Structural basis of substrate recognition in thiopurine s-methyltransferase

Thiopurine S-methyltransferase (TPMT) modulates the cytotoxic effects of thiopurine prodrugs such as 6-mercaptopurine by methylating them in a reaction using S-adenosyl- l-methionine as the donor. Patients with TPMT variant allozymes exhibit diminished levels of protein and/or enzyme activity and are at risk for thiopurine drug-induced toxicity. We have determined two crystal structures of murine TPMT, as a binary complex with the product S-adenosyl- l-homocysteine and as a ternary complex with S-adenosyl- l-homocysteine and the substrate 6-mercaptopurine, to 1.8 and 2.0 A resolution, respectively. Comparison of the structures reveals that an active site loop becomes ordered upon 6-mercaptopurine binding. The positions of the two ligands are consistent with the expected S N2 reaction mechanism. Arg147 and Arg221, the only polar amino acids near 6-mercaptopurine, are highlighted as possible participants in substrate deprotonation. To probe whether these residues are important for catalysis, point mutants were prepared in the human enzyme. Substitution of Arg152 (Arg147 in murine TPMT) with glutamic acid decreases V max and increases K m for 6-mercaptopurine but not K m for S-adenosyl- l-methionine. Substitution at this position with alanine or histidine and similar substitutions of Arg226 (Arg221 in murine TPMT) result in no effect on enzyme activity. The double mutant Arg152Ala/Arg226Ala exhibits a decreased V max and increased K m for 6-mercaptopurine. These observations suggest that either Arg152 or Arg226 may participate in some fashion in the TPMT reaction, with one residue compensating when the other is altered, and that Arg152 may interact with substrate more directly than Arg226, consistent with observations in the murine TPMT crystal structure.     

Thiopurine methyltransferase biochemical genetics: Human lymphocyte activity

The level of human erythrocyte (RBC) thiopurine methyltransferase (TPMT) activity is inherited as a monogenic trait. Experiments were performed to determine whether the level of TPMT activity in the human lymphocyte is regulated in parallel with RBC TPMT. Supernatants of lymphocyte homogenates contained TPMT activity. Lymphocyte TPMT activity was maximal at a reaction pH of 6.6. The apparent K _m value for 6-mercaptopurine, the thiopurine substrate for the reaction, was 8.1×10^–4 m, and the apparent K _m value for S-adenosyl-l-methionine, the methyl donor for the reaction, was 3.6×10^–6 m. The average TPMT activity in lymphocytes isolated from blood of 55 randomly selected subjects was 11.0±0.4 units/10⁹ cells (mean ± SE), with a range of from 4.8 to 17.7 units/10⁹ cells. There was a significant correlation of relative RBC with relative lymphocyte TPMT activity in blood samples from these 55 subjects, with a correlation coefficient of 0.563 (P<0.001). The correlation coefficient for RBC with platelet enyzme activities in these same subjects was also highly significant (r=0.680, P<0.001). Blood samples from four previously identified subjects who were homozygous for the allele TPMT ^L, subjects who lacked detectable RBC enzyme activity, also lacked detectable lymphocyte and platelet TPMT activities. These results were compatible with the conclusion that the genetic polymorphism which regulates RBC TPMT activity also regulates the level of human lymphocyte and platelet TPMT activities.Supported in part by NIH Grants GM 28157 and NS 11014. Dr. Weinshilboum is a Burroughs Wellcome Scholar in Clinical Pharmacology.     

Structural basis of allele variation of human thiopurine-S-methyltransferase

Human thiopurine S-methyltransferase (TPMT) exhibits considerable person-to-person variation in activity to thiopurine drugs. We have produced an N-terminal truncation of human TPMT protein, crystallized the protein in complex with the methyl donor product S-adenosyl-L-homocysteine, and determined the atomic structure to the resolution of 1.58 and 1.89 A, respectively, for the seleno-methionine incorporated and wild type proteins. The structure of TPMT indicates that the naturally occurring amino acid polymorphisms scatter throughout the structure, and that the amino acids whose alteration have the most influence on function are those that form intra-molecular stabilizing interactions (mainly van der Waals contacts). Furthermore, we have produced four TPMT mutant proteins containing variant alleles of TPMT*2, *3A, *3B, and *3C and examined the structure-function relationship of the mutant proteins based on their expression and solubility in bacteria and their thermostability profile.     

