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Triosephosphate isomerase

Triosephosphate isomerase (TPI), also known as TIM, is a dimeric enzyme that catalyzes the reversible interconversion of the glycolytic intermediates dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde 3-phosphate (GAP), a crucial step in glycolysis that ensures the efficient utilization of both triose phosphates for downstream ATP production.^[1] This reaction, classified under EC 5.3.1.1, proceeds via a proton transfer mechanism involving a cis-enediolate intermediate, with the enzyme achieving near-diffusion-limited catalytic efficiency (k_cat ≈ 500 s⁻¹ for the forward reaction and ≈ 5,000 s⁻¹ for the reverse), making it one of the most highly evolved biocatalysts known.^[1] TPI is ubiquitously expressed in eukaryotes and prokaryotes, encoded by the TPI1 gene in humans, and plays a pivotal role in cellular energy metabolism by preventing the wasteful accumulation of DHAP, which could otherwise lead to side reactions like phosphate elimination.^[2] Structurally, TPI features a conserved (β/α)₈-barrel fold, often referred to as the TIM barrel, consisting of eight parallel β-strands surrounded by eight α-helices, with the active site located at the C-terminal end of the barrel within the dimer interface.^[1] Key catalytic residues include Glu165 (or Glu167 in some species) acting as the base for proton abstraction, His95 for stabilizing the enediolate oxyanion, and loops such as loop-6 (residues 166–176) that dynamically close over the substrate to exclude water and enhance specificity.^[1] This architecture not only facilitates the enzyme's high turnover but also underscores its evolutionary conservation, as the TIM barrel represents one of the most ancient and versatile protein folds in nature.^[1] Beyond its core glycolytic function, TPI exhibits moonlighting activities, including nuclear localization where it influences histone acetylation, cancer cell proliferation (e.g., in lung adenocarcinoma), and interactions with proteins like tau in neurodegenerative contexts or SUR1-KIR6.2 in insulin secretion regulation.^[2] Mutations in TPI1, particularly the prevalent Glu105Asp variant, cause triosephosphate isomerase deficiency (TPID), a rare autosomal recessive disorder characterized by chronic hemolytic anemia, progressive neuromuscular dysfunction, cardiomyopathy, and increased infection susceptibility, often leading to early childhood mortality due to impaired enzyme stability rather than loss of catalytic activity.^[2] These clinical manifestations highlight TPI's indispensable role in human physiology and its potential as a therapeutic target in metabolic and oncogenic diseases.

Biological Function

Role in Glycolysis

Triosephosphate isomerase (TPI), classified as EC 5.3.1.1, serves as the fifth enzyme in the glycolytic pathway, where it catalyzes the reversible isomerization of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde 3-phosphate (G3P).^[1] This step follows the cleavage of fructose-1,6-bisphosphate by aldolase, which produces one molecule each of DHAP and G3P, allowing TPI to interconvert them and ensure both triose phosphates can proceed through the lower half of glycolysis.^[3] The reaction equilibrium strongly favors DHAP, with an overall equilibrium constant (K_eq = [DHAP]/[G3P]) of approximately 22 at 25°C, resulting in about 96% DHAP and 4% G3P under equilibrium conditions.^[1] Despite this bias, the net flux in glycolysis is directed toward G3P production due to the rapid consumption of G3P by downstream enzymes, including glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which maintains low G3P levels and drives the isomerization forward.^[4] TPI is essential for efficient glycolysis across all domains of life, enabling the complete utilization of glucose-derived carbons by converting the DHAP produced from aldolase into G3P, thereby preventing a metabolic bottleneck where half of the carbons would otherwise accumulate as unused DHAP.^[5] Without TPI activity, glycolysis would be severely impaired, limiting ATP and NADH generation from the payoff phase and disrupting energy homeostasis in cells reliant on this pathway.^[3]

Involvement in Other Pathways

Triosephosphate isomerase (TPI) catalyzes the reversible interconversion of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P), enabling its participation in gluconeogenesis by facilitating the conversion of G3P to DHAP, which is subsequently utilized in the synthesis of fructose-1,6-bisphosphate by aldolase.^[6] This reversibility ensures efficient flux through the pathway under conditions requiring glucose production, such as fasting or intensive exercise.^[7] In parasitic organisms like trypanosomes, TPI exhibits elevated activity and distinct isoforms localized to glycosomes, rendering it a promising drug target due to the parasites' reliance on glycolysis for ATP in bloodstream forms.^[8] Inhibition of TPI disrupts energy metabolism selectively in these pathogens, as demonstrated by compounds like rabeprazole that reduce TPI activity and impair Trypanosoma cruzi viability without significantly affecting host enzymes.^[9] Similar targeting strategies have been explored for other parasites, including Plasmodium falciparum and trematodes such as Fasciola hepatica, exploiting structural differences in parasitic TPI.^[10]^[11] TPI plays minor roles in methylglyoxal detoxification by interconverting triose phosphates, thereby preventing the accumulation of DHAP, a precursor to the toxic metabolite methylglyoxal formed under high glycolytic flux or oxidative stress.^[12] Elevated methylglyoxal levels induce TPI expression, which reduces DHAP and mitigates downstream glycation damage to proteins and nucleic acids.^[13] Additionally, TPI contributes to cross-talk with the non-oxidative pentose phosphate pathway by equilibrating G3P, a key intermediate that feeds into transketolase and transaldolase reactions for nucleotide and NADPH production.^[14] Organism-specific variations in TPI function include moonlighting roles beyond catalysis, such as nuclear localization in response to cellular stress, where it influences gene expression and metabolic reprogramming.^[5] In eukaryotes, DHAP derived from TPI activity serves as a precursor for lipid signaling molecules, like glycerol-3-phosphate, which mediate stress responses including inflammation and apoptosis.^[15] These non-glycolytic functions highlight TPI's evolutionary adaptability across species.

