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Deoxyguanosine, also known as dG, belongs to the class of organic compounds known as purine 2'-deoxyribonucleosides. Purine 2'-deoxyribonucleosides are compounds consisting of a purine linked to a ribose which lacks a hydroxyl group at position 2’. Deoxyguanosine is a nucleoside consisting of the base guanine and the sugar deoxyribose. Deoxyguanosine is one of the four deoxyribonucleosides that make up DNA. Deoxyguanosine exists in all living species, ranging from bacteria to plants to humans. Deoxyguanosine participates in a number of enzymatic reactions. In particular, deoxyguanosine can be biosynthesized from 2'-deoxyguanosine 5'-monophosphate through the enzyme known as cytosolic purine 5'-nucleotidase. In addition, deoxyguanosine can be converted into 2'-deoxyguanosine 5'-monophosphate (dGMP); which is mediated by the enzyme deoxyguanosine kinase. Deoxyguanosine is involved in the rare, inherited metabolic disorder called the purine nucleoside phosphorylase deficiency (PNP deficiency). In particular PNP deficiency is characterized by elevated levels of dGTP (deoxyguanosine triphosphate). PNP accounts for approximately 4% of patients with severe combined immunodeficiency (PMID: 1931007). PNP-deficient patients suffer from recurrent infections, usually beginning in the first year of life. Two thirds of patients have evidence of neurologic disorders with spasticity, developmental delay and mental retardation. Deoxyguanosine can be converted to 8-hydroxy-deoxyguanosine (8-OHdG) due to hydroxyl radical attack at the C8 of guanine. 8-hydroxy-deoxyguanosine is a sensitive marker of the DNA damage This damage, if left unrepaired, has been proposed to contribute to mutagenicity and cancer promotion.

N-Acetyl-L-methionine or N-Acetylmethionine, belongs to the class of organic compounds known as N-acyl-alpha amino acids. N-acyl-alpha amino acids are compounds containing an alpha amino acid which bears an acyl group at its terminal nitrogen atom. N-Acetylmethionine can also be classified as an alpha amino acid or a derivatized alpha amino acid. Technically, N-Acetylmethionine is a biologically available N-terminal capped form of the proteinogenic alpha amino acid L-methionine. N-acetyl amino acids can be produced either via direct synthesis of specific N-acetyltransferases or via the proteolytic degradation of N-acetylated proteins by specific hydrolases. N-terminal acetylation of proteins is a widespread and highly conserved process in eukaryotes that is involved in protection and stability of proteins (PMID: 16465618). About 85% of all human proteins and 68% of all yeast proteins are acetylated at their N-terminus (PMID: 21750686). Several proteins from prokaryotes and archaea are also modified by N-terminal acetylation. The majority of eukaryotic N-terminal-acetylation reactions occur through N-acetyltransferase enzymes or NAT’s (PMID: 30054468). These enzymes consist of three main oligomeric complexes NatA, NatB, and NatC, which are composed of at least a unique catalytic subunit and one unique ribosomal anchor. The substrate specificities of different NAT enzymes are mainly determined by the identities of the first two N-terminal residues of the target protein. The human NatA complex co-translationally acetylates N-termini that bear a small amino acid (A, S, T, C, and occasionally V and G) (PMID: 30054468). NatA also exists in a monomeric state and can post-translationally acetylate acidic N-termini residues (D-, E-). NatB and NatC acetylate N-terminal methionine with further specificity determined by the identity of the second amino acid. N-acetylated amino acids, such as N-acetylmethionine can be released by an N-acylpeptide hydrolase from peptides generated by proteolytic degradation (PMID: 16465618). In addition to the NAT enzymes and protein-based acetylation, N-acetylation of free methionine can also occur. In particular, N-Acetylmethionine can be biosynthesized from L-methionine and acetyl-CoA by the enzyme methionine N-acetyltransferase (EC 2.3.1.66). Excessive amounts N-acetyl amino acids including N-acetylmethionine (as well as N-acetylglycine, N-acetylserine, N-acetylglutamine, N-acetylglutamate, N-acetylalanine, N-acetylleucine and smaller amounts of N-acetylthreonine, N-acetylisoleucine, and N-acetylvaline) can be detected in the urine with individuals with acylase I deficiency, a genetic disorder (PMID: 16465618). Aminoacylase I is a soluble homodimeric zinc binding enzyme that catalyzes the formation of free aliphatic amino acids from N-acetylated precursors. In humans, Aminoacylase I is encoded by the aminoacylase 1 gene (ACY1) on chromosome 3p21 that consists of 15 exons (OMIM 609924). Individuals with aminoacylase I deficiency will experience convulsions, hearing loss and difficulty feeding (PMID: 16465618). ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. Many N-acetylamino acids, including N-acetylmethionine are classified as uremic toxins if present in high abundance in the serum or plasma (PMID: 26317986; PMID: 20613759). Uremic toxins are a diverse group of endogenously produced molecules that, if not properly cleared or eliminated by the kidneys, can cause kidney damage, cardiovascular disease and neurological deficits (PMID: 18287557).

