Cofactor Pyridoxal Research Articles

A facile synthesis of polyethyleneimine based fluorescent polymeric nanorods using vitamin B6 cofactor as cross-linker for ratiometric detection of doxorubicin.

Polyethyleneimine (PEI) based fluorescent polymeric nanorods with high quantum yield (87.21%) were synthesized by crosslinking and self-assembly of PEI by vitamin B6 cofactor pyridoxal 5'-phosphate (PLP). The fluorescent PEIPLP polymeric nanorods were employed for the ratiometric detection of doxorubicin (DOX). With the addition of DOX to the PEIPLP nanorods, the fluorescent intensity was decreased at 510nm and concomitantly enhanced at 590nm due to the fluorescence resonance energy transfer (FRET) process. The selective and specific ratiometric fluorescence response from the PEIPLP nanorods can be employed to detect DOX down to 10 nM. Thepractical utility of the PEIPLP nanorods was examined by detecting DOX in human serum.

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate.

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID, toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5'-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.IMPORTANCEArchaea are one of the three domains of life, classified as a phylogenetically distinct lineage. There is a paucity of known enzyme structures from organisms of this domain, and this is often exacerbated by characteristically difficult growth conditions and a lack of readily available molecular biology toolkits to study proteins in archaeal cells. As a result, there is a gap in knowledge concerning the mechanisms governing archaeal protein behavior and their impacts on both the environment and human health; case in point, the synthesis of the widely utilized cofactor pyridoxal 5'-phosphate (PLP; a vitamer of vitamin B6, which humans cannot produce). By leveraging the power of single-particle cryo-EM and map-to-primary sequence identification, we determine the native structure of PLP synthase from cellular lysate. Our workflow allows the (i) rapid examination of new or less characterized systems with minimal sample requirements and (ii) discovery of structural states inaccessible by recombinant expression.

PLP-Dependent Enzyme Methionine γ-Lyase: Insights into the Michaelis Complex from Molecular Dynamics and Free Energy Simulations.

Methionine γ-lyase (MGL) breaks down methionine, with the help of its cofactor pyridoxal-5'-phosphate (PLP), or vitamin B6. Methionine depletion is damaging for cancer cells but not normal cells, so MGL is of interest as a therapeutic protein. To increase our understanding and help engineer improved activity, we focused on the reactive, Michaelis complex between MGL, covalently bound PLP, and substrate Met. is not amenable to crystallography, as it proceeds to products. Experimental activity measurements helped exclude a mechanism that would bypass . We then used molecular dynamics and alchemical free energy simulations to elucidate its structure and dynamics. We showed that the PLP phosphate has a pKa strongly downshifted by the protein, whether Met is present or not. Met binding affects the structure surrounding the reactive atoms. With Met, the Schiff base linkage between PLP and a nearby lysine shifts from a zwitterionic, keto form to a neutral, enol form that makes it easier for Met to approach its labile, target atom. The Met ligand also stabilizes the correct orientation of the Schiff base, more strongly than in simulations without Met, and in agreement with structures in the Protein Data Bank, where the Schiff base orientation correlates with the presence or absence of a co-bound anion or substrate analogue in the active site. Overall, the Met ligand helps organize the active site for the enzyme reaction by reducing fluctuations and shifting protonation states and conformational populations.

Phosphoserine Aminotransferase Pathogenetic Variants in Serine Deficiency Disorders: A Functional Characterization.

In humans, the phosphorylated pathway (PP) converts the glycolytic intermediate D-3-phosphoglycerate (3-PG) into L-serine through the enzymes 3-phosphoglycerate dehydrogenase, phosphoserine aminotransferase (PSAT) and phosphoserine phosphatase. From the pathogenic point of view, the PP in the brain is particularly relevant, as genetic defects of any of the three enzymes are associated with a group of neurometabolic disorders known as serine deficiency disorders (SDDs). We recombinantly expressed and characterized eight variants of PSAT associated with SDDs and two non-SDD associated variants. We show that the pathogenetic mechanisms in SDDs are extremely diverse, including low affinity of the cofactor pyridoxal 5'-phosphate and thermal instability for S179L and G79W PSAT, loss of activity of the holo form for R342W PSAT, aggregation for D100A PSAT, increased Km for one of the substrates with invariant kcats for S43R PSAT, and a combination of increased Km and decreased kcat for C245R PSAT. Finally, we show that the flux through the in vitro reconstructed PP at physiological concentrations of substrates and enzymes is extremely sensitive to alterations of the functional properties of PSAT variants, confirming PSAT dysfunctions as a cause of SSDs.