Molecular Structure

Overall Architecture

Triosephosphate isomerase (TPI) is a homodimeric enzyme, with each subunit comprising approximately 250 amino acids and a molecular mass of about 27 kDa, resulting in a total molecular weight of roughly 54 kDa for the dimer.^[16]^[17] The core structure of each subunit features a canonical (βα)₈ TIM barrel fold, consisting of eight parallel β-strands arranged in a cylindrical core, each connected by an α-helix on the outer surface, forming a closed barrel approximately 30 Å in diameter.^[18] This architecture positions the substrate-binding site at the C-terminal end of the β-barrel, facilitating efficient catalysis.^[1] The TIM barrel fold was first identified in the crystal structure of chicken muscle TPI, determined in 1975 at 2.5 Å resolution (PDB: 1TIM), marking it as the inaugural example of this motif in structural biology.^[19]^[20] Since then, the TIM barrel has emerged as one of the most prevalent protein folds, adopted by over 10% of all known enzymes across diverse metabolic functions.^[21] TPI serves as the archetypal representative of this fold, with its robust and versatile architecture enabling high catalytic efficiency while maintaining structural integrity.^[22] The dimer interface of TPI is formed primarily by interactions from loops connecting the β-strands and α-helices of adjacent subunits, involving approximately 40 residues per subunit and stabilized by multiple salt bridges (e.g., involving conserved arginines and aspartates) and extensive hydrophobic contacts.^[23]^[24] Dimerization is essential for stability but does not mediate allosteric regulation or cooperativity between subunits, as the active sites are independent and the enzyme operates without inter-subunit communication influencing catalysis.^[1] Despite this conservation, TPI exhibits variations across species that reflect evolutionary adaptations. The fold and key structural elements are highly preserved, with, for example, about 90% sequence identity between human and chicken TPI, ensuring similar overall architecture. Prokaryotic TPIs, such as those from bacteria like Escherichia coli, retain the core TIM barrel with subunit lengths of approximately 250 amino acids.^[25] This structural conservation underscores TPI's fundamental role in glycolysis across all domains of life.

Active Site Features

The active site of triosephosphate isomerase (TIM) is located at the C-terminal end of the (β/α)₈ barrel domain, where it is lined by key residues contributed primarily from the loops connecting the β-strands.^[1] Prominent among these are Glu165, which functions as the nucleophilic base, and His95, which acts as an acid/base catalyst, both positioned to facilitate proton transfer during isomerization.^[26] These residues form a compact pocket with short, bifurcated hydrogen bonds that optimize geometry for catalysis.^[27] A hallmark feature is the flexible loop comprising residues 166–176, which undergoes rapid conformational changes to enclose the substrate upon binding.^[28] This loop closes over the active site in less than 1 millisecond, effectively excluding bulk water and enhancing reaction specificity by stabilizing the bound triose phosphate in a planar orientation.^[29] The motion involves a ~7 Å displacement at the loop tip, driven by hinge regions at its ends, and is essential for preventing premature release of intermediates.^[30] Substrate binding occurs through an array of hydrogen bonds that anchor the phosphate and carbonyl groups without requiring metal cofactors.^[1] For instance, residues such as Ser211, Tyr208, and Asn11 form interactions with the phosphate moiety, while His95 hydrogen-bonds to the carbonyl oxygen, positioning the substrate optimally for enolization.^[31] This non-metal-dependent architecture underscores TIM's efficiency as a "perfectly evolved" enzyme.^[32] High-resolution crystal structures have illuminated these features, including the human TIM structure (PDB: 1WYI) determined at 2.2 Å resolution in 2005, which reveals the open-loop conformation.^[33] Inhibitor-bound forms, such as those with 2-phosphoglycolate (PDB: 1HTI), mimic the enediol intermediate, showing how the closed loop and catalytic residues coordinate the transition state analogue.^[34] These structures confirm the site's dynamic adaptability while maintaining a TIM barrel scaffold that encloses the reaction.^[35]

Catalytic Mechanism

Reaction Pathway

Triosephosphate isomerase (TPI) catalyzes the reversible isomerization of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde 3-phosphate (G3P), a key step in glycolysis that interconverts the two triose phosphates.