Indole is an aromatic heterocyclic organic compound. It has a bicyclic structure, consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. The participation of the nitrogen lone electron pair in the aromatic ring means that indole is not a base, and it does not behave like a simple amine. Indole is a microbial metabolite and it can be produced by bacteria as a degradation product of the amino acid tryptophan. It occurs naturally in human feces and has an intense fecal smell. At very low concentrations, however, indole has a flowery smell and is a constituent of many flower scents (such as orange blossoms) and perfumes. As a volatile organic compound, indole has been identified as a fecal biomarker of Clostridium difficile infection (PMID: 30986230). Natural jasmine oil, used in the perfume industry, contains around 2.5% of indole. Indole also occurs in coal tar. Indole has been found to be produced in a number of bacterial genera including Alcaligenes, Aspergillus, Escherichia, and Pseudomonas (PMID: 23194589, 2310183, 9680309). Indole plays a role in bacterial biofilm formation, bacterial motility, bacterial virulence, plasmid stability, and antibiotic resistance. It also functions as an intercellular signalling molecule (PMID: 26115989). Recently, it was determined that the bacterial membrane-bound histidine sensor kinase (HK) known as CpxA acts as a bacterial indole sensor to facilitate signalling (PMID: 31164470). It has been found that decreased indole concentrations in the gut promote bacterial pathogenesis, while increased levels of indole in the gut decrease bacterial virulence gene expression (PMID: 31164470). As a result, enteric pathogens sense a gradient of indole concentrations in the gut to migrate to different niches and successfully establish an infection.

A racemate comprising equimolar amounts of N-acetyl-L-methionine and N-acetyl-D-methionine." []

Aesculetin, also known as cichorigenin or cichoriin aglucon, belongs to the class of organic compounds known as 6,7-dihydroxycoumarins. These are coumarins bearing two hydroxyl groups at positions 6 and 7 of the coumarin skeleton, respectively. Aesculetin is found, on average, in the highest concentration within sherries. Aesculetin has also been detected, but not quantified, in several different foods, such as horseradish, carrots, dandelions, grape wines, and highbush blueberries. This could make aesculetin a potential biomarker for the consumption of these foods.

A 3'-deoxyribonucleoside having guanine as the nucleobase." []

Anabasine is a pyridine and piperidine alkaloid found in the Tree Tobacco (Nicotiana glauca) plant, a close relative of the common tobacco plant (Nicotiana tabacum). It is a structural isomer of, and chemically similar to, nicotine. Its principal (historical) industrial use is as an insecticide. Anabasine is a nicotinic receptor agonist toxin and Cholinesterase inhibitor which acts upon the nicotinic acetylcholine receptors. Anabasine is an unstable yellow liquid which is succeptable to light, heat and moisture. It's decomposition products include Nitrogen oxides, carbon monoxide, irritating and toxic fumes and gases and carbon dioxide.

2'-O-Methyladenosine is a methylated adenine residue. 2'-O-Methyladenosine is a naturally occurring 2'-O-methylpurine nucleoside with long lasting hypotensive properties; resistance of 2'-O-methyladenosine against adenosine deaminase is thought to contribute to prolonged activity. 2'-O-Methyladenosine occurs in human fluids, and they increase in urines of untreated adenosine deaminase (ADA) deficient patients (OMIM 608958). (PMID: 9539952, 6980397).

