DeCure's autonomous Rare AI scientist is researching a drug-repurposing hypothesis for glycine N-methyltransferase deficiency — screening already-approved drugs against its 2-gene Open Targets disease module to publish open-access research. Research is fast; the path to publication is funded in milestone stages.
Disease moduleGlycine N-methyltransferase deficiency maps to a 2-gene Open Targets module — the target space DeCure's AI scientist screens approved drugs against.
DeCure.ai methodSignature reversal (LINCS) plus network proximity (STRING) rank already-approved drugs likely to perturb this module — the same engine that produces DeCure.ai's repurposing hypotheses.
Repurposing thesisScreening approved medicines against this disease module, then publishing the evidence for the strongest candidate. Known pharmacology and human exposure data make the first question sharper — they do not establish safety or efficacy in a new indication.
Research record
01
ResearchComing soon
Candidate research + dossier — target rationale, drug-repurposing thesis and evidence pack.proof: Published dossier + on-chain hash
02
ValidationComing soon
In-vitro biological validation at a contract research org (CRO).proof: CRO contract + in-vitro report
03
Peer review & paperComing soon
Peer-reviewed paper published open-access (preprint + journal).proof: DOI + open-access link + on-chain hash
Current lead
No approved-drug candidate for glycine n-methyltransferase deficiency is corroborated in the literature DeepSearch retrieved. Some conditions are managed with non-pharmacological care — a device, surgery or physical therapy — rather than a medicine; that may be the case here, or the literature we found may simply be too sparse yet to support a drug-repurposing angle.
Molecular view
glycine N-methyltransferase (GNMT) — GNMT is one of the genes genetically linked to this disease in Open Targets — shown as context, not as a drug target we're pursuing: no approved-drug candidate for this disease is yet corroborated in the literature we found.
Loading structure…
helix sheet apo structuredrag to rotate · scroll to zoom
RCSB Protein Data Bank · entry 2AZT · 2.7 Å · ligand none (apo structure). Experimental structure, not a prediction.
What the evidence adds up to
Glycine N-methyltransferase (GNMT) is a key regulatory enzyme in methyl group metabolism, abundant in liver, where it uses excess S-adenosylmethionine to methylate glycine to sarcosine. Its activity is inhibited when the natural folate ligand 5-methyltetrahydropteroylpentaglutamate is bound. In 1989, purified rat GNMT was phosphorylated in vitro by the catalytic subunit of cAMP-dependent protein kinase, increasing its activity approximately 2-fold; binding of the folate ligand first inhibited that phosphorylation. Freshly isolated rat hepatocytes incorporated 32P-labelled inorganic phosphate into the protein, and chemical analysis showed about 0.55 mol of phosphate per mol of GNMT subunit. In 2006, the crystal structure of rat GNMT complexed with 5-methyltetrahydrofolate showed two folate binding sites in the intersubunit areas of the tetramer, each formed primarily by N-terminal regions and other regions of paired subunits; binding experiments confirmed one tetramer binds two folate molecules. The N-terminal fragments must have conformational freedom for enzymatic reaction, and folate in that position provides a mechanism for inhibition.
In 1987, rat liver glycine methyltransferase was completely inactivated by 5,5'-dithiobis(2-nitrobenzoic acid); treatment with KCN reactivated it, yielding a 4-fold greater Km for glycine. Kinetics showed one cysteine residue involved. Reaction with iodoacetate led to partial inactivation, retaining about 22% of initial activity; carboxymethylation of Cys-282 was responsible for loss of activity. Cys-185, Cys-246, and Cys-262 were also modified upon prolonged incubation with iodoacetate. 5'-[p-(Fluorosulfonyl)benzoyl]adenosine inactivated the enzyme by forming one disulfide per subunit, with radioactivity distributed equally among Cys-185, Cys-246, Cys-262, and Cys-282 after reduction.