\ce{HOCH2C(=O)CH2OPO3^{2-} ⇌ O=CHCH(OH)CH2OPO3^{2-}}

The standard free energy change for this equilibrium (ΔG°') is approximately +7.5 kJ/mol, favoring DHAP by a ratio of about 96:4 under physiological conditions.^[36] The mechanism proceeds via a suprafacial shift of a proton from C1 to C2 (or vice versa), mediated by an enediolate intermediate without the formation of a covalent enzyme-substrate adduct.^[37] This pathway lowers the activation barrier of the uncatalyzed reaction (estimated at ~107 kJ/mol) by approximately 52 kJ/mol through electrostatic stabilization and precise proton shuttling.^[38]^[39] In the forward direction (DHAP to G3P), the catalytic base Glu165 deprotonates the pro-R hydrogen at C1 of DHAP, generating the enediolate anion, while His95 acts as an acid to protonate the carbonyl oxygen, yielding a cis-enediol(ate) intermediate.^[40] The intermediate then rotates 180° around the C1–C2 bond to reorient the groups.^[37] Finally, Glu165 reprotonates C2 from the opposite face, and His95 deprotonates the oxygen at C1 (formerly the carbonyl oxygen), forming the aldehyde group of G3P. The reverse reaction (G3P to DHAP) follows a symmetric pathway, with Glu165 and His95 exchanging roles as base and acid.^[40] The overall process is stereospecific, retaining configuration at both C1 and C2.^[38] The critical roles of Glu165 and His95 have been confirmed through site-directed mutagenesis studies. Replacement of Glu165 with alanine (Glu165Ala) abolishes activity, resulting in a greater than 9000-fold reduction in k_cat, as the mutant lacks the essential base for proton abstraction.^[41] Likewise, substitution of His95 with glutamine (His95Gln) impairs electrophilic catalysis and intermediate stabilization, decreasing k_cat by 10⁴-fold.

Kinetic and Inhibitory Properties

Triosephosphate isomerase (TPI) exhibits diffusion-limited kinetics, with the specificity constant k_\text{cat}/K_\text{M} approaching $10^8 to $10^9 M^{-1} s^{-1}, indicating that the enzyme operates at the physical limit set by substrate diffusion rather than intrinsic chemical barriers. For the conversion of glyceraldehyde 3-phosphate (G3P) to dihydroxyacetone phosphate (DHAP), typical values include a turnover number k_\text{cat} of approximately 4300 s^{-1} and a Michaelis constant K_\text{M} of about 0.4 mM in chicken muscle TPI, while the reverse reaction shows a lower k_\text{cat} of around 430 s^{-1} and K_\text{M} of 0.97 mM. These parameters underscore TPI's efficiency in glycolysis, where every substrate encounter leads to productive catalysis.^[42]^[43] The thermodynamic profile of the reaction reveals a low activation free energy barrier \Delta G^\ddagger of approximately 12 kcal/mol, enabling the rapid interconversion without significant energetic hurdles beyond diffusion. This profile positions TPI as a "perfect enzyme," as described by Knowles, where evolutionary optimization has eliminated all internal commitments, leaving no room for further improvement in catalytic proficiency.^[30] TPI is subject to inhibition by various compounds that target its active site or conformational dynamics. Competitive inhibitors such as 2-phosphoglycolate, which mimics the enediol intermediate, bind with a dissociation constant K_i of about 20-26 \muM, effectively blocking substrate access. Non-competitive inhibitors like sulfate and arsenate ions interfere by binding near the active site and disrupting the flexible loop (residues 168-177) essential for catalysis, with inhibition constants in the millimolar range depending on pH and species.^[44] The enzyme's activity is pH-dependent, with an optimum around 7-8, reflecting the ionization states of key residues like His95 and Glu165 that facilitate proton transfer via the enediol intermediate. At this pH, the pKa of His95 is shifted downward (below 7) to enhance its role in stabilizing the transition state. Mesophilic TPIs maintain stability up to about 50°C, beyond which thermal denaturation disrupts the dimer interface and active site integrity.^[1]^[43]^[45] Species variations in TPI properties influence inhibitor sensitivity; for instance, TPIs from parasitic organisms like Trypanosoma and Giardia are more susceptible to oxidative inactivation due to exposed cysteines near the active site, guiding the design of selective antiparasitic agents that exploit this vulnerability without affecting human TPI.^[10]^[46]