7,8-dihydroxycoumarin is a hydroxycoumarin. Daphnetin is a natural product found in Sinacalia tangutica, Solanum tuberosum, and other organisms with data available.

Ginnalin B is a natural product found in Acer pycnanthum and Acer rubrum with data available.

This compound was observed experimentally in |FRAME: TAX-853| (unpublished data, X. Feng, University Medical Center Groningen).

2H-isoindole is an isoindole and a polycyclic heteroarene. It is a tautomer of a 1H-isoindole. Benzopyrroles with the nitrogen at the number two carbon, in contrast to INDOLES which have the nitrogen adjacent to the six-membered ring.

Nothofagin

Hydroquinone, also known as benzene-1,4-diol, is an aromatic organic compound which is a type of phenol, having the chemical formula C6H4(OH)2. Its chemical structure has two hydroxyl groups bonded to a benzene ring in a para position. Hydroquinone is commonly used as a biomarker for benzene exposure. The presence of hydroquinone in normal individuals stems mainly from direct dietary ingestion, catabolism of tyrosine and other substrates by gut bacteria, ingestion of arbutin-containing foods, cigarette smoking, and the use of some over-the-counter medicines. Hydroquinone is a white granular solid at room temperature and pressure. The hydroxyl groups of hydroquinone are quite weakly acidic. Hydroquinone can lose an H+ from one of the hydroxyls to form a monophenolate ion or lose an H+ from both to form a diphenolate ion. Hydroquinone has a variety of uses principally associated with its action as a reducing agent which is soluble in water. It is a major component of most photographic developers where, with the compound Metol, it reduces silver halides to elemental silver.

A dideoxynucleoside compound in which the 3'-hydroxy group on the sugar moiety has been replaced by an azido group. This modification prevents the formation of phosphodiester linkages which are needed for the completion of nucleic acid chains. The compound is a potent inhibitor of HIV replication, acting as a chain-terminator of viral DNA during reverse transcription. It improves immunologic function, partially reverses the HIV-induced neurological dysfunction, and improves certain other clinical abnormalities associated with AIDS. Its principal toxic effect is dose-dependent suppression of bone marrow, resulting in anemia and leukopenia. [PubChem]

4-amino-4-deoxychorismate, also known as adc, belongs to dicarboxylic acids and derivatives class of compounds. Those are organic compounds containing exactly two carboxylic acid groups. 4-amino-4-deoxychorismate is soluble (in water) and a weakly acidic compound (based on its pKa). 4-amino-4-deoxychorismate can be found in a number of food items such as chives, narrowleaf cattail, green vegetables, and chicory leaves, which makes 4-amino-4-deoxychorismate a potential biomarker for the consumption of these food products. 4-amino-4-deoxychorismate exists in E.coli (prokaryote) and yeast (eukaryote).

P-phenetidine is a colorless to dark red liquid. (NTP, 1992) 4-ethoxyaniline is an aromatic ether that is aniline in which the hydrogen at position 4 is replaced by an ethoxy group. It is a hydrolysis metabolite of phenacetin. It has a role as a drug metabolite. It is a substituted aniline, an aromatic ether and a primary amino compound. Used in the manufacture of acetophenetidin.

Protocatechuic acid 4-glucoside is a member of the class of compounds known as phenolic glycosides. Phenolic glycosides are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. Protocatechuic acid 4-glucoside is soluble (in water) and a weakly acidic compound (based on its pKa). Protocatechuic acid 4-glucoside can be found in a number of food items such as rosemary, jostaberry, rubus (blackberry, raspberry), and highbush blueberry, which makes protocatechuic acid 4-glucoside a potential biomarker for the consumption of these food products.

A monohydroxybenzoic acid that is 2,5-dihydroxybenzoic acid in which the phenolic hydrogen at position 2 has been replaced by a beta-D-glucosyl residue." []

Dimethyl maleate belongs to the class of organic compounds known as fatty acid esters. These are carboxylic ester derivatives of a fatty acid. Dimethyl maleate is the methyl ester of maleic acid and the cis-isomer of dimethyl fumarate. Dimethyl maleate is a commonly used thiol-alkylating agent and enjoys widespread use in many organic synthesis (e.g. as a dienophile for diene syntheses). In the production of plastics, pigments, pharmaceuticals, and agricultural products, dimethyl maleate is used as an additive and an intermediate. In the production of paints, adhesives, and copolymers, dimethyl maleate is used as an intermediate.