In 2018, three cases of nonketotic hyperglycinemia were reported from India, with two novel mutations in the aminomethyltransferase (AMT) gene: c.14_15insT (p.Ser6LysfsTer22) and c.259-2A>T, both adversely affecting the protein. Prenatal diagnosis in one family showed an unaffected fetus in the third pregnancy. AMT protein is pivotal for synthesis of 5,10-methylene tetrahydrofolate, the first metabolite in one-carbon metabolism that regulates DNA synthesis, repair, and methylation. A 2009 reply to a letter described that GNMT knockout mice, with complete absence of enzyme activity and protein, developed very high liver S-adenosylmethionine levels. At 3 months, male knockout mice had fatty liver and fibrosis; after 8 months, all knockout mice had hepatocellular carcinoma, resulting from overmethylation of RASSF1 and SOCS2 promoters. The Chen group’s GNMT knockout animals also developed hepatocellular carcinoma at about 17 months of age. In 1975, Kerr noted GNMT was not present in fast-growing liver hepatomas and was present at low levels in slower growing tumours.
What is still missing is any clinical trial or therapeutic intervention for GNMT deficiency in humans. No drug has been tested in patients with this condition. The animal models show a clear link between loss of GNMT, elevated S-adenosylmethionine, and liver cancer, but translating that into a treatment would require a trial design that can safely modulate methyl group metabolism, adequate funding for a rare disease, and patient stratification by genotype and disease stage.
Evidence
Retrieved by DeepSearch across 234,678,978 indexed works and resolved on OpenAlex — ranked by citations, including the results that did not work.
Journal of Biological Chemistry · 1989 · 49 citations · open access
Phosphorylation Modulates the Activity of Glycine N-Methyltransferase, a Folate Binding Protein
AbstractGlycine N-methyltransferase (EC 2.1.1.20) was recently identified as a major folate binding protein of rat liver cytosol (Wagner, C., and Cook, R. J. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 3631-3634). Activity of the enzyme is inhibited when the natural folate ligand, 5-methyltetrahydropteroylpentaglutamate (5-CH3-H4PteGlu5), is bound. It has been suggested that glycine N-methyltransferase plays a role in regulating the availability of methyl groups in the liver. Purified transferase was phosphorylated in vitro by the catalytic subunit of cAMP-dependent protein kinase. If 5-CH3-H4PteGlu5 was first bound to the transferase, phosphorylation was inhibited. Phosphorylation of glycine N-methyltransferase in vitro increased its activity approximately 2-fold. 5-CH3-H4PteGlu5 inhibited the activity of newly phosphorylated enzyme as well as native enzyme. Freshly isolated rat hepatocytes incorporated 32P-labeled inorganic phosphate into this folate binding protein. Chemical analysis of purified enzyme showed about 0.55 mol of phosphate present per mol of glycine N-methyltransferase subunit. These results indicate that phosphorylation of glycine N-methyltransferase may provide a mechanism for modulating the activity of this enzyme and support its role in regulating the availability of methyl groups.
Journal of Biological Chemistry · 2006 · 25 citations · open access
5-Methyltetrahydrofolate Is Bound in Intersubunit Areas of Rat Liver Folate-binding Protein Glycine N-Methyltransferase
AbstractGlycine N-methyltransferase (GNMT) is a key regulatory enzyme in methyl group metabolism. It is abundant in the liver, where it uses excess S-adenosylmethionine (AdoMet) to methylate glycine to N-methylglycine (sarcosine) and produces S-adenosylhomocysteine (AdoHcy), thereby controlling the methylating potential of the cell. GNMT also links utilization of preformed methyl groups, in the form of methionine, to their de novo synthesis, because it is inhibited by a specific form of folate, 5-methyltetrahydrofolate. Although the structure of the enzyme has been elucidated by x-ray crystallography of the apoenzyme and in the presence of the substrate, the location of the folate inhibitor in the tetrameric structure has not been identified. We report here for the first time the crystal structure of rat GNMT complexed with 5-methyltetrahydrofolate. In the GNMT-folate complex, two folate binding sites were located in the intersubunit areas of the tetramer. Each folate binding site is formed primarily by two 1-7 N-terminal regions of one pair of subunits and two 205-218 regions of the other pair of subunits. Both the pteridine and p-aminobenzoyl rings are located in the hydrophobic cavities formed by Tyr5, Leu207, and Met215 residues of all subunits. Binding experiments in solution also confirm that one GNMT tetramer binds two folate molecules. For the enzymatic reaction to take place, the N-terminal fragments of GNMT must have a significant degree of conformational freedom to provide access to the active sites. The presence of the folate in this position provides a mechanism for its inhibition.