Genetics and Expression

Gene Organization and Isoforms

The human TPI1 gene, located on chromosome 12p13.31, spans approximately 3.5 kb and consists of 7 exons, encoding the triosephosphate isomerase enzyme.^[47]^[48] The canonical transcript produces a mature protein of 249 amino acids, as documented in UniProt entry P60174.^[49] In humans, TPI1 exhibits limited isoform diversity, primarily through alternative promoter usage and splicing, resulting in three documented isoforms, though the canonical 249-amino-acid form predominates in cytosolic function.^[49] Rare splicing variants have been observed in some eukaryotes, such as those conferring plastid targeting signals in plants like Arabidopsis thaliana, enabling compartmentalized activity in chloroplasts.^[50] In contrast, prokaryotic homologs, including those from bacteria and archaea, typically lack such signal peptides, reflecting their cytoplasmic localization without organelle-specific targeting.^[51] Over 20 pathogenic variants in TPI1 have been identified, primarily missense mutations disrupting enzyme stability or dimerization.^[52] The most common is the Glu104Asp substitution (also denoted as Glu105Asp due to numbering variations; c.315G>C), which destabilizes the dimeric structure and accounts for approximately 80% of reported cases, with evidence of a founder effect in certain populations such as those of Northern European descent.^[53]^[54] Sequence conservation of triosephosphate isomerase is exceptionally high, with approximately 50% amino acid identity between bacterial and eukaryotic homologs, underscoring its ancient origin and essential role in glycolysis.^[51] This conservation facilitates codon optimization strategies in biotechnological expression systems, where synthetic TPI1 variants are engineered for enhanced production in heterologous hosts like yeast or E. coli.^[55]

Regulation and Evolutionary Conservation

Triosephosphate isomerase (TPI) expression is upregulated in proliferating cells, particularly under hypoxic conditions, where hypoxia-inducible factor 1α (HIF-1α) binds to the TPI1 promoter to enhance transcription, supporting increased glycolytic flux in low-oxygen environments. In cancer cells, post-translational modifications such as phosphorylation at serine residues (e.g., Ser21) further modulate TPI activity, promoting metabolic reprogramming and tumor progression. Recent research as of 2024 has identified additional layers of regulation, such as long non-coding RNA (lncRNA)-mediated upregulation of TPI1 promoting self-renewal and chemoresistance in cancer stem cells, and LDHA-induced histone lactylation enhancing TPI1 transcription in osteoarthritis development.^[56]^[57] Unlike many glycolytic enzymes, TPI lacks known allosteric regulators, with its activity primarily controlled by substrate availability within the glycolytic pathway, ensuring efficient interconversion of dihydroxyacetone phosphate and glyceraldehyde-3-phosphate without feedback inhibition. The TIM barrel fold of TPI represents one of the most ancient protein structures, tracing its origins to the last universal common ancestor (LUCA) approximately 4 billion years ago, as evidenced by its presence across all domains of life. Horizontal gene transfer has occurred in certain bacteria, such as in symbiotic associations, contributing to metabolic adaptations. In plants, paralogous TPI isoforms have evolved for specialized chloroplast functions, facilitating non-phosphorylating pathways in photosynthesis. Conservation is particularly stringent at the active site, where key residues like histidine, glutamate, and lysine remain invariant across species to preserve catalytic efficiency. Divergence is observed in peripheral loops, enabling adaptations such as enhanced thermostability in hyperthermophilic organisms; for instance, TPI from Thermotoga maritima maintains activity at 90°C due to rigidified loop structures that prevent unfolding.

Pathophysiology and Clinical Relevance

Enzyme Deficiency Disorders

Triosephosphate isomerase deficiency (TPID), also known as triose phosphate isomerase deficiency, is a rare autosomal recessive multisystem disorder caused by pathogenic variants in the TPI1 gene, which encodes the glycolytic enzyme triosephosphate isomerase. First described in 1965, the condition arises from severely impaired enzyme function, leading to disrupted glycolysis and accumulation of metabolic intermediates. With fewer than 100 cases reported worldwide, TPID has an estimated incidence of less than 1 in 5 million live births, reflecting its extreme rarity.^[58]^[59]^[60] Clinically, TPID manifests primarily in infancy with chronic nonspherocytic hemolytic anemia, often presenting at birth with jaundice and reticulocytosis due to premature destruction of red blood cells. Neurological symptoms emerge progressively around 6 months to 1 year of age, including hypotonia, muscle weakness, developmental delay, dystonia, and seizures, culminating in severe neurodegeneration. Additional features encompass cardiomyopathy, recurrent infections from impaired white blood cell function, and respiratory insufficiency, contributing to high mortality; most patients do not survive beyond early childhood, with death often occurring by age 5-8 years due to respiratory failure or infection in severe cases. The Glu105Asp (p.Glu105Asp) variant represents a common mutation, accounting for approximately 79% of alleles in northern European pedigrees.^[59]^[53]^[54] At the pathophysiological level, residual TPI activity is typically below 5% of normal, causing a metabolic bottleneck in glycolysis that elevates dihydroxyacetone phosphate (DHAP) levels up to 40-60-fold in erythrocytes and other tissues. This DHAP accumulation promotes oxidative stress through depletion of antioxidants like reduced glutathione and alpha-tocopherol, alongside increased production of the toxic byproduct methylglyoxal, which induces protein glycation, oxidation, and nitrosation. Tissue-specific effects are pronounced in erythrocytes, driving hemolytic anemia via altered membrane integrity and rigidity, and in neurons, where oxidative damage and reduced prolyl oligopeptidase activity exacerbate neurodegeneration.^[61]^[62]^[63] Diagnosis relies on biochemical assays demonstrating reduced TPI enzymatic activity (often 2-5% of normal) and elevated DHAP in erythrocytes or fibroblasts, with confirmation via targeted sequencing of the TPI1 gene to identify biallelic variants. Prenatal diagnosis is feasible through chorionic villus sampling or amniocentesis for at-risk pregnancies, enabling early detection of fetal enzyme deficiency. Animal models provide insights into disease mechanisms; complete Tpi1 knockout mice exhibit embryonic lethality, underscoring the enzyme's essential role, while partial deficiency models, such as those harboring the homozygous Glu105Asp mutation, recapitulate hemolytic anemia, shortened lifespan, and neuromuscular deficits observed in humans.^[59]^[64]