Isovaleric acid, is a natural fatty acid found in a wide variety of plants and essential oils. Isovaleric acid is clear colorless liquid that is sparingly soluble in water, but well soluble in most common organic solvents. It has been suggested that isovaleric acid from pilot whales, a species frequently consumed in the Faroe Islands, may be the unusual dietary factor in prolonged gestation in the population of the Faroe Islands. Previous studies suggested that was due to the high intake of n-3 polyunsaturated fatty acids has been, but fatty acid data for eicosapentaenoic acid (EPA) and docosahexanoic acid (DHA) in blood lipids of Faroese and Norwegians was reviewed in terms of the type of fish eaten (mostly lean white fish with DHA much greater than EPA); the popular lean fish, thus, probably provides too little EPA to produce a marked effect on human biochemistry (PMID 2646392). Isovaleric acid is found to be associated with isovaleric acidemia, which is an inborn error of metabolism.

Folic acid or folate, is a vitamin that belongs to the class of compounds known as pterins. Chemically, folate consists of three distinct chemical moieties linked together. A pterin (2-amino-4-hydroxy-pteridine) linked by a methylene bridge to a p-aminobenzoyl group that in turn is linked through an amide linkage to glutamic acid. It is a member of the vitamin B family and is primarily known as vitamin B9. Folate is required for the body to make DNA and RNA and metabolize amino acids necessary for cell division for the hematopoietic system. As humans cannot make folate, it is required in the diet, making it an essential nutrient (i.e. a vitamin). Folate occurs naturally in many foods including mushrooms, spinach, yeast, green leaves, and grasses (poaceae). Folic acid, being biochemically inactive, is converted to tetrahydrofolic acid and methyltetrahydrofolate by the enzyme known as dihydrofolate reductase. Tetrahydrofolate and methyltetrahydrofolate are transported across cells by receptor-mediated endocytosis where they are needed to maintain normal erythropoiesis, synthesize purine and thymidylate nucleic acids, interconvert amino acids and generate formic acid. Folic acid is used in the treatment and prevention of folate deficiencies and megaloblastic anemia. Folic acid is also used as a supplement by women during pregnancy to reduce the risk of neural tube defects (NTDs) in babies. Low levels in early pregnancy are believed to be the cause of more than half of babies born with NTDs (PMID: 28097362). Folic acid is also a microbial metabolite produced by Bifidobacterium and Lactobacillus (PMID: 22254078).

Theobromine, or 3,7-Dimethylxanthine, is the principle alkaloid in Theobroma cacao (the cacao bean) and other plants. A xanthine alkaloid that is used as a bronchodilator and as a vasodilator. It has a weaker diuretic activity than theophylline and is also a less powerful stimulant of smooth muscle. It has practically no stimulant effect on the central nervous system. It was formerly used as a diuretic and in the treatment of angina pectoris and hypertension. Theobromine is a bitter alkaloid of the methylxanthine family, which also includes the similar compounds theophylline and caffeine. Despite its name, the compound contains no bromine. Theobromine is derived from Theobroma, the genus of the cacao tree, which is composed of the Greek roots theo ("God") and broma ("food"), meaning "food of the gods". It is the primary alkaloid found in cocoa and chocolate, and is one of the causes for chocolate's mood-elevating effects. The amount found in chocolate is small enough that chocolate can be safely consumed by humans in large quantities, but animals that metabolize theobromine more slowly, such as cats and dogs, can easily consume enough chocolate to cause chocolate poisoning. Theobromine is a stimulant frequently confused with caffeine. Theobromine has very different effects on the human body from caffeine; it is a mild, lasting stimulant with a mood improving effect, whereas caffeine has a strong, immediate effect and increases stress. In medicine, it is used as a diuretic, vasodilator, and myocardial stimulant. There is a possible association between prostate cancer and theobromine. Theobromine is a contributing factor in acid reflux because it relaxes the esophageal sphincter muscle, allowing stomach acid access to the esophagus.