Journal of Biological Chemistry · 1988 · 21 citations · open access
Rat liver glycine methyltransferase. Cooperative binding of S-adenosylmethionine and loss of cooperativity by removal of a short NH2-terminal segment.
AbstractRat liver glycine methyltransferase, a homotetramer, exhibits sigmoidal rate behavior with respect to S-adenosylmethionine (Ogawa, H., and Fujioka, M. (1982) J. Biol. Chem. 257, 3447-3452). The binding experiment shows that the sigmoidicity observed in initial velocity kinetics is explained by the cooperative binding of S-adenosylmethionine to the catalytic sites residing on each subunit. Limited proteolysis of glycine methyltransferase with trypsin in the presence of S-adenosylmethionine yields an enzyme lacking the NH2-terminal 8 residues. The proteolytically modified enzyme retains a tetrameric structure. The truncated enzyme shows no cooperativity with respect to S-adenosylmethionine binding and kinetics. It has values of Vmax and Km for glycine identical to those of the native enzyme, but a 3-fold lower [S]0.5 value for S-adenosylmethionine. The proteolytic modification is without effect on the circular dichroism and fluorescence spectra. Furthermore, the protein fluorescence of the modified enzyme is quenched upon addition of S-adenosylmethionine to the same extent as observed with the native enzyme. These results suggest that a short NH2-terminal segment, which lies outside the active site, is important for communication between subunits.
Function and reactivity of sulfhydryl groups of rat liver glycine methyltransferase
AbstractRat liver glycine methyltransferase is completely inactivated by 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB). Treatment of the inactivated enzyme with KCN results in a reactivated enzyme having values of Vmax and S0.5 for S-adenosyl-L-methionine comparable to those of the native enzyme and about a 4-fold greater Km value for glycine. Kinetics of inactivation and reactivation show that one cysteine residue is involved in this process. Reaction of the methyltransferase with iodoacetate leads to partial inactivation of the enzyme; about 22% of the initial activity is retained in the modified enzyme. The relationship between the loss of enzyme activity and the number of iodoacetate molecules incorporated and the sequence analysis of peptides containing the modified residues indicate that carboxymethylation of Cys-282 is responsible for loss of activity. The observations that the activity of the cyanylated glycine methyltransferase shows no decrease upon incubation with iodoacetate and, conversely, the residual activity associated with the iodoacetate-modified enzyme is not abolished by DTNB suggest that Cys-282 is also involved in the inactivation by DTNB. Besides this residue, Cys-185, Cys-246, and Cys-262 are modified upon prolonged incubation with iodoacetate. 5'-[p-(Fluorosulfonyl)benzoyl]adenosine (FSBA) inactivates glycine methyltransferase by forming 1 disulfide/subunit [Fujioka, M., & Ishiguro, Y. (1986) J. Biol. Chem. 261, 6346-6351]. Despite this stoichiometry, treatment of the FSBA-inactivated enzyme with unlabeled iodoacetate and then with iodo[14C]acetate after reduction with 2-mercaptoethanol and subsequent peptide analysis show that the incorporated radioactivity is distributed equally among Cys-185, Cys-246, Cys-262, and Cys-282.(ABSTRACT TRUNCATED AT 250 WORDS)
Journal of Pediatric Genetics · 2018 · 4 citations · open access
Identification of Two Novel Mutations in Aminomethyltransferase Gene in Cases of Glycine Encephalopathy
AbstractIn this study, we report three cases of nonketotic hyperglycinemia (NKHG) diagnosed biochemically and molecularly. Clinical exome analysis in two families revealed two novel mutations in the aminomethyltransferase (AMT) gene, that is, c.14_15insT (p.Ser6LysfsTer22) and c.259-2A > T, both of them adversely affecting the protein. This is the first report of AMT gene mutations in NKHG from India. Prenatal diagnosis in the first family showed an unaffected fetus in the third pregnancy. The role of AMT protein is pivotal for the synthesis of 5,10-methylene tetrahydrofolate, the first metabolite in one-carbon metabolism that regulates DNA synthesis, repair, and methylation.