Four human thiopurine s-methyltransferase alleles severely affect protein structure and dynamics

Thiopurine S-methyltransferase (TPMT) metabolizes cytotoxic thiopurine drugs used in the treatment of leukemia and inflammatory bowel disease. TPMT is a major pharmacogenomic target with 23 alleles identified to date. Several of these alleles cause rapid protein degradation and/or aggregation, making it extremely difficult to study the structural impact of the TPMT polymorphisms experimentally. We, therefore, have performed multiple molecular dynamics simulations of the four most common alleles [TPMT*2 (A80P), *3A (A154T/Y240C), *3B (A154T) and *3C (Y240C)] to investigate the molecular mechanism of TPMT inactivation at an atomic level. The A80P polymorphism in TPMT*2 disrupts helix α3 bordering the active site, which breaks several salt-bridge interactions and opens up a large cleft in the protein. The A154T polymorphism is located within the co-substrate binding site. The larger threonine alters the packing of substrate-binding residues (P68, L69, Y166), increasing the solvent exposure of the polymorphic site. This packing rearrangement may account for the complete lack of activity in the A154T mutant. The Y240C polymorphism is located in β-strand 9, distant from the active site. Side-chain contacts between residue 240 and helix α8 are lost in TPMT*3C. Residues 154 and 240 in TPMT*3A are connected through a hydrogen-bonding network. The dual polymorphisms result in a flattened, slightly distorted protein structure and an increase in the thiopurine-binding site solvent accessibility. The two variants that undergo the most rapid degradation in vivo, TPMT*2 and *3A, are also the most deformed in the simulations.     

S-adenosylhomocysteine hydrolases as the primary target enzymes in androgen regulation of methylation complexes

tRNA methylation complexes consisting of S-adenosylmethionine (AdoMet) synthetase, tRNA methylases, and S-adenosylhomocysteine (AdoHcy) hydrolase have been prepared from rat Novikoff hepatoma cells. The existence of the ternary enzyme complex is supported by dissociation and reconstitution of the ternany tRNA methylation complexes. In rat prostate and testis, two isozymes each for AdoMet synthetase and AdoHcy hydrolase are detected. The K_m (methionine) values for the two AdoMet synthetases are 3.1 and 23.7 μm and the K_m (adenosine) values for the two AdoHcy hydrolases are 0.33 and 1.8 μm. Correspondingly, two groups of methylation complexes are detectable, sedimenting in a sucrose gradient as 7 S and 8 S. The 7 S complexes are composed of AdoMet synthetase and AdoHcy hydrolase with the higher K_m values, and the 8 S complexes are composed of the respective isozymes with the lower K_m values. tRNA methylation complexes belong to the 8 S group. In hormone-depleted rat prostates and testes following hypophysectomy, the specific activities of AdoMet synthetases, tRNA methylases, and AdoHcy hydrolases are decreased severely, but are restored promptly after administration of testosterone. Thus, methylation enzymes are responsive to the regulation by steroid hormone. AdoHcy hydrolases from hormone-depleted tissues are unstable, and ternary tRNA methylation complexes are easily dissociable into individual activities. The stability of AdoHcy hydrolases is markedly improved by testosterone, and the integrity of ternary tRNA methylation complexes is maintained in the presence of testosterone. These results suggest that AdoHcy hydrolases are the primary target enzymes in adrogen regulation of methylation complexes.     

Methylation of selenocysteine catalysed by thiopurine S-methyltransferase

Background

Methylation driven by thiopurine S-methylatransferase (TPMT) is crucial for deactivation of cytostatic and immunosuppressant thiopurines. Despite its remarkable integration into clinical practice, the endogenous function of TPMT is unknown.

