DeCure for Pyruvate kinase deficiency of red cells
DeCure's autonomous Rare AI scientist is researching a drug-repurposing hypothesis for pyruvate kinase deficiency of red cells — screening already-approved drugs against its 3-gene Open Targets disease module to publish open-access research. Research is fast; the path to publication is funded in milestone stages.
Disease modulePyruvate kinase deficiency of red cells maps to a 3-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 pyruvate kinase deficiency of red cells 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
farnesyl diphosphate synthase (FDPS) — FDPS 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 1-hydroxy-2-imidazo[1,2-a]pyridin-3-ylethane-1,1-diyldrag to rotate · scroll to zoom
RCSB Protein Data Bank · entry 2VF6 · 2.1 Å · ligand (1-HYDROXY-2-IMIDAZO[1,2-A]PYRIDIN-3-YLETHANE-1,1-DIYL)BIS(PHOSPHONIC ACID) (M0N). Experimental structure, not a prediction.
What the evidence adds up to
In 15 patients with pyruvate kinase deficiency, ex vivo treatment with AG-348 (mitapivat) increased enzymatic activity in all patient cells after 24 hours, with a mean increase of 1.8-fold (range 1.2–3.4). ATP levels rose by a mean of 1.5-fold (range 1.0–2.2), similar to the 1.6-fold increase in control cells. PK thermostability, which was strongly reduced in deficient red cells, improved with AG-348, increasing residual activity 1.4- to more than 10-fold compared with vehicle-treated samples. The effect was minimal in cells with very low or undetectable PK-R protein levels. In half of the patients, treatment was associated with increased red cell deformability.
A second small molecule activator, AG-519, was tested in 32 healthy subjects across four dose cohorts (25 mg to 375 mg twice daily for 14 days). Dose-dependent increases in ATP and decreases in 2,3-diphosphoglycerate were observed, consistent with increased PK-R activity. The drug was well tolerated with no serious adverse events; one case of probable drug-induced grade 2 thrombocytopenia occurred at 375 mg and resolved rapidly. AG-519 did not show the aromatase inhibitory effects seen with AG-348.
Earlier work from 1976 reported that sulphydryl compounds produced a striking in vitro correction of qualitative and, in one case, quantitative PK defects. In vivo, correction was produced in two patients with clinical improvement in one. However, the authors concluded that the PK abnormality might be an epiphenomenon of a primary unknown defect involving red cell thiol groups, not the cause of the haemolytic anaemia. A 1994 study of PK deficiency in the Amish identified a point mutation (CGC to CAC at nucleotide 1436, Arg to His at residue 479) in the C domain of R-type PK, a region essential for intersubunit contact and allosteric regulation. Patient red cells showed increased ouabain-insensitive potassium efflux (142–145% of normal) not inhibited by furosemide.
Measurement of 3-phosphoglycerate (3PG) was described as a valuable diagnostic aid for functional PK deficiency, with reticulocytosis having minimal effect on 3PG levels compared with other glycolytic intermediates or PK activity itself. What remains missing is evidence from adequately powered, randomised trials in patients with PK deficiency that demonstrate sustained haematological improvement, reduction in haemolysis, or transfusion independence. The relationship between ex vivo or biomarker changes and clinical outcomes is not established. Patient stratification by residual PK protein level may be necessary, as suggested by the minimal response in cells with very low PK-R.
Evidence
Retrieved by DeepSearch across 234,678,978 indexed works and resolved on OpenAlex — ranked by citations, including the results that did not work.
Haematologica · 2020 · 80 citations · open access
AG-348 (Mitapivat), an allosteric activator of red blood cell pyruvate kinase, increases enzymatic activity, protein stability, and ATP levels over a broad range of PKLR genotypes
AbstractPyruvate kinase (PK) deficiency is a rare hereditary disorder affecting red cell (RBC) glycolysis, causing changes in metabolism including a deficiency in ATP. This affects red cell homeostasis, promoting premature removal of RBCs from the circulation. In this study we characterized and evaluated the effect of AG-348, an allosteric activator of PK that is currently in clinical trials for treatment of PK deficiency, on RBCs and erythroid precursors from PK-deficient patients. In 15 patients ex vivo treatment with AG-348 resulted in increased enzymatic activity in all patient cells after 24 hours (mean increase 1.8-fold, range 1.2-3.4). ATP levels increased (mean increase 1.5-fold, range 1.0-2.2) similar to control cells (mean increase 1.6-fold, range, 1.4-1.8). Generally, PK thermostability was strongly reduced in PK-deficient RBCs. Ex vivo treatment with AG-348 increased residual activity 1.4 to >10-fold than residual activity of vehicle-treated samples. Protein analyses suggests that a sufficient level of PK protein is required for cells to respond to AG-348 treatment ex-vivo, as treatment effects were minimal in patient cells with very low or undetectable levels of PK-R. In half of the patients, ex vivo treatment with AG-348 was associated with an increase in RBC deformability. These data support the hypothesis that drug intervention with AG-348 effectively upregulates PK enzymatic activity and increases stability in PK-deficient RBCs over a broad range of PKLR genotypes. The concomitant increase in ATP levels suggests that glycolytic pathway activity may be restored. AG-348 treatment may represent an attractive way to correct the underlying pathologies of PK deficiency. (AG-348 is currently in clinical trials for the treatment of PK deficiency. ClinicalTrials.gov: NCT02476916, NCT03853798, NCT03548220, NCT03559699).