AbstractThe letter by Chen and colleagues begins by questioning our findings in “Loss of the Glycine N-Methyltransferase Gene Leads to Steatosis and Hepatocellular Carcinoma in Mice,”1 and finishes by claiming their group is the first to demonstrate that GNMT (glycine N-methyltransferase) is a liver cancer susceptibility gene. Our group published a description of the preparation and properties of a mouse GNMT knockout in 2006.2 The strategy used was gene targeting and we replaced the first exon with part of the promoter region and intron 1 (1.90 kb) with the NEO gene (1.85 kb). In this article, we reported the complete absence of enzyme activity and enzyme protein by western blotting in 3-month-old knockout mouse livers using a polyclonal antibody. Because GNMT is a major consumer of methyl groups from S-adenosylmethionine (SAMe), this resulted in very high levels of liver SAMe. In 2007, Dr. Chen's group published an article in HEPATOLOGY titled “Glycine N-Methyltransferase−/− Mice Develop Chronic Hepatitis and Glycogen Storage Disease in the Liver”.3 They described a strategy similar to that we used to generate a GNMT knockout mouse. They replaced a fragment of the Gnmt gene containing exons 1-4 and part of exon 5 with the NEO gene. This article was concerned with the phenotype of their knockout mouse model as having glycogen storage disease as stated in the title of their article. They examined knockout male and female mice at 11 weeks of age and 9 months of age but made no reference to the development of liver cancer. In 2008, we published the HEPATOLOGY study that Dr. Chen takes issue with.1 At the age of 3 months, male knockout mice developed fatty liver and fibrosis; after 8 months, all knockout mice had hepatocellular carcinoma (HCC). HCC development was a result of overmethylation of RASSF1 and SOCS2 promoters. Then, after our discovery of HCC in our GNMT−/− animals, the Chen group found that their GNMT−/− animals also developed HCC at about 17 months of age.4 Most surprising in Dr. Chen's letter is the contention that our GNMT knockout mouse is not a complete knockout based on the dubious designation of a 51-nucleotide to 52-nucleotide sequence as a gene “promoter” with no documentation to justify this. They contend that our mouse model generates a protein truncated by 73 amino acids. Our use of polyclonal antibody showed no signal smaller than that of 32 kDa (intact GNMT) upon western blotting. Moreover, if such internal start sites were indeed functional, truncated forms of GNMT would be apparent in wild-type animals. In summary, we are confused by Dr. Chen's linkage of his claim to have been the first to identify GNMT as a liver cancer susceptibility gene to the erroneous claim of technical deficiencies in our work. It should be noted here that in 1975 Dr. Kerr pointed out that GNMT was not present in fast-growing liver hepatomas and was present at a low level in slower growing tumors.5, 6 Zigmund Luka*, M. Luz Martínez-Chantar , Shelly C. Lu , Conrad Wager* §, José M. Mato , * Department of Biochemistry, Vanderbilt University, Nashville, TN, CIC bioGUNE, CIBERehd, Technology Park of Bizkaia, Bizkaia, Spain, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University Southern California, Los Angeles, CA, § Tennessee Valley Department of Medical Affairs Medical Center, Nashville, TN.
AbstractIn this study, we report three cases of nonketotic hyperglycinemia (NKHG) diagnosed biochemically and molecularly. Clinical exome analysis in two families revealed two novel mutations in the aminomethyltransferase (AMT) gene, that is, c.14_15insT (p.Ser6LysfsTer22) and c.259-2A > T, both of them adversely affecting the protein. This is the first report of AMT gene mutations in NKHG from India. Prenatal diagnosis in the first family showed an unaffected fetus in the third pregnancy. The role of AMT protein is pivotal for the synthesis of 5,10-methylene tetrahydrofolate, the first metabolite in one-carbon metabolism that regulates DNA synthesis, repair, and methylation.
Specific staining of glycine <i>N</i>‐methyltransferase
AbstractGlycine N-methyltransferase from rabbit, human, rat and pig livers was separated by isoelectric focusing and a specific functional staining method was developed through the detection of sarcosine produced from the methylation of glycine. Isozyme patterns obtained in the various species tested differ both in the number of bands and apparent isoelectric points. These differences may explain the contradictory data on the subunit structure and glycosylation status of the enzyme reported so far.
Disease module: DeepOracle (Open Targets). Structures: RDKit from PubChem SMILES. Literature: retrieved by DeepSearch across 234,678,978 indexed works (targeted per-candidate search), resolved on OpenAlex.
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