Mercaptopurine pharmacogenetics: Monogenic inheritance of erythrocyte thiopurine methyltransferase activity

Thiopurine methyltransferase (TPMT) catalyzes thiopurine S-methylation, an important metabolic pathway for drugs such as 6-mercaptopurine. Erythrocyte (RBC) TPMT activity was measured in blood samples from 298 randomly selected subjects. Of the subjects, 88.6% were included in a subgroup with high enzyme activity (13.50 ± 1.86 U, mean ± SD), 11.1% were included in a subgroup with intermediate activity (7.20 ± 1.08 U), and 0.3% had undetectable activity. This distribution conforms to Hardy-Weinberg predictions for the autosomal codominant inheritance of a pair of alleles for low and high TPMT activity, TPMT^L and TPMT^H, with gene frequencies of .059 and .941, respectively. If RBC TPMT activity is inherited in an autosomal codominant fashion, then subjects homozygous for TPMT^H would have high enzyme activity, subjects heterozygous for the two alleles would have intermediate activity, and subjects homozygous for TPMT^L would have undetectable activity. The segregation of RBC TPMT activity among 215 first-degree relatives in 50 randomly selected families and among 35 members of two kindreds and one family selected because they included probands with undetectable RBC enzyme activity were also compatible with the autosomal codominant inheritance of RBC TPMT. For example, in eight matings between subjects with intermediate activity (presumed genotype TPMT^L TPMT^H) and subjects with high activity (presumed genotype TPMT^H TPMT^H), 47% (8/17) of the offspring had intermediate activity. This value is very similar to the 50% figure expected on the basis of autosomal codominant inheritance (χ²_[1] = .059). Further experiments are required to determine whether this genetic polymorphism for an important drug metabolizing enzyme may represent one factor in individual variations in sensitivity to thiopurines.     

A stereospecific colorimetric assay for (S,S)-adenosylmethionine quantification based on thiopurine methyltransferase-catalyzed thiol methylation

S-Adenosyl-L-methionine (AdoMet) which is biologically synthesized by AdoMet synthetase bears an S configuration at the sulfur atom. The chiral sulfonium spontaneously racemizes to form a mixture of S and R isomers of AdoMet under physiological conditions or normal storage conditions. The chirality of AdoMet greatly affects its activity; the R isomer is not accepted as a substrate for AdoMet-dependent methyltransferases. We report a stereospecific colorimetric assay for (S,S)-adenosylmethionine quantification based on an enzyme-coupled reaction in which (S,S)-AdoMet reacts with 2-nitro-5-thiobenzoic acid to form AdoHcy and 2-nitro-5-methylthiobenzoic acid. The transformation is catalyzed by recombinant human thiopurine S-methyltransferase (TPMT, EC 2.1.1.67) and is associated with a large spectral change at 410 nm. Accumulation of the S-adenosylhomocysteine (AdoHcy) product, a feedback inhibitor of TPMT, slows the assay. AdoHcy nucleosidase (EC 3.2.2.9) irreversibly cleaves AdoHcy to adenine and S-ribosylhomocysteine, significantly shortening the assay time to less than 10 min. The assay is linear from 5 to at least 60 microM (S,S)-AdoMet.     

A new hexanuclear rhenium cluster complex with six terminal acetate ligands: Synthesis, structure, and properties of K4[Re6S8(CH3COO)6]·8H2O

A room-temperature reaction between [Re₆S₈(OH)₆]⁴⁻ and acetic acid in an aqueous solution resulted in the substitution of all terminal hydroxo groups by acetate ligands, affording a new hexanuclear anionic rhenium cluster complex [Re₆S₈(CH₃COO)₆]⁴⁻. The complex was isolated as a potassium salt with the composition of K₄[Re₆S₈(CH₃COO)₆]·8H₂O (1) and characterized by X-ray single-crystal diffraction and elemental analyses, IR, ¹H NMR, UV-Vis, and luminescence spectroscopies.     

