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Deoxyinosine is a nucleoside that is formed when hypoxanthine is attached to a deoxyribose ring (also known as a ribofuranose) via a beta-N9-glycosidic bond. Deoxyinosine is found in DNA while inosine is found in RNA. Inosine is a nucleic acid important for RNA editing. Adenosine deaminase (ADA) catalyzes the conversion of adenosine and deoxyadenosine to inosine and deoxyinosine, respectively. ADA-deficient individuals suffer from severe combined immunodeficiency (SCID) and are unable to produce significant numbers of mature T or B lymphocytes. This occurs as a consequence of the accumulation of ADA substrates or their metabolites. Inosine is also an intermediate in a chain of purine nucleotides reactions required for muscle movements. Moreover, deoxyinosine is found to be associated with purine nucleoside phosphorylase (PNP) deficiency, which is an inborn error of metabolism.

Glutaric acid is a simple five-carbon linear dicarboxylic acid. Glutaric acid is naturally produced in the body during the metabolism of some amino acids, including lysine and tryptophan. Glutaric acid may cause irritation to the skin and eyes. When present in sufficiently high levels, glutaric acid can act as an acidogen and a metabotoxin. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Chronically high levels of glutaric acid are associated with at least three inborn errors of metabolism, including glutaric aciduria type I, malonyl-CoA decarboxylase deficiency, and glutaric aciduria type III. Glutaric aciduria type I (glutaric acidemia type I, glutaryl-CoA dehydrogenase deficiency, GA1, or GAT1) is an inherited disorder in which the body is unable to completely break down the amino acids lysine, hydroxylysine, and tryptophan due to a deficiency of mitochondrial glutaryl-CoA dehydrogenase (EC 1.3.99.7, GCDH). Excessive levels of their intermediate breakdown products (e.g. glutaric acid, glutaryl-CoA, 3-hydroxyglutaric acid, glutaconic acid) can accumulate and cause damage to the brain (and also other organs). Babies with glutaric acidemia type I are often born with unusually large heads (macrocephaly). Macrocephaly is amongst the earliest signs of GA1. GA1 also causes secondary carnitine deficiency because glutaric acid, like other organic acids, is detoxified by carnitine. Abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). These can progress to heart, liver, and kidney abnormalities, seizures, coma, and possibly death. These are also the characteristic symptoms of untreated glutaric aciduria. Many affected children with organic acidemias experience intellectual disability or delayed development. In adults, acidosis or acidemia is characterized by headaches, confusion, feeling tired, tremors, sleepiness, and seizures. Treatment of glutaric aciduria is mainly based on the restriction of lysine intake, supplementation of carnitine, and an intensification of therapy during intercurrent illnesses. The major principle of dietary treatment is to reduce the production of glutaric acid and 3-hydroxyglutaric acid by restriction of natural protein, in general, and of lysine, in particular (PMID: 17465389, 15505398). Glutaric acid has also been found in Escherichia (PMID: 30143200).

Methylsuccinic acid (CAS: 498-21-5) is a normal metabolite found in human fluids. Increased urinary levels of methylsuccinic acid (together with ethylmalonic acid) are the main biochemical measurable features in ethylmalonic encephalopathy (OMIM: 602473), a rare metabolic disorder with an autosomal recessive mode of inheritance that is clinically characterized by neuromotor delay, hyperlactic acidemia, recurrent petechiae, orthostatic acrocyanosis, and chronic diarrhea (PMID:12382164). The underlying biochemical defect involves isoleucine catabolism (PMID:9667231). Methylsuccinic acid levels were found to have decreased in the urine of animals under D-serine-induced nephrotoxicity (D-serine causes selective necrosis of the proximal straight tubules in the rat kidney) (PMID:15596249). Moreover, methylsuccinic acid is found to be associated with ethylmalonic encephalopathy, isovaleric acidemia, and medium-chain acyl-CoA dehydrogenase deficiency, which are also inborn errors of metabolism.