Molecular abnormality of erythrocyte pyruvate kinase deficiency in the Amish
AbstractAbstract We describe the cellular and molecular biologic studies of the erythrocyte pyruvate kinase (PK) deficiency of the Amish deme in Pennsylvania. Nucleotide sequencing of the patient's PK gene showed a point mutation, CGC to CAC, corresponding to no. 1436 from the translational initiation site of the R-type PK (R-PK) mRNA, and it caused a single amino acid substitution from Arg to His at the 479th amino acid residue of the R-PK. The substituted Arg residue is located in the C domain of PK subunit, that is essential for both the intersubunit contact and the allosteric regulation. Because this enzyme shows the catalytic activity only as a dimer or tetramer, it is rational that the structural alteration would result in severe PK deficiency. To elucidate the effect of the PK deficiency on red blood cell (RBC) membrane, we performed the cellular studies of the patients' RBCs. Ouabain-insensitive K+ efflux was increased to 142% to 145% of normal controls and not inhibited by furosemide, as previously observed in HbSC disease RBCs.
British Journal of Haematology · 1976 · 35 citations
Effects of Sulphydryl Compounds on Abnormal Red Cell Pyruvate Kinase
AbstractThe effect of some sulphydryl compounds on two new variants of red cell pyruvate kinase (ATP: pyruvate phosphotransferase, PK) is reported. In vitro a striking correction has been obtained of both the qualitative and, in one case, the quantitative defect of red cell PK. In vivo, a correction of the qualitative and quantitative abnormalities has been produced in both patients, with clinical improvement of one of them. These findings, together with the unexpected results in respect to the functional properties of PK found in the affected members of the two families studied, suggest that the PK abnormality is not the cause of the haemolytic anaemia, but an epiphenomenon of a primary unknown defect that apparently involves the red cell thiol groups.
British Journal of Haematology · 1987 · 15 citations
Red cell 3‐phosphoglycerate level as a diagnostic aid in pyruvate kinase deficiency
AbstractA case of pyruvate kinase (PK) deficiency is described in which the diagnosis was aided by measurement of the 3-phosphoglycerate (3PG) concentration. Review of the literature on the levels of red cell metabolites in 52 families with PK deficiency confirmed that a rise in 3PG is a valuable indicator of a functional deficiency of PK. Estimation of 3PG is relatively easy (and accurate). Furthermore, reticulocytosis, which sometimes makes the diagnosis of PK deficiency more difficult, has minimal effect on the level of 3PG in comparison with all other glycolytic intermediates or PK activity.
American Journal of Hematology · 1981 · 14 citations
Thirteen cases of pyruvate kinase deficiency found in Japan
AbstractThirteen cases of pyruvate kinase (PK) deficiency, considered to be heterozygous for different PK mutants because of no consanguinities in their parents, were characterized by the International Committee for Standardization in Haematology (ICSH) recommended methods. These deficiency cases are named PK "Kagoshima," PK "Kyoto," PK "Takamatsu," PK "Abeno," PK "Kobe," PK "Marugame," PK "Hoenzaka," PK "Osaka," PK "Motomachi," PK "Gifu," PK "Hiroshima" PK "Matsumoto," and PK "Tama." The characteristics of mutant PK enzymes suggest that the cause of chronic hemolysis depends mainly on decreased affinity for phosphoenolpyruvate, thermolability, increased inhibition by adenosine triphosphate, and low activation by fructose-1, 6-diphosphate.