Sources of S-adenosyl-l-homocysteine background in measuring protein arginine N-methyltransferase activity using tandem mass spectrometry

S-Adenosyl-l-homocysteine (AdoHcy) background signal in reactions with protein arginine N-methyltransferase 1 is investigated using an ultrahigh-performance liquid chromatography tandem mass spectrometry assay that measures AdoHcy. We identify three sources of AdoHcy background: enzymatic automethylation, AdoHcy contamination in commercial S-adenosyl-l-methionine (AdoMet), and nonenzymatic pseudo-first-order formation of AdoHcy from AdoMet. We propose a potential mechanism for the nonenzymatic production of AdoHcy and illustrate strategies for mitigating background AdoHcy that can be applied to any assay.     

S-adenosyl-L-homocysteine hydrolase and methylation disorders: Yeast as a model system

S-adenosyl-L-methionine (AdoMet)-dependent methylation is central to the regulation of many biological processes: more than 50 AdoMet-dependent methyltransferases methylate a broad spectrum of cellular compounds including nucleic acids, proteins and lipids. Common to all AdoMet-dependent methyltransferase reactions is the release of the strong product inhibitor S-adenosyl-L-homocysteine (AdoHcy), as a by-product of the reaction. S-adenosyl-L-homocysteine hydrolase is the only eukaryotic enzyme capable of reversible AdoHcy hydrolysis to adenosine and homocysteine and, thus, relief from AdoHcy inhibition. Impaired S-adenosyl-L-homocysteine hydrolase activity in humans results in AdoHcy accumulation and severe pathological consequences. Hyperhomocysteinemia, which is characterized by elevated levels of homocysteine in blood, also exhibits a similar phenotype of AdoHcy accumulation due to the reversal of the direction of the S-adenosyl-L-homocysteine hydrolase reaction. Inhibition of S-adenosyl-L-homocysteine hydrolase is also linked to antiviral effects. In this review the advantages of yeast as an experimental system to understand pathologies associated with AdoHcy accumulation will be discussed.     

Capillary electrophoresis determination of thiopurine methyl transferase activity in erythrocytes

Thiopurine S-methyltransferase (TPMT) catalyzes methylation of thiopurine drugs (e.g. 6-mercaptopurine, azathioprine). Decreased activity of TPMT is associated with hematopoietic toxicity after administration of standard doses of the drugs. We developed capillary electrophoretic method for determination of TPMT enzyme activity in erythrocytes. Limit of quantification of the method is 1.5 μmol/L (S/N = 6). The recovery of 6-methylmercaptopurine was 87.5–94.8%, imprecision value (as CV, n = 10) was 1.68% (within-day) and 2.53% (between-day). Erythrocyte TPMT activities were measured in 60 healthy adult volunteers.     

New mono and dinuclear arene ruthenium chloro complexes containing ester substituents

The dinuclear arene ruthenium complexes [RuCl₂{C₆H₅(CH₂)₃OCO-p-C₆H₄-OC₈H₁₇}]₂ (1) and [RuCl₂{p-C₆H₄(CH₂COOCH₂CH₃)₂}]₂ (2) have been obtained by dehydrogenation of the corresponding cyclohexadiene derivative with ruthenium chloride hydrate. The single-crystal X-ray structure analysis of 2 shows the arene ligands to be involved in slipped-parallel π-π stacking interactions with neighbouring molecules, thus forming infinite chains along the b-axis. The dinuclear complexes 1 and 2 react with two equivalents of triphenylphosphine (PPh₃) to give in excellent yield the corresponding mononuclear phosphine complexes [RuCl₂{C₆H₅(CH₂)₃OCO-p-C₆H₄-OC₈H₁₇}(PPh₃)] (3) and [RuCl₂{p-C₆H₄(CH₂COOCH₂CH₃)₂}(PPh₃)] (4), respectively. The single-crystal X-ray structure analysis of 4 reveals the formation of a dimer through two C-H?Cl interactions in the solid state.     