Dimethylmalonic acid is a dicarboxylic acid that is malonic acid in which both methylene hydrogens have been replaced by methyl groups. It has a role as a fatty acid synthesis inhibitor. Dimethylmalonic acid, also known as 2,2-dimethylmalonate or propanedioate, belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups. Dimethylmalonic acid is a very hydrophobic molecule, practically insoluble in water, and relatively neutral.

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.

A 5'-deoxyribonucleoside in which hypoxanthine is attached to 5-deoxyribofuranose via a beta-N(9)-glycosidic bond." []

(S)-2-Acetolactate is an intermediate in the biosynthesis of valine, leucine and isoleucine (KEGG ID C06010 ). It is the sixth to last step in the synthesis of protein and is converted from 2-hydroxy-3-methyl-2-oxobutanoate via the enzyme acetolactate synthase [EC:2.2.1.6]. It is then converted to 3-hydroxy-3-methyl-2-oxobutanoate via the enzyme ketol-acid reductoisomerase [EC:1.1.1.86].

A 5'-deoxyribonucleoside in which hypoxanthine is attached to 5-deoxyribofuranose via a beta-N(9)-glycosidic bond." []

Maltol, also known as E636 or fema 2656, belongs to the class of organic compounds known as pyranones and derivatives. Pyranones and derivatives are compounds containing a pyran ring which bears a ketone. Some synthetic derivatives of maltol, developed at the University of Urbino, showed limited in vitro antiproliferative activity towards cancer cells lines, perhaps inducing apoptosis in these cells. Maltol is a sweet, baked, and bread tasting compound. Maltol has been detected, but not quantified, in several different foods, such as milk and milk products, nuts, soy beans, pepper (c. annuum), and coffee and coffee products. Maltol's sweetness adds to the odor of freshly baked bread, and is used as a flavor enhancer (INS Number 636) in breads and cakes. Related to this property, maltol has been reported to greatly increase aluminum uptake in the body and to increase the oral bioavailability of gallium and iron. Maltol is a naturally occurring organic compound that is used primarily as a flavor enhancer. It is a white crystalline powder that is soluble in hot water, chloroform, and other polar solvents. Maltol is registered as a flavor component in the EU. Maltol, like related 3-hydroxy-4-pyrones such as kojic acid, binds to hard metal centers such as Fe3+, Ga3+, Al3+, and VO2+. It is known in the European E number food additive series as E636. Because it has the odor of cotton candy and caramel, maltol is used to impart a sweet aroma to fragrances.

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.

3'-deoxyinosine is a purine 3'-deoxyribonucleoside that is inosine in which the hydroxy group at position 3' is replaced by a hydrogen.

2-Oxovaleric acid is an alpha-ketoacid is a metabolite usually found in human biofluids. Ketoacids have been known to play an important part in the metabolism of valine, leucine, isoleucine. 2-Oxovaleric acid presence has been determined in human blood serum and urine in numerous scientific documents, although its origin remains unclear. (PMID: 11482739, 9869358, 3235498).

alpha-Ketoisovaleric acid is an abnormal metabolite that arises from the incomplete breakdown of branched-chain amino acids. alpha-Ketoisovaleric acid is a neurotoxin, an acidogen, and a metabotoxin. A neurotoxin causes damage to nerve cells and nerve tissues. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Chronically high levels of alpha-ketoisovaleric acid are associated with maple syrup urine disease. MSUD is a metabolic disorder caused by a deficiency of the branched-chain alpha-keto acid dehydrogenase complex (BCKDC), leading to a buildup of the branched-chain amino acids (leucine, isoleucine, and valine) and their toxic by-products (ketoacids) in the blood and urine. The symptoms of MSUD often show in infancy and lead to severe brain damage if untreated. MSUD may also present later depending on the severity of the disease. If left untreated in older individuals, during times of metabolic crisis, symptoms of the condition include uncharacteristically inappropriate, extreme, or erratic behaviour and moods, hallucinations, anorexia, weight loss, anemia, diarrhea, vomiting, dehydration, lethargy, oscillating hypertonia and hypotonia, ataxia, seizures, hypoglycemia, ketoacidosis, opisthotonus, pancreatitis, rapid neurological decline, and coma. In maple syrup urine disease, the brain concentration of branched-chain ketoacids can increase 10- to 20-fold. This leads to a depletion of glutamate and a consequent reduction in the concentration of brain glutamine, aspartate, alanine, and other amino acids. The result is a compromise of energy metabolism because of a failure of the malate-aspartate shuttle and a diminished rate of protein synthesis (PMID: 15930465). alpha-Ketoisovaleric acid is a keto-acid, which is a subclass of organic acids. Abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). These can progress to heart, liver, and kidney abnormalities, seizures, coma, and possibly death. These are also the characteristic symptoms of untreated MSUD. Many affected children with organic acidemias experience intellectual disability or delayed development.