Purification and characterization of tomato arginine decarboxylase and its inhibition by the bacterial small molecule phevamine A

Polyamines play essential roles in plant growth and survival. Arginine decarboxylase (ADC), which converts arginine to agmatine, catalyzes the first step in polyamine biosynthesis from arginine. However, few biochemical studies with purified plant ADCs have been conducted to evaluate their catalytic efficiency. Tomato genome encodes two arginine decarboxylases: SlADC1 and SlADC2, which are critical for growth, development, and immune responses against bacterial pathogens. We expressed and purified soluble SlADC1 as a recombinant protein fused with maltose-binding protein tag from E. coli Rosetta 2(DE3) cells. Using the purified fusion protein, we characterized the biochemical properties of SlADC1 in vitro and explored it as a target of the bacterial small molecule phevamine A. We confirmed that the activity of SlADC1 depends on the cofactor pyridoxal 5′-phosphate. SlADC1 is specific toward l-arginine and its kinetic parameters were measured using a liquid chromatography-mass spectrometry method. Phevamine A is a competitive inhibitor of SlADC1 and reduces the activity of SlADC1 at high micromolar concentrations. Our purification and biochemical characterization of SlADC1 sets the stage for inhibition studies of this enzyme.

Vitamin B6 Cofactor-Conjugated Fluorescent Polymeric Nanoparticles for Nanomolar Detection of Cu(II) and Fe(II) and Their Application in Edible Items

In the present study, vitamin B6 cofactor pyridoxal 5′-phosphate (PLP)-conjugated yellow-emitting polymeric nanoparticles (NPs) were synthesized, characterized, and applied for the sensing of metal ions. The branched polyethyleneimine (PEI) was cross-linked by adding formaldehyde and self-aggregated to form the cyan-blue-emitting PEIF NPs. The covalent conjugation of PLP over the surface of PEIF NPs via forming an imine linkage between the −NH2 group present over PEIF and the −CHO group of PLP formed the yellow-emitting PEIFPLP NPs. The spectroscopic (ultraviolet–visible (UV–vis), fluorescence, Fourier-transform infrared (FTIR), and X-ray photoelectron spectroscopy (XPS)) and high-resolution transmission electron microscopy (HRTEM) analyses were performed to characterize the PEIFPLP NPs. The PEIFPLP NPs showed good photostability, and the fluorescence emission at 552 nm (λex = 450 nm) was stable over a wide pH range from 2 to 12. In the metal ions’ sensing experiments, the fluorescence emission of PEIFPLP NPs was quenched by Cu(II) and Fe(II) among the other examined metal ions such as Ca(II), Mg(II), Cd(II), Mn(II), Co(II), Ni(II), Zn(II), Fe(III), Pt(II), Pb(II), Cr(III), Hg(II), Al(III), and Cu(I). The static quenching occurred due to the electron transfer from the excited PEIFPLP NPs to the partially filled d-orbital of Cu(II) and Fe(II). The PEIFPLP NPs showed good linearity between 2.4 × 10–6 to 1.9 × 10–5 and 7.4 × 10–6 to 2.2 × 10–5 M with a nanomolar detection limit of 17 and 31 nM for Cu(II) and Fe(II), respectively. Further, the analytical applicability of the developed PEIFPLP NPs was validated by quantifying Cu(II) and Fe(II) ions in fruits, vegetables, and environmental water samples.

Fluorescence Sensing of pH and p-Nitrophenol Using an AIEE Active Pyridoxal Derived Schiff Base.

