may play a role in the initiation of Hypochlorite-induced Lipid peroxidation. (PMID: 9260000, Biofactors. 1997;6(2):181-90.). D009676 - Noxae > D016877 - Oxidants
beta-N-Acetylglucosamine
beta-N-Acetylglucosamine is an acylaminosugar, which is an organic compound containing a sugar linked to a chain through an N-acyl group. This compound is water-soluble. Glycosylation with beta-N-acetylglucosamine is one of the most common post-translational modifications. All animals and plants dynamically attach and remove beta-N-acetylglucosamine at serine and threonine residues on myriad nuclear and cytoplasmic proteins. beta-N-Acetylglucosamine cycling, which is tightly regulated by the concerted actions of two highly-conserved enzymes, serves as a nutrient and stress sensor. Proteins glycosylated with beta-N-acetylglucosamine can be found in almost every intracellular compartment and almost every functional class (PMID: 17460662).
Hydrogen Ion
Hydrogen ion, also known as proton or h+, is a member of the class of compounds known as other non-metal hydrides. Other non-metal hydrides are inorganic compounds in which the heaviest atom bonded to a hydrogen atom is belongs to the class of other non-metals. Hydrogen ion can be found in a number of food items such as lowbush blueberry, groundcherry, parsley, and tarragon, which makes hydrogen ion a potential biomarker for the consumption of these food products. Hydrogen ion exists in all living organisms, ranging from bacteria to humans. In humans, hydrogen ion is involved in several metabolic pathways, some of which include cardiolipin biosynthesis cl(i-13:0/a-25:0/a-21:0/i-15:0), cardiolipin biosynthesis cl(a-13:0/a-17:0/i-13:0/a-25:0), cardiolipin biosynthesis cl(i-12:0/i-13:0/a-17:0/a-15:0), and cardiolipin biosynthesis CL(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)/18:1(11Z)/22:5(7Z,10Z,13Z,16Z,19Z)). Hydrogen ion is also involved in several metabolic disorders, some of which include de novo triacylglycerol biosynthesis TG(20:3(8Z,11Z,14Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)/22:5(7Z,10Z,13Z,16Z,19Z)), de novo triacylglycerol biosynthesis TG(18:2(9Z,12Z)/20:0/20:4(5Z,8Z,11Z,14Z)), de novo triacylglycerol biosynthesis TG(18:4(6Z,9Z,12Z,15Z)/18:3(9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)), and de novo triacylglycerol biosynthesis TG(24:0/20:5(5Z,8Z,11Z,14Z,17Z)/24:0). A hydrogen ion is created when a hydrogen atom loses or gains an electron. A positively charged hydrogen ion (or proton) can readily combine with other particles and therefore is only seen isolated when it is in a gaseous state or a nearly particle-free space. Due to its extremely high charge density of approximately 2×1010 times that of a sodium ion, the bare hydrogen ion cannot exist freely in solution as it readily hydrates, i.e., bonds quickly. The hydrogen ion is recommended by IUPAC as a general term for all ions of hydrogen and its isotopes. Depending on the charge of the ion, two different classes can be distinguished: positively charged ions and negatively charged ions . Hydrogen ion is recommended by IUPAC as a general term for all ions of hydrogen and its isotopes. Depending on the charge of the ion, two different classes can be distinguished: positively charged ions and negatively charged ions. Under aqueous conditions found in biochemistry, hydrogen ions exist as the hydrated form hydronium, H3O+, but these are often still referred to as hydrogen ions or even protons by biochemists. [Wikipedia])
Hypothiocyanite
As it is an organic compound, hypothiocyanite occurs naturally in the antimicrobial immune system of the human respiratory tract in a redox reaction catalyzed by the enzyme lactoperoxidase. It has been researched extensively for its capabilities as an alternative antibiotic as it is harmless to human body cells while being cytotoxic to bacteria. Of late, the exact processes for making hypothiocyanite have been patented as such an effective antimicrobial has many commercial applications. Whether or not this antimicrobial compound comprises the entirety of the immune system of the respiratory tract remains to be seen.; Hypothiocyanite is the anion [OSCN]- and the conjugate base of hypothiocyanous acid. It is an organic compound part of the thiocyanates as it contains the functional group SCN. It is formed when an oxygen is singly bonded to the thiocyanate group. Hypothiocyanous acid (HOSCN) is a fairly weak acid as its acid dissociation constant is 5.3 [HMDB] As it is an organic compound, hypothiocyanite occurs naturally in the antimicrobial immune system of the human respiratory tract in a redox reaction catalyzed by the enzyme lactoperoxidase. It has been researched extensively for its capabilities as an alternative antibiotic as it is harmless to human body cells while being cytotoxic to bacteria. Of late, the exact processes for making hypothiocyanite have been patented as such an effective antimicrobial has many commercial applications. Whether or not this antimicrobial compound comprises the entirety of the immune system of the respiratory tract remains to be seen. Hypothiocyanite is the anion [OSCN]- and the conjugate base of hypothiocyanous acid. It is an organic compound part of the thiocyanates as it contains the functional group SCN. It is formed when an oxygen is singly bonded to the thiocyanate group. Hypothiocyanous acid (HOSCN) is a fairly weak acid as its acid dissociation constant is 5.3. D000890 - Anti-Infective Agents
H2O
An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. Water. CAS Common Chemistry. CAS, a division of the American Chemical Society, n.d. https://commonchemistry.cas.org/detail?cas_rn=7732-18-5 (retrieved 2024-10-17) (CAS RN: 7732-18-5). Licensed under the Attribution-Noncommercial 4.0 International License (CC BY-NC 4.0).