Chiroptical properties of diastereomeric five-coordinate Pt(II)–olefin complexes. Molecular structure of [PtCl2{(S,S)-(E)-CNCHCHCN}(R,R)-{C6H5CH(CH3)N(CH3)CH2}2]·C6H6

The chiroptical properties of five-coordinate diastereomeric complexes of general formula [PtCl₂(R,R)-{C₆H₅CH(CH₃)N(CH₃)CH₂}₂{olefin}], with olefin ligands having electron-withdrawing substituents, have been investigated. The sign of CD bands in the 28 000–30 000 cm⁻¹ region appears to be correlated to the absolute configuration of the prochiral coordinated alkene. Single-crystal X-ray diffraction structure determination has been performed on the single diastereomer [PtCl₂(E-but-2-enedinitrile)(R,R)-{C₆H₅CH(CH₃)N(CH₃)CH₂}₂]· C₆H₆. The compound crystallizes in the monoclinic space group C2 with a = 17.842(2), b = 8.466(1), c = 10.464(1) Å, β = 109.34(1)°, Z = 2. The number of observed reflections was 1943 and the final R and R_w values were 0.020 and 0.028 respectively. Trigonal-bipyramidal geometry is observed around the Pt atom, with the two Cl atoms in axial positions. The unsaturated ligand lies in the equatorial plane disclosing S,S absolute configuration.     

Thiopurine methyltransferase: a review and a clinical pilot study

Thiopurine methyltransferase (TPMT) is an important enzyme in the metabolism of 6-mercaptopurine (6MP), which is used in the treatment of acute lymphoblastic leukemia (ALL). TPMT catalyzes the formation of methylthioinosine monophosphate (MetIMP), which is cytotoxic for cultured cell lines, and it plays a role in detoxification of 6MP. Population studies show a genetic polymorphism for TMPT with both high and low activity alleles. About 1 of 300 subjects is homozygous for the low activity. The function TPMT plays in detoxification or therapeutic efficacy of 6MP in vivo is not clear. In this article the genetic polymorphism of TPMT is reviewed and the contribution of TPMT to the cytotoxic action, or detoxification, of 6MP in children with ALL is discussed. Induction of TPMT activity has been described during the treatment for ALL. We performed a pilot study on the influence of high-dose 6MP infusions (1300 mg/m² in 24 h) on TPMT activity of peripheral blood mononuclear cells (pMNC) of eleven patients with ALL. The TPMT activities were in, or, above the normal range. There was no statistically significant difference between the TPMT activities before and after the 6MP infusions. MetIMP levels in pMNC increased during successive courses. This might be explained by TPMT induction, but other explanations are plausible as well. Twenty five percent of the TPMT assays failed, because less than the necessary 5·10⁶ pMNC could be isolated from the blood of leukopenic patients. Red blood cells can not be used for TPMT measurements, since transfusions are frequently required during the treatment with 6MP infusions. Therefore, the influence of high-dose 6MP infusions on TPMT activity can only be investigated further when a TMPT assay which requires less pMNC has been developed.     

Phenome-Wide Association Studies on a Quantitative Trait: Application to TPMT Enzyme Activity and Thiopurine Therapy in Pharmacogenomics

Phenome-Wide Association Studies (PheWAS) investigate whether genetic polymorphisms associated with a phenotype are also associated with other diagnoses. In this study, we have developed new methods to perform a PheWAS based on ICD-10 codes and biological test results, and to use a quantitative trait as the selection criterion. We tested our approach on thiopurine S-methyltransferase (TPMT) activity in patients treated by thiopurine drugs. We developed 2 aggregation methods for the ICD-10 codes: an ICD-10 hierarchy and a mapping to existing ICD-9-CM based PheWAS codes. Eleven biological test results were also analyzed using discretization algorithms. We applied these methods in patients having a TPMT activity assessment from the clinical data warehouse of a French academic hospital between January 2000 and July 2013. Data after initiation of thiopurine treatment were analyzed and patient groups were compared according to their TPMT activity level. A total of 442 patient records were analyzed representing 10,252 ICD-10 codes and 72,711 biological test results. The results from the ICD-9-CM based PheWAS codes and ICD-10 hierarchy codes were concordant. Cross-validation with the biological test results allowed us to validate the ICD phenotypes. Iron-deficiency anemia and diabetes mellitus were associated with a very high TPMT activity (p = 0.0004 and p = 0.0015, respectively). We describe here an original method to perform PheWAS on a quantitative trait using both ICD-10 diagnosis codes and biological test results to identify associated phenotypes. In the field of pharmacogenomics, PheWAS allow for the identification of new subgroups of patients who require personalized clinical and therapeutic management.     