An easy-to-prepare aggregation-induced emission enhancement (AIEE) active Schiff base NPY was synthesized by condensing vitamin B6 cofactor pyridoxal with 3-hydroxy-2-naphthoic hydrazide, and employed for the fluorescent sensing of pH and p-nitrophenol (p-NP). The AIEE phenomenon of NPY was investigated in mixed DMSO/H2O medium. The weakly yellow-fluorescent NPY (λem = 535nm) in pure DMSO turned to a bright cyan-fluorescent NPY (λem = 490nm) upon addition of poor solvent water. The DLS and SEM analyses supported the self-aggregation of NPY that restricted the intramolecular rotation and activated the excited state intramolecular proton transfer (ESIPT) process. The AIEE luminogen (AIEEgen) NPY containing 90% of water fraction (fwater) was employed for the fluorescent sensing of pH. AIEEgen NPY displays three distinct fluorescent pH windows: non-fluorescent below pH 3.0 and above pH 10.0, cyan fluorescent between pH 3.0 to 8.0, and yellow fluorescent between pH 8.0 to 10.0. AIEEgen NPY was also applied for the detection of nitroaromatics in HEPES buffer (10% DMSO, 10 mM, pH 7.0). The addition of p-NP selectively quenched the fluorescent intensity of AIEEgen NPY with an estimated detection limit of 1.73 µM. The analytical utility of AIEEgen NPY was examined by quantifying p-NP in different real water samples.

Self-sufficient biocatalysts constructed using chitin-based microspheres

The concomitant recycling of enzymes and co-factors is a big challenge in biocatalysis. In this study, co-immobilization of the enzyme and the co-factor pyridoxal 5′-phosphate was achieved using chitin-based microspheres as the support. Chitin/chitosan composite microspheres were prepared and then modified with polyethyleneimine. Three pyridoxal 5′-phosphate-independent enzymes were used to demonstrate that the self-sufficient biocatalysts based on chitin/chitosan composite microspheres and polyethyleneimine modified microspheres displayed good generalizability for high recycling efficiency of both enzyme and pyridoxal 5′-phosphate. Furthermore, the self-sufficient biocatalysts were applied in the continuous flow production of cadaverine and maintained good continuous catalysis without the exogenous addition of pyridoxal 5′-phosphate, suggesting that this co-immobilization platform shows promise for application in industrial biocatalysis.

Sodium glutamate and glutamic acid decarboxylase as alternative for classical chemical leavening in wheat (pan)cake batter systems

We investigated the use of sodium glutamate and glutamic acid decarboxylase (GAD) as alternative for classical chemical leavening systems (CCLS) in batter-derived bakery products. In the presence of its cofactor pyridoxal 5′-phosphate, GAD catalyses (sodium) glutamate conversion into carbon dioxide and γ-aminobutyric acid. Based on its high recombinant production yield in Escherichia coli and high in vitro specific activity, GAD from Streptococcus thermophilus was selected from a series of GADs for further research. The enzymatic leavening system (ELS) and CCLS were compared in terms of efficiency of carbon dioxide release in pancake batter at 50 °C. At this temperature, the ELS led to the highest leavening. In pancake baking, fast heating resulted in swift inactivation of the GAD, leading to reduced leavening. In cream cake baking, however, the slower heating rate allowed the ELS to exert its activity for a longer period under the conditions used, resulting in more leavening than with the CCLS. Sucrose affected the ELS neither in pancake batter nor in cake batter, but resulted in increased batter leavening due to the increased batter viscosity.

Pyridoxal derived red-emitting aggregates for the ratiometric sensing of pH and copper(II)

The research on aggregation-induced emission (AIE) continue to gain a bourgeoning interest for their extensive applications in different field including sensing and biosensing. In this study, the red-emitting rod-type aggregates L (λex = 375 nm, λem = 597 nm) was prepared facilely in two steps, i.e., the vitamin B6 cofactor pyridoxal was first condensed with the p-phenylenediamine followed by the DMSO solution of the orange precipitate formed was allowed to self-aggregate by adding poor solvent. Upon self-aggregation of L, the restriction of intramolecular motion and the ESIPT phenomenon play the key role in emitting red fluorescence at 597 nm. The pH dependent emission study of the aggregates L revealed three distinct pH windows: red-emitting between pH 5.4 to 9.1, green emitting above pH 9.9 and non-fluorescent in acidic pH. The aggregates L in HEPES buffer (5% DMSO, 10 mM, pH = 7.4) showed a selective turn-off response towards Cu2+ with a good linearity between 4.8 and 14.7 μM and a detection limit of 2.7 μM. The quenching was occurred due to the non-fluorescent complex formed between L and Cu2+ in the ground state. Addition of strong chelating agent EDTA reversed the quenched fluorescence of L. To improve the practical utility, the turn-off sensor L was converted into a ratiometric sensor for Cu2+ by adding an optimized amount of fluorescein (Fl) dye. The dual emitting L@Fl showed fluorescence quenching at 597 nm whereas concomitant enhancement at 515 nm because of the energy transfer mechanism. The developed ratiometric sensor showed improved detection limit of 0.72 μM. Finally, the practical utility of both L as turn-off sensor and L@Fl as ratiometric sensor was examined by quantifying Cu2+ concentration in different real samples.