Therapeutic Targeting and Recent Research

Triosephosphate isomerase (TPI) has emerged as a promising drug target in parasitic diseases due to structural differences between parasite and human enzymes, particularly at the dimer interface and active site, allowing for species-selective inhibition. In trypanosomiasis caused by Trypanosoma species, inhibitors targeting TPI disrupt glycolysis in the parasite's glycosomes, a compartment absent in humans. A 2022 review highlights advances in designing benzothiazole, benzoxazole, and sulfhydryl-based inhibitors that bind to these species-specific pockets in T. cruzi and T. brucei TPI, achieving selective inactivation with minimal human enzyme disruption. For instance, phosphoglycolate analogs have been explored as transition-state mimics, showing potent inhibition of trypanosomal TPI (IC₅₀ values in the micromolar range) through coordination with catalytic residues like Glu-167, though in vivo efficacy remains under evaluation. Similar strategies apply to other parasites; a 2020 study on Fasciola hepatica TPI identified compound 187, a curcuminoid derivative, which reduced parasite load by 100% in vitro and protected mice from infection in vivo, reducing liver pathology by targeting non-conserved interface residues (K14, H96). A 2025 high-resolution crystal structure of F. hepatica TPI further supports drug targeting by highlighting species-specific interface residues.^[65] These findings underscore the potential of exploiting ~50% sequence divergence at parasite TPI interfaces for antiprotozoal therapies. In cancer, TPI overexpression supports the Warburg effect by enhancing glycolytic flux, making it a viable therapeutic target, particularly in tumors reliant on aerobic glycolysis. Elevated TPI levels have been documented in glioblastoma, correlating with aggressive phenotypes and poor prognosis, as TPI facilitates rapid interconversion of glycolytic intermediates to sustain ATP production under hypoxia. A 2023 analysis proposes targeting post-translationally modified TPI (e.g., deamidated or phosphorylated forms) in cancer cells, where such modifications accumulate selectively, unlike in normal tissues; thiol-reactive agents like rabeprazole inhibit deamidated TPI in breast cancer models, reducing proliferation by 50-70% in vitro without affecting wild-type enzyme. Knockdown studies via siRNA in pancreatic ductal adenocarcinoma cells demonstrate that TPI silencing impairs glycolysis and cell growth, sensitizing tumors to inhibitors like 2-deoxyglucose, though no phase I clinical trials specifically for TPI modulation were reported by 2023. These approaches highlight TPI's role in metabolic vulnerabilities, with ongoing research prioritizing PTM-specific inhibitors to avoid off-target effects in non-cancerous cells. Recent structural studies have advanced understanding of TPI dynamics, informing therapeutic design. High-resolution X-ray crystallography of human TPI mutants, such as the V154M variant associated with deficiency (PDB: 7SX1, released 2022), reveals altered loop flexibility near the active site, impacting substrate binding and stability. Computational modeling with AlphaFold2 has been applied to predict structures of TPI deficiency variants (e.g., E105D, common in triosephosphate isomerase deficiency or TPID), showing destabilization of the TIM barrel fold and increased aggregation propensity, which aids in silico screening for stabilizers. A 2023 study integrated AlphaFold predictions with molecular dynamics to model how these mutations disrupt enediolate intermediate formation, providing insights for variant-specific therapies. These tools address gaps in modeling rare TPID alleles, enabling prediction of clinical severity without exhaustive crystallography. Therapeutic prospects for TPID, a rare glycolytic enzymopathy causing hemolytic anemia and neurodegeneration, include gene editing and replacement strategies, though challenges persist. Preclinical explorations of CRISPR-Cas9 editing of the TPI1 gene aim to correct mutations like E105D in hematopoietic stem cells, with 2023 reviews suggesting potential for ex vivo therapy to restore enzyme activity and mitigate neuropathy. Enzyme replacement therapy faces significant hurdles due to the blood-brain barrier, which limits delivery to the central nervous system where neurodegeneration predominates; high-dose infusions achieve peripheral correction but yield <5% brain penetration in metabolic disease models. Supportive measures like ketogenic diets show promise in stabilizing mutant TPI, but curative options remain experimental. In 2025, high-throughput screening identified small-molecule stabilizers for TPID mutants, improving folding and activity by 2-3 fold in patient-derived fibroblasts, advancing potential therapies.^[66] High-throughput screening efforts post-2020 have identified novel TPI modulators to bridge therapeutic gaps. A 2021 phenotypic screen of ~100,000 compounds uncovered small-molecule stabilizers for TPID mutants, enhancing protein folding and activity by 2-3 fold in patient-derived fibroblasts, with leads advancing to hit-to-lead optimization. For parasitic targets, virtual HTS of parasite TPI structures (2022-2024) yielded ~10 novel scaffolds targeting interface pockets, including hybrid phosphoglycolate derivatives with sub-micromolar potency against T. brucei TPI and selectivity indices >100 over human enzyme. These screens, combining AlphaFold-predicted models with biochemical assays, accelerate lead discovery for both antiparasitic and anticancer applications, emphasizing the need for in vivo validation to translate findings into clinical candidates.