Anagliptin,a potent dipeptidyl peptidase IV inhibitor: its single-crystal structure and enzyme interactions

Abstract

The single-crystal structure of anagliptin, N-[2-({2-[(2S)-2-cyanopyrrolidin-1-yl]-2-oxoethyl}amino)-2-methylpropyl]-2-methylpyrazolo[1,5-a]pyrimidine-6-carboxamide, was determined. Two independent molecules were held together by intermolecular hydrogen bonds, and the absolute configuration of the 2-cyanopyrrolidine ring delivered from l-prolinamide was confirmed to be S. The interactions of anagliptin with DPP-4 were clarified by the co-crystal structure solved at 2.85?Å resolution. Based on the structure determined by X-ray crystallography, the potency and selectivity of anagliptin were discussed, and an SAR study using anagliptin derivatives was performed.     

Förster resonance energy transfer measurements of cofactor‐dependent effects on protein arginine N‐methyltransferase homodimerization

Protein arginine N‐methyltransferase (PRMT) dimerization is required for methyl group transfer from the cofactor S‐adenosyl‐L ‐methionine (AdoMet) to arginine residues in protein substrates, forming S‐adenosyl‐L ‐homocysteine (AdoHcy) and methylarginine residues. In this study, we use Förster resonance energy transfer (FRET) to determine dissociation constant (K_D) values for dimerization of PRMT1 and PRMT6. By attaching monomeric Cerulean and Citrine fluorescent proteins to their N‐termini, fluorescent PRMTs are formed that exhibit similar enzyme kinetics to unconjugated PRMTs. These fluorescent proteins are used in FRET‐based binding studies in a multi‐well format. In the presence of AdoMet, fluorescent PRMT1 and PRMT6 exhibit 4‐ and 6‐fold lower dimerization K_D values, respectively, than in the presence of AdoHcy, suggesting that AdoMet promotes PRMT homodimerization in contrast to AdoHcy. We also find that the dimerization K_D values for PRMT1 in the presence of AdoMet or AdoHcy are, respectively, 6‐ and 10‐fold lower than the corresponding values for PRMT6. Considering that the affinity of PRMT6 for AdoHcy is 10‐fold higher than for AdoMet, PRMT6 function may be subject to cofactor‐dependent regulation in cells where the methylation potential (i.e., ratio of AdoMet to AdoHcy) is low. Since PRMT1 affinity for AdoMet and AdoHcy is similar, however, a low methylation potential may not affect PRMT1 function.     

Ab initio computational insight into the ion-pair SN2 reaction of lithium isothiocyanate and methyl fluoride in the gas phase and in acetone solution

The ion-pair S_N2 reaction LiNCS + CH₃F with two mechanisms, inversion and retention, was investigated at the MP2(full)/6-311+G**//HF/6-311+G** level in the gas phase and in acetone solution. All HF-optimized structures were confirmed by vibrational frequency analysis. Based on IRC analyses, eight possible reaction pathways in the title reaction are proposed. The inversion mechanism through a six-membered-ring transition-state structure is the most favorable. Methyl thiocyanate should form preferentially in the gas phase and the more stable methyl isothiocyanate will be the main product in CH₃COCH₃. The retardation of the reaction in CH₃COCH₃ solution was attributed to the differences in the solvation free energies in the separated reactants and transition structures. All of the theoretical results are consistent with the experiment.     

A copper(II) coordination polymer with alternating double EO-azido bridges and mixed EO-azido/alkoxo double bridges

A new one-dimensional (1D) copper(II) complex, [Cu₂(dpk · CH₂O)(N₃)₃]_n (dpk · CH₂OH = unimethylated diol of di-2-pyridyl ketone) (1), has been synthesized and characterized. X-ray crystal structure study reveals that 1 is composed of 1D copper(II) chain with alternating double EO-azido bridges and mixed EO-azido/alkoxo double bridges. The magnetic determination indicates that ferromagnetic interaction dominates in this new 1D S = 1/2 system.