Pyridoxal Derived AIEgen for Fluorescence Turn-off Sensing of Cu2+ and Fe2+ Ions and Fluorescence Imaging of Latent Fingerprints.

Schiff base 4-((E)-((E)-(2-hydroxybenzylidene)hydrazono)methyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol (HSP) was synthesized by condensing vitamin B6 cofactor pyridoxal with salicylaldehyde hydrazone, and characterized by standard spectroscopic techniques (FT-IR, 1H NMR, 13C NMR, and ESI-MS). The solution of HSP in DMSO/HEPES (10mM, pH = 7.4) mixed solvents with varying HEPES fractions (fw) from 0 to 95% showed aggregation-induced emission (AIE). The AIE active HSP in 95% HEPES gave intense fluorescent emission at 570nm was employed for the detection of metal ions. The fluorescence of HSP was quenched upon adding Cu2+ and Fe2+ ions. The association constant (Ka) of the Schiff base HSPwith Cu2+and Fe2+ions was estimated as 4.08 × 105M-1 and 1.23 × 105M-1, respectively by using the online analysis tool BindFit v0.5. The HSP showed the detection limit down to 1.75µM and 1.89µM for Cu2+ and Fe2+ ions, respectively. Further, the aggregates of HSP were applied to visualize latent fingerprints (LFPs) over a non-porous glass slide.

Crystal structure of Sphingobacterium multivorum serine palmitoyltransferase complexed with tris(hydroxymethyl)aminomethane.

Serine palmitoyltransferase (SPT) catalyses the first reaction in sphingolipid biosynthesis: the decarboxylative condensation of L-serine (L-Ser) and palmitoyl-CoA to form 3-ketodihydrosphingosine. SPT from Sphingobacterium multivorum has been isolated and its crystal structure in complex with L-Ser has been determined at 2.3 Å resolution (PDB entry 3a2b). However, the quality of the crystal was not good enough to judge the conformation of the cofactor molecule and the orientations of the side chains of the amino-acid residues in the enzyme active site. The crystal quality was improved by revision of the purification procedure and by optimization of both the crystallization procedure and the post-crystallization treatment conditions. Here, the crystal structure ofSPT complexed with tris(hydroxymethyl)aminomethane (Tris), a buffer component, was determined at 1.65 Å resolution. The protein crystallized at 20°C and diffraction data were collected from the crystals to a resolution of 1.65 Å. The crystal belonged to the tetragonal space group P41212, with unit-cell parameters a = b = 61.32, c = 208.57 Å. Analysis of the crystal structure revealed C4-C5-C5A-O4P (77°) and C5-C5A-O4P-P (-143°) torsion angles in the phosphate-group moiety of the cofactor pyridoxal 5'-phosphate (PLP) that are more reasonable than those observed in the previously reported crystal structure (14° and 151°, respectively). Furthermore, the clear electron density showing a Schiff-base linkage between PLP and the bulky artificial ligand Tris indicated exceptional flexibility of the active-site cavity of this enzyme. These findings open up the possibility for further study of the detailed mechanisms of substrate recognition and catalysis by this enzyme.

Rewiring of the protein–protein–metabolite interactome during the diauxic shift in yeast