References

[1]
Triosephosphate isomerase: a highly evolved biocatalyst - PMC
Triosephosphate isomerase (TIM) is a glycolytic enzyme that very fast interconverts dihydroxyacetone phosphate and d-glyceraldehyde-3-phosphate.
[2]
Newly discovered roles of triosephosphate isomerase including ...
Jan 31, 2023 · Triosephosphate isomerase (TPI) is best known as a glycolytic enzyme that interconverts the 3-carbon sugars dihydroxyacetone phosphate (DHAP) ...
[3]
The Remarkable Role of Triosephosphate Isomerase in Diabetes ...
This work reviews the complex role of the enzyme triosephosphate isomerase (TIM) (EC 5.3.1.1) within the context of diabetes, a prevalent metabolic disorder ...
[4]
Triosephosphate Isomerase, Jeremy R. Knowles, and W. John Albery
The reaction is reversible, with the equilibrium constant close to unity (22 in the direction of DHAP for the total concentrations of DHAP and G3P; 340 for the ...
[5]
Newly discovered roles of triosephosphate isomerase including ...
Jan 31, 2023 · Loss of TPI function results in the recessive disease TPI Deficiency (TPI Df). Recently, numerous lines of evidence suggest the TPI protein has ...
[6]
Physiology, Gluconeogenesis - StatPearls - NCBI Bookshelf - NIH
Nov 13, 2023 · Triose phosphate isomerase isomerizes glyceraldehyde 3 ... Gluconeogenesis reactions are highly endergonic and, thus, easily reversible.<|separator|>
[7]
Gluconeogenesis - an overview | ScienceDirect Topics
... reactions are virtually reversible (phosphoglycerate mutase, phosphoglycerokinase, triose phosphate isomerase, and aldolase). The reaction of fructose-1,6 ...
[8]
Crystal structure of triosephosphate isomerase from Trypanosoma ...
cruzi (18), Trypanosoma brucei (14, 19), and Plasmodium falciparum (20) have been considered targets for drug design, respectively, against Chagas' disease, ...<|separator|>
[9]
Repurposing of rabeprazole as an anti- Trypanosoma cruzi drug that ...
This study demonstrates that rabeprazole inhibits both cell viability and triosephosphate isomerase activity in T. cruzi epimastigotes.
[10]
Novel and selective inactivators of Triosephosphate isomerase with ...
Feb 13, 2020 · Triosephosphate isomerase (TIM), an enzyme of the glycolytic pathway, has emerged as a useful drug target in many parasites, including Fasciola hepatica TIM ( ...
[11]
Characterization of stress and methylglyoxal inducible triose ... - NIH
Our result shows that increases in MG leads to the increase in TPI which results in decrease of DHAP and consequently decrease in the level of toxic MG.
[12]
Increased formation of methylglyoxal and protein glycation ...
Triosephosphate isomerase deficiency is associated with the accumulation of dihydroxyacetonephosphate (DHAP) to abnormally high levels, ...
[13]
Review Triosephosphate isomerase deficiency: New insights into an ...
TPI deficiency is an autosomal recessive multisystem genetic disease coupled with hemolytic anemia and neurological disorder frequently leading to death in ...
[14]
The Remarkable Role of Triosephosphate Isomerase in Diabetes ...
DHAP can influence mTORC1 activation through indirect metabolic signaling; abundant DHAP levels indicate abundant glucose availability, which cells interpret as ...
[15]
Triose Phosphate Isomerase - Proteopedia, life in 3D
Mar 8, 2020 · The TPI tertiary structure is the classic example of the "TIM barrel" fold (see image at left). The TPI structure is shown on the right (PDB ...
[16]
Journal Article Primary structure of human triosephosphate isomerase.
The enzyme is a dimeric molecule consisting of two identical polypeptide chains with 248 amino acid residues and a calculated subunit molecular mass of 26,750 ...Missing: kDa | Show results with:kDa
[17]
The TIM-barrel fold: a versatile framework for efficient enzymes
Mar 16, 2001 · The TIM-barrel fold is an eightfold repeat of (βα) units, with eight parallel β-strands covered by eight α-helices, and is the most common ...
[18]
Structure of chicken muscle triose phosphate isomerase ... - PubMed
Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 angstrom resolution using amino acid sequence data. Nature. 1975 ...Missing: crystal PDB 1TIM
[19]
1TIM: STRUCTURE OF TRIOSE PHOSPHATE ISOMERASE FROM ...
Atomic coordinates for triose phosphate isomerase from chicken muscle. · Total Structure Weight: 53.16 kDa · Atom Count: 3,740 · Modeled Residue Count: 494 ...Missing: crystal 1975
[20]
The TIM Barrel Architecture Facilitated the Early Evolution of Protein ...