Safety, Tolerability, Pharmacokinetics and Pharmacodynamics of Multiple Doses of AG-519, an Allosteric Activator of Pyruvate Kinase-R, in Healthy Subjects
AbstractAbstract BACKGROUND Pyruvate kinase (PK) deficiency is a congenital hemolytic anemia caused by deficiency of the glycolytic enzyme red cell PK (PK-R) due to mutations in the PKLR gene. PK catalyzes the last enzymatic step in the glycolytic pathway and is the main source of adenosine triphosphate (ATP) production in red blood cells. PKLR mutations lead to defective proteins that are hypothesized to reduce ATP levels in red cells, leading to hemolysis. Small molecule allosteric activation of PK-R resulting in increases in ATP and decreases in 2,3-diphosphoglycerate (2,3-DPG) in healthy volunteers has been observed with an earlier molecule, AG-348, the first small molecule PK-R activator to enter clinical trials (Yang et al. EHA 2015, S138). AG-519 is the second small molecule PK-R activator to enter clinical trials. AG-519 is a potent, highly selective and orally bioavailable PK-R activator devoid of the aromatase inhibitory effects that were observed with AG-348. AIMS AG-519 is currently being tested in a randomized, double-blind, phase 1 study in healthy volunteers (NCT02630927), with the objective of identifying a safe and pharmacodynamically active dose and schedule to support potential ongoing development in patients with PK deficiency. Here we report the first 4 cohorts of the multiple ascending dose (MAD) phase of this study. The single ascending dose (SAD) phase of the study and the first two cohorts of the MAD phase of the study have been reported previously (Barbier et al. EHA 2016, P752). METHODS Healthymen and women (non-childbearing potential) aged 18-60 years who provided informed consent were eligible. The MAD phase of the study consisted of 5 dose cohorts. The dose levels administered were determined during interim data reviews of each completed MAD cohort, as well as data from completed SAD cohorts. At each dose level, 8 subjects were enrolled and randomized to receive AG-519 (n=6) or placebo (n=2) twice daily (BID; approximately every 12 hours) for 14 days. Safety assessments included adverse events (AEs), vital signs, electrocardiogram and clinical laboratory parameters. Serial blood samples were drawn to measure plasma concentrations of AG-519 and whole blood concentrations of 2,3-DPG and ATP for pharmacokinetic and pharmacodynamic (PD) assessments. RESULTS Data are available for 32 subjects enrolled across 4 dose cohorts in the MAD phase of the study: 8 subjects each in cohort 1 (125 mg BID), cohort 2 (375 mg BID), cohort 3 (25 mg BID), and cohort 4 (300 mg BID). Blinded safety reviews indicated that multiple doses up to 375 mg have been well tolerated with no serious AEs or dose-limiting toxicities reported to date. One case of probable drug-induced Grade 2 thrombocytopenia was previously reported in 1 subject in the 375 mg cohort; the event was rapidly reversible with no clinical sequelae. The protocol was amended to require daily monitoring of platelets in subsequent cohorts and no other subjects have developed thrombocytopenia during treatment. The preliminary analysis of free testosterone and estradiol confirmed the absence of aromatase inhibitory activity. AG-519 steady-state was reached the third day after the first dose based on trough concentration values. The clearance of AG-519 after multiple doses was similar to that observed after single doses in the SAD cohorts. Dose-dependent increases in ATP in blood (Figure 1) and decreases in 2,3-DPG in blood correlated with dose-dependent increases in exposure of AG-519, with a peak effect at or below 375 mg BID. ATP response at 25 mg appears to be greater than 50% of maximal response. Results from the fifth MAD cohort, which evaluated the PD results with 10 mg BID, will be presented. ATP = adenosine triphosphate; BID = twice daily CONCLUSION AG-519 is well tolerated in healthy subjects at doses ranging from 25 mg to 375 mg BID for 14 days. The robust dose-dependent changes in ATP and 2,3-DPG concentrations in blood from healthy volunteers are consistent with increased activity of PK-R, the expected PD effect of AG-519. These data support the hypothesis that AG-519 may be able to enhance glycolytic activity in red cells of patients with PK deficiency to address the underlying cause of the disease. Figure 1 Change of ATP concentration in blood from baseline Figure 1. Change of ATP concentration in blood from baseline Disclosures Barbier: Agios Pharmaceuticals, Inc.: Employment, Equity Ownership. Bodie:Agios Pharmaceuticals, Inc.: Employment, Equity Ownership. Connor:Agios Pharmaceuticals, Inc.: Employment, Equity Ownership. Merica:Agios Pharmaceuticals, Inc.: Employment, Equity Ownership. Kung:Agios Pharmaceuticals, Inc.: Employment, Equity Ownership. Le:Agios Pharmaceuticals, Inc.: Employment, Equity Ownership. Yang:Agios Pharmaceuticals, Inc.: Employment, Equity Ownership. Kosinski:Agios Pharmaceuticals, Inc.: Employment, Equity Ownership. Silverman:Agios Pharmaceuticals, Inc.: Employment, Equity Ownership. Yuan:Agios Pharmaceuticals, Inc.: Employment, Equity Ownership. Bowden:Agios Pharmaceuticals, Inc.: Employment, Equity Ownership. Cohen:Agios Pharmaceuticals, Inc.: Consultancy.
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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