In budding yeast Saccharomyces cerevisiae, the switch from aerobic fermentation to respiratory growth is separated by a period of growth arrest, known as the diauxic shift, accompanied by a significant metabolic rewiring, including the derepression of gluconeogenesis and the establishment of mitochondrial respiration. Previous studies reported hundreds of proteins and tens of metabolites accumulating differentially across the diauxic shift transition. To assess the differences in the protein–protein (PPIs) and protein–metabolite interactions (PMIs) yeast samples harvested in the glucose-utilizing, fermentative phase, ethanol-utilizing and early stationary respiratory phases were analysed using isothermal shift assay (iTSA) and a co-fractionation mass spectrometry approach, PROMIS. Whereas iTSA monitors changes in protein stability and is informative towards protein interaction status, PROMIS uses co-elution to delineate putative PPIs and PMIs. The resulting dataset comprises 1627 proteins and 247 metabolites, hundreds of proteins and tens of metabolites characterized by differential thermal stability and/or fractionation profile, constituting a novel resource to be mined for the regulatory PPIs and PMIs. The examples discussed here include (i) dissociation of the core and regulatory particle of the proteasome in the early stationary phase, (ii) the differential binding of a co-factor pyridoxal phosphate to the enzymes of amino acid metabolism and (iii) the putative, phase-specific interactions between proline-containing dipeptides and enzymes of central carbon metabolism.

MitoNEET's Reactivity of Lys55 toward Pyridoxal Phosphate Demonstrates its Activity as a Transaminase Enzyme.

MitoNEET is a [2Fe-2S] redox active mitochondrial protein belonging to the CDGSH iron-sulfur domain (CISD) family of proteins. MitoNEET has been implicated as a potential target for drug development to treat various disorders, including type-2 diabetes, cancer, and Parkinson's disease. However, the specific cellular function(s) for mitoNEET still remains to be fully elucidated, and this presents a significant roadblock in rational drug development. Here, we show that mitoNEET binds the enzymatic cofactor pyridoxal phosphate (PLP) specifically at only one of its 11 lysine residues, Lys55. Lys55 is part of the soluble portion of the protein and is in a hydrogen-bonding network with the histidine residue that ligates the [2Fe-2S] cluster. In the presence of mitoNEET, PLP catalyzes the transamination reaction of the amino acid cysteine and the alpha-keto acid 2-oxoglutarate to form 3-mercaptopyruvate and glutamate. This work identifies, for the first time, mitoNEET as an enzyme with cysteine transaminase activity.

Fluorescent turn-on sensing of albumin proteins (BSA and ovalbumin) using vitamin B6 cofactor derived Schiff base.

The detection of albumin proteins with high accuracy by facile analytical approaches is important for the diagnosis of various diseases. This manuscript introduced an easy-to-prepare Schiff base L by condensing vitamin B6 cofactor pyridoxal 5'-phosphate (PLP) with 2-aminothiophenol for the fluorescence turn-on sensing of bovine serum albumin (BSA) and ovalbumin (OVA). The weakly emissive L showed a significant fluorescence enhancement at 485 and 490 nm in the presence of OVA and BSA with an estimated sensitivity limit of 1.7 µM and 0.3 µM, respectively. The formation of protein-ligand complex restricted the free intramolecular rotation of L is expected to show the selective fluorescence enhancement. The molecular docking and molecular dynamics simulations were performed to examine the binding affinity and modes between BSA/OVA and L. The practical utility of L as a fluorescent turn-on sensor was validated by quantifying BSA and OVA in various real biological samples of milk, serum, egg white and urine with good recovery percentages.

Structure and Enzymatic Activity of an Intellectual Disability-Associated Ornithine Decarboxylase Variant, G84R.

Ornithine decarboxylase (ODC) is a rate-limiting enzyme for the synthesis of polyamines (PAs). PAs are required for proliferation, and increased ODC activity is associated with cancer and neural over-proliferation. ODC levels and activity are therefore tightly regulated, including through the ODC-specific inhibitor, antizyme AZ1. Recently, ODC G84R has been reported as a partial loss-of-function variant that is associated with intellectual disability and seizures. However, G84 is distant from both the catalytic center and the ODC homodimerization interface. To understand how G84R modulates ODC activity, we have determined the crystal structure of ODC G84R in both the presence and the absence of the cofactor pyridoxal 5-phosphate. The structures show that the replacement of G84 by arginine leads to hydrogen bond formation of R84 with F420, the last residue of the ODC C-terminal helix, a structural element that is involved in the AZ1-mediated proteasomal degradation of ODC. In contrast, the catalytic center is essentially indistinguishable from that of wildtype ODC. We therefore reanalyzed the catalytic activity of ODC G84R and found that it is rescued when the protein is purified in the presence of a reducing agent to mimic the reducing environment of the cytoplasm. This suggests that R84 may exert its neurological effects not through reducing ODC catalytic activity but through misregulation of its AZ1-mediated proteasomal degradation.