Jan 5, 2016 · The triosephosphate isomerase (TIM) barrel protein fold is a structurally repetitive architecture that is present in approximately 10% of all enzymes.
[21]
TIM-Finder: A new method for identifying TIM-barrel proteins
Dec 14, 2009 · One of the top ten superfolds is the triosephosphate isomerase (TIM)-barrel fold (Figure 1A). It was first observed in triosephosphate isomerase ...
[22]
Side chain interactions within the triosephosphate isomerase dimer ...
... are a total of 42 residues involved in dimer interface, with 29 hydrogen bonds and 4 salt bridges stabilizing the interaction. The amino acid side ...
[23]
Interchain Salt Bridges | Hydrophobic Interfaces | Quaternary Structure
Introduction. Triose-phosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of two sugar triose phosphates, dihydroxyacetone ...
[24]
Crystal structure of recombinant human triosephosphate isomerase ...
The chicken and human enzymes have an RMS difference of 0.69 A for 484 equivalent residues and about 90% sequence identity. Complementary mutations ensure a ...
[25]
Triose-phosphate Isomerase (TIM) of the Psychrophilic ...
Jan 23, 1998 · The vTIM structure is very similar to the structure of eTIM, in agreement with the high sequence identity. The comparison of the structures of ...Experimental Procedures · Results And Discussion · X-Ray Structure
[26]
Enzyme Architecture: Amino Acid Side-Chains That Function To ...
Jun 4, 2018 · The active site is highly compact, with unusually short and bifurcated hydrogen bonds for both catalytic Glu-165 and His-95 residues. The ...
[27]
Optimal alignment for enzymatic proton transfer: Structure of ... - PNAS
The active site is highly compact, with unusually short and bifurcated hydrogen bonds for both catalytic Glu-165 and His-95 residues. The carboxylate oxygen of ...
[28]
The Loop Opening/Closing Motion of the Enzyme Triosephosphate ...
To explore the origin of the large-scale motion of triosephosphate isomerase's flexible loop (residues 166 to 176) at the active site, several simulation ...
[29]
Active site loop motion in triosephosphate isomerase - PubMed
Mar 18, 2003 · The motion of this loop was monitored using laser induced temperature-jump relaxation spectroscopy at nanosecond to millisecond time resolution.
[30]
Loop Motion in Triosephosphate Isomerase Is Not a Simple Open ...
Oct 26, 2018 · Crystal structures of TIM typically show an open or a closed conformation of loop 6, with the tip of the loop moving ∼7 Å between conformations.
[31]
Structure of Plasmodium falciparum Triose-phosphate Isomerase-2 ...
One of the conformations of Ser-211 makes strong hydrogen bonds with the residues at the tip of loop 6. The other residues, Tyr-208, Gly-209, and Gly-210, also ...
[32]
Triose-phosphate Isomerase (TIM) of the Psychrophilic ...
Neither cofactors nor metal ions are required in this reaction, and there is no evidence of allostery or cooperativity among the subunits. Figure 1. The ...
[33]
RCSB PDB - 1WYI: human triosephosphate isomerase of new crystal form
### Summary of 1WYI Structure
[34]
https://www.rcsb.org/structure/1HTI
[35]
Structure of a high-resolution crystal form of human triosephosphate ...
A high-resolution structure of human triosephosphate isomerase was obtained from crystals improved by means of the gel-tube method.
[36]
Substrate product equilibrium on a reversible enzyme ... - PNAS
There is no evidence for a bound form of the aldehyde GAP (i.e., no second carbonyl connected to a methylene) nor for an enediol(ate) triose phosphate (which ...
[37]
an analogue of the intermediate on the reaction pathway - PubMed
The glycolytic enzyme triosephosphate isomerase (TIM) catalyzes the interconversion of the three-carbon sugars dihydroxyacetone phosphate (DHAP) and ...
[38]
Perfection in enzyme catalysis: the energetics of triosephosphate ...
Knowles, and W. John Albery ... Triosephosphate Isomerase-Catalyzed Reaction: Verification of Methodology and Analysis of Reaction Mechanisms.
[39]
Triosephosphate isomerase - EMBL-EBI
TIM is a glycolytic enzyme that catalyses the central reaction in the glycolytic pathway, the interconversion of D-glyceraldehyde 3-phosphate (GAP) and ...
[40]
the role of the fully conserved glutamic acid 97 residue - PubMed
The control mutant, E165A, which lacks the key catalytic base, shows an approximately 9000-fold drop in activity. The integrity of the overall fold and ...
[41]
Free-energy profile for the reaction catalyzed by triosephosphate ...
Free-energy profile for the reaction catalyzed by triosephosphate ... Active-Site Glu165 Activation in Triosephosphate Isomerase and Its Deprotonation Kinetics.