Thiocyanate
A pseudohalide anion obtained by deprotonation of the thiol group of thiocyanic acid.
Thiocyanate
Thiocyanate is analogous to the cyanate ion, [OCN]-, wherein oxygen is replaced by sulfur. [SCN]- is one of the pseudohalogens, due to the similarity of its reactions to that of halide ions. Thiocyanate was formerly known as rhodanide (from a Greek word for rose) because of the red color of its complexes with iron. Thiocyanates are typically colorless. Cyanide ions can react with cystine to yield thicocyanate. This reaction occurs to a slight extent even in neutral solution, but is more pronounced in alkaline solutions of cystine. In addition to this non-enzymatic route, cyanide produced in vivo can be converted in part to thiocyanate by sulfur transferase systems. The thiocyanate ion can be oxidized at acid pH by hydrogen peroxide to generate sulfate and cyanide. The reaction is catalyzed by hemoglobin acting as a peroxidase. Thiocyanate is analogous to the cyanate ion, [OCN]-, wherein oxygen is replaced by sulfur. [SCN]- is one of the pseudohalogens, due to the similarity of its reactions to that of halide ions. Thiocyanate was formerly known as rhodanide (from a Greek word for rose) because of the red color of its complexes with iron. Thiocyanates are typically colorless. Cyanide ions can react with cystine to yield thicocyanate. This reaction occurs to a slight extent even in neutral solution, but is more pronounced in alkaline solutions of cystine. In addition to this non-enzymatic route, cyanide produced in vivo can be converted in part to thiocyanate by sulfur transferase systems. The thiocyanate ion can be oxidized at acid pH by hydrogen peroxide to generate sulfate and cyanide. The reaction is catalyzed by hemoglobin acting as a peroxidase. A study shows that thiocyanate has a protective effect in lung in cystic fibrosis, and an anti-inflammatory effect in arterial endothelial cells, a neuronal cell line, and a pancreatic beta cell line (PMID: 19918082). Thiocyanate has been identified as a uremic toxin according to the European Uremic Toxin Working Group (PMID: 22626821).
Ferriheme b
C34H30FeN4O4-4 (614.1616329999999)
COVID info from COVID-19 Disease Map Corona-virus Coronavirus SARS-CoV-2 COVID-19 SARS-CoV COVID19 SARS2 SARS
hydrogen peroxide
A - Alimentary tract and metabolism > A01 - Stomatological preparations > A01A - Stomatological preparations > A01AB - Antiinfectives and antiseptics for local oral treatment An inorganic peroxide consisting of two hydroxy groups joined by a covalent oxygen-oxygen single bond. D - Dermatologicals > D08 - Antiseptics and disinfectants > D08A - Antiseptics and disinfectants S - Sensory organs > S02 - Otologicals > S02A - Antiinfectives > S02AA - Antiinfectives C254 - Anti-Infective Agent > C28394 - Topical Anti-Infective Agent D009676 - Noxae > D016877 - Oxidants > D010545 - Peroxides D000890 - Anti-Infective Agents
HYPOCHLOROUS ACID
A chlorine oxoacid with formula HOCl; a weak, unstable acid, it is the active form of chlorine in water. D009676 - Noxae > D016877 - Oxidants
chitin
COVID info from PDB, Protein Data Bank, clinicaltrial, clinicaltrials, clinical trial, clinical trials An N-acetyl-D-glucosamine having beta-configuration at the anomeric centre. Corona-virus Coronavirus SARS-CoV-2 COVID-19 SARS-CoV COVID19 SARS2 SARS