Fluorescent pH sensing and MnO2 nanosphere directed turn-on sensing of glutathione using pyridoxal 5′-phosphate modified polydopamine nanoparticles

The water-soluble fluorescent organic nanoparticles (PDAPLP NPs) was synthesized by the oxidation of dopamine in the presence of vitamin B6 cofactor pyridoxal 5′-phosphate (PLP). The fluorescent intensity of PDAPLP NPs was quenched in the presence of MnO2 nanospheres due to the energy transfer process occurred from the PDAPLP NPs to MnO2 nanospheres. The fluorescence was restored upon addition of GSH to the PDAPLP_MnO2 nanocomposite due to the redox transformation of Mn(IV) to Mn(II). The fluorescence turn-on response allowed to detect GSH down to 0.31 µM. The developed nanoprobing approach was fast (response time < 2 min), simple and highly selective. The practical utility of the PDAPLP_MnO2 nanoprobe was validated by quantifying GSH in real saliva samples. In addition, the PDAPLP NPs was applied for the fluorescence sensing of pH. The cyan-blue fluorescent PDAPLP NPs between pH 2.0 to 7.0 turned to green-fluorescent above pH 7.0 in the basic pH.

Pyridoxamine 5’-Phosphate Oxidase Deficiency: A Potentially Treatable Epileptic Encephalopathy

Pyridoxal phosphate-responsive neonatal epileptic encephalopathy due to pyridoxamine-5-primephosphate oxidase deficiency is a rare cause of epileptic encephalopathy. A neonate with this condition presents early in life with refractory seizures which does not respond to conventional anti-epileptic medications, depressed level of consciousness, and severe psychomotor retardation if left untreated. Early initiation of active cofactor pyridoxal-5’-phophate can be curative. We are describing a rare neurometabolic condition; the first case in the Kingdom of Bahrain to the best of our knowledge. Keywords: Pyridoxal-5’-phosphate, pyridoxamine 5’-phosphate oxidase, pyridoxine dependent epilepsy, epileptic encephalopathy, neonatal seizure

Vitamin B6 cofactor-directed fluorescent “turn-on” detection of alkaline-phosphatase activity using bovine serum albumin-functionalized Mn–ZnS quantum dots

Alkaline phosphatase (ALP) activity was detected using bovine serum albumin (BSA)-functionalized manganese-doped zinc sulfide (Mn–ZnS) quantum dots (QDs), and the phosphate substrate was the vitamin-B6 cofactor pyridoxal 5′-phosphate (PLP).

(+)-Sesamin, a sesame lignan, is a potent inhibitor of gut bacterial tryptophan indole-lyase that is a key enzyme in chronic kidney disease pathogenesis

The progression of chronic kidney disease (CKD) increases the risks of cardiovascular morbidity and end-stage kidney disease. Indoxyl sulfate (IS), which is derived from dietary l-tryptophan by the action of bacterial l-tryptophan indole-lyase (TIL) in the gut, serves as a uremic toxin that exacerbates CKD-related kidney disorder. A mouse model previously showed that inhibition of TIL by 2-aza-l-tyrosine effectively reduced the plasma IS level, causing the recovery of renal damage. In this study, we found that (+)-sesamin and related lignans, which occur abundantly in sesame seeds, inhibit intestinal bacteria TILs. Kinetic studies revealed that (+)-sesamin and sesamol competitively inhibited Escherichia coli TIL (EcTIL) with Ki values of 7 μM and 14 μM, respectively. These Ki values were smaller than that of 2-aza-l-tyrosine (143 μM). Molecular docking simulation of (+)-sesamin- (or sesamol-)binding to EcTIL predicted that these inhibitors potentially bind near the active site of EcTIL, where the cofactor pyridoxal 5′-phosphate is bound, consistent with the kinetic results. (+)-Sesamin is a phytochemical with a long history of consumption and is generally regarded as safe. Hence, dietary supplementation of (+)-sesamin encapsulated in enteric capsules could be a promising mechanism-based strategy to prevent CKD progression. Moreover, the present findings would provide a new structural basis for designing more potent TIL inhibitors for the development of mechanism-based therapeutic drugs to treat CKD.