[42]
[PDF] t. triose phosphate isomerase
The equilibrium constant between DHAP and GAP is 0.05 (Eq. T.2), so dihydroxyacetone phosphate is actually preferred at equilibrium. However, GAP is rapidly ...
[43]
Active Site Properties of Monomeric Triosephosphate Isomerase ...
Using site-directed mutagenesis, it is shown here that Lys 13 and His 95 are nevertheless essential for optimal catalysis by monoTIM: monoTIM-K13A is completely ...Missing: glutamine kcat
[44]
Probing the role of highly conserved residues in triosephosphate ...
Jul 23, 2015 · The four T75 mutants and Q64E behave like the wild-type enzyme in precipitating at temperatures > 50 °C. The Q64N mutant exhibits a thermal ...
[45]
Perturbation of the Dimer Interface of Triosephosphate Isomerase ...
Looking for molecules to eliminate the parasite, we have targeted a central enzyme of the glycolytic pathway: triosephosphate isomerase (TIM). The homodimeric ...
[46]
Entry - *190450 - TRIOSEPHOSPHATE ISOMERASE 1; TPI1 - OMIM
► Gene Structure Brown et al. (1985) found that the functional TPI1 gene spans 3.5 kb and contains 7 exons.Missing: size | Show results with:size
[47]
7167 - Gene ResultTPI1 triosephosphate isomerase 1 [ (human)]
TPI1 encodes an enzyme that catalyzes the isomerization of glyceraldehydes 3-phosphate and dihydroxy-acetone phosphate in glycolysis and gluconeogenesis.Missing: yeast prokaryotic terminal
[48]
TPI1 - Triosephosphate isomerase - Homo sapiens (Human) - UniProt
Oct 7, 2020 · Triosephosphate isomerase (TPI1) is a metabolic enzyme that catalyzes the interconversion between DHAP and G3P in glycolysis and ...
[49]
The Plastid Isoform of Triose Phosphate Isomerase Is Required for ...
An extensive query of the public Arabidopsis EST databases revealed two splice variants for this putative plastid TPI mRNA (At2g21170.1 and At2g21170.2).
[50]
Evidence that eukaryotic triosephosphate isomerase is of alpha ...
We have cloned and sequenced genes for triosephosphate isomerase (TPI) from the gamma-proteobacterium Francisella tularensis, the green non-sulfur bacterium ...Missing: conservation | Show results with:conservation
[51]
Triose Phosphate Isomerase Deficiency Is Caused by Altered ... - NIH
Dec 20, 2006 · Triosephosphate isomerase (TPI) deficiency is an autosomal recessive disorder caused by various mutations in the gene encoding the key glycolytic enzyme TPI.Plasmid Construction And... · Yeast Strains And... · Results<|control11|><|separator|>
[52]
Evidence for Founder Effect of the Glu104Asp Substitution ... - PubMed
The origin of the Glu104Asp mutation was defined by haplotype analysis using a novel G/A polymorphism at nucleotide 2898 of the TPI gene.Missing: Ashkenazi Jews
[53]
Child Neurology: Triosephosphate isomerase deficiency
Sep 1, 2020 · The pathogenic variant, Glu105Asp substitution (previously described as p.Glu104Asp), is the most frequent, accounting for approximately 80% of ...
[54]
Scalable protein production by Komagataella phaffii enabled by ...
Apr 20, 2024 · It could be worthwhile to consider altering the codon usage of the TPI1 gene or testing other stronger, weaker or differently regulated ...
[55]
https://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-024-02368-3
[56]
615512 - TRIOSEPHOSPHATE ISOMERASE DEFICIENCY; TPID
A number sign (#) is used with this entry because triosephosphate isomerase deficiency (TPID) is caused by homozygous or compound heterozygous mutation in the ...
[57]
Triosephosphate isomerase deficiency - Genetics - MedlinePlus
Aug 1, 2014 · Triosephosphate isomerase deficiency is a disorder characterized by a shortage of red blood cells (anemia), movement problems, increased susceptibility to ...Missing: Ureaplasma | Show results with:Ureaplasma
[58]
Triosephosphate isomerase deficiency: consequences of an ... - NIH
Triosephosphate isomerase (TPI) deficiency is a unique glycolytic enzymopathy coupled with neurodegeneration.
[59]
Increased formation of methylglyoxal and protein ... - PubMed
Triosephosphate isomerase deficiency is associated with the accumulation of dihydroxyacetonephosphate (DHAP) to abnormally high levels, ...Missing: pathophysiology | Show results with:pathophysiology
[60]
https://medlineplus.gov/genetics/condition/triosephosphate-isomerase-deficiency/
[61]
Murine model of triosephosphate isomerase deficiency with anemia ...
Nov 9, 2022 · Here we report a CRISPR generated mouse model of TPI Df. The model exhibits reduced longevity, anemia, and severe neurobehavioral deficits.