Phloroglucinol is a benzenetriol. It is an organic compound that is used in the synthesis of pharmaceuticals and explosives. This molecule exists in two forms, or tautomers, 1,3,5-trihydroxybenzene, which has phenol-like, and 1,3,5-cyclohexanetrione (phloroglucin), which has ketone-like character. These two tautomers are in equilibrium. Phloroglucinol is a useful intermediate because it is polyfunctional. 1,3,5-Trihydroxybenzene has been found to be a metabolite in Pseudomonas (PMID: 15826166).

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.

Cytosine, also known as C, belongs to the class of organic compounds known as pyrimidones. Pyrimidones are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. Cytosine is also classified as a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at position 2). Cytosine is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine (uracil in RNA). The nucleoside of cytosine is cytidine. In Watson-Crick base pairing, cytosine forms three hydrogen bonds with guanine. Cytosine was discovered and named by Albrecht Kossel and Albert Neumann in 1894 when it was hydrolyzed from calf thymus tissues. Cytosine exists in all living species, ranging from bacteria to plants to humans. Within cells, cytosine can undergo several enzymatic reactions. It can be methylated into 5-methylcytosine by an enzyme called DNA methyltransferase (DNMT) or be methylated and hydroxylated to make 5-hydroxymethylcytosine. The DNA methyltransferase (DNMT) family of enzymes transfer a methyl group from S-adenosyl-l-methionine (SAM) to the 5’ carbon of cytosine in a molecule of DNA. High levels of cytosine can be found in the urine of individuals with severe combined immunodeficiency syndrome (SCID). Cytosine concentrations as high as (23-160 mmol/mol creatinine) were detected in SCID patients compared to normal levels of <2 mmol/mol creatinine (PMID: 262183).

2-aminonaphthalene belongs to the family of Naphthalenes. These are compounds containing a naphthalene moiety, which consists of two fused benzene rings.

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

Triacetate lactone is a member of 2-pyranones. It is a conjugate acid of a triacetate lactone oxoanion. 4-Hydroxy-6-methyl-2-pyrone is a natural product found in Rigidoporus sanguinolentus with data available.

Alanylleucine is a dipeptide composed of alanine and leucine. It is an incomplete breakdown product of protein digestion or protein catabolism. Some dipeptides are known to have physiological or cell-signaling effects although most are simply short-lived intermediates on their way to specific amino acid degradation pathways following further proteolysis.

In the lysine degradation IV pathway, glutarate semialdehyde reacts with NADP+ and H2O to produce glutarate, NADPH, and H+. In this pathway, glutarate semialdehyde is produced by the reaction between 5-aminopentanoate and 2-ketoglutarate, with L-glutamate as a byproduct. The enzyme responsible for this reaction is 5-aminovalerate aminotransferase. In the lysine degradation III pathway, glutarate semialdehyde reacts with NAD+ and H2O to produce glutarate and NADH. In this pathway, glutarate semialdehyde is produced by the reaction between 5-aminopentanoate and 2-ketoglutarate, with L-glutamate as a byproduct. The enzyme responsible for this reaction is 5-aminovalerate aminotransferase.

A naphthylamine that is naphthalene substituted by an amino group at position 1." []

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.