1
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Shanker VR, Bruun TU, Hie BL, Kim PS. Inverse folding of protein complexes with a structure-informed language model enables unsupervised antibody evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572475. [PMID: 38187780 PMCID: PMC10769282 DOI: 10.1101/2023.12.19.572475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Large language models trained on sequence information alone are capable of learning high level principles of protein design. However, beyond sequence, the three-dimensional structures of proteins determine their specific function, activity, and evolvability. Here we show that a general protein language model augmented with protein structure backbone coordinates and trained on the inverse folding problem can guide evolution for diverse proteins without needing to explicitly model individual functional tasks. We demonstrate inverse folding to be an effective unsupervised, structure-based sequence optimization strategy that also generalizes to multimeric complexes by implicitly learning features of binding and amino acid epistasis. Using this approach, we screened ~30 variants of two therapeutic clinical antibodies used to treat SARS-CoV-2 infection and achieved up to 26-fold improvement in neutralization and 37-fold improvement in affinity against antibody-escaped viral variants-of-concern BQ.1.1 and XBB.1.5, respectively. In addition to substantial overall improvements in protein function, we find inverse folding performs with leading experimental success rates among other reported machine learning-guided directed evolution methods, without requiring any task-specific training data.
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Affiliation(s)
- Varun R. Shanker
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Theodora U.J. Bruun
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian L. Hie
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter S. Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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2
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Neti SS, Wang B, Iwig DF, Onderko EL, Booker SJ. Enzymatic Fluoromethylation Enabled by the S-Adenosylmethionine Analog Te-Adenosyl- L-(fluoromethyl)homotellurocysteine. ACS CENTRAL SCIENCE 2023; 9:905-914. [PMID: 37252363 PMCID: PMC10214534 DOI: 10.1021/acscentsci.2c01385] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Indexed: 05/31/2023]
Abstract
Fluoromethyl, difluoromethyl, and trifluoromethyl groups are present in numerous pharmaceuticals and agrochemicals, where they play critical roles in the efficacy and metabolic stability of these molecules. Strategies for late-stage incorporation of fluorine-containing atoms in molecules have become an important area of organic and medicinal chemistry as well as synthetic biology. Herein, we describe the synthesis and use of Te-adenosyl-L-(fluoromethyl)homotellurocysteine (FMeTeSAM), a novel and biologically relevant fluoromethylating agent. FMeTeSAM is structurally and chemically related to the universal cellular methyl donor S-adenosyl-L-methionine (SAM) and supports the robust transfer of fluoromethyl groups to oxygen, nitrogen, sulfur, and some carbon nucleophiles. FMeTeSAM is also used to fluoromethylate precursors to oxaline and daunorubicin, two complex natural products that exhibit antitumor properties.
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Affiliation(s)
- Syam Sundar Neti
- Department
of Chemistry, Department of Biochemistry and Molecular Biology, and Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Bo Wang
- Department
of Chemistry, Department of Biochemistry and Molecular Biology, and Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - David F. Iwig
- Department
of Chemistry, Department of Biochemistry and Molecular Biology, and Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Elizabeth L. Onderko
- Department
of Chemistry, Department of Biochemistry and Molecular Biology, and Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Squire J. Booker
- Department
of Chemistry, Department of Biochemistry and Molecular Biology, and Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
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3
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A bioinformatics approach to the identification of novel deleterious mutations of human TPMT through validated screening and molecular dynamics. Sci Rep 2022; 12:18872. [PMID: 36344599 PMCID: PMC9640560 DOI: 10.1038/s41598-022-23488-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022] Open
Abstract
Polymorphisms of Thiopurine S-methyltransferase (TPMT) are known to be associated with leukemia, inflammatory bowel diseases, and more. The objective of the present study was to identify novel deleterious missense SNPs of TPMT through a comprehensive in silico protocol. The initial SNP screening protocol used to identify deleterious SNPs from the pool of all TPMT SNPs in the dbSNP database yielded an accuracy of 83.33% in identifying extremely dangerous variants. Five novel deleterious missense SNPs (W33G, W78R, V89E, W150G, and L182P) of TPMT were identified through the aforementioned screening protocol. These 5 SNPs were then subjected to conservation analysis, interaction analysis, oncogenic and phenotypic analysis, structural analysis, PTM analysis, and molecular dynamics simulations (MDS) analysis to further assess and analyze their deleterious nature. Oncogenic analysis revealed that all five SNPs are oncogenic. MDS analysis revealed that all SNPs are deleterious due to the alterations they cause in the binding energy of the wild-type protein. Plasticity-induced instability caused by most of the mutations as indicated by the MDS results has been hypothesized to be the reason for this alteration. While in vivo or in vitro protocols are more conclusive, they are often more challenging and expensive. Hence, future research endeavors targeted at TPMT polymorphisms and/or their consequences in relevant disease progressions or treatments, through in vitro or in vivo means can give a higher priority to these SNPs rather than considering the massive pool of all SNPs of TPMT.
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4
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Insights into methionine S-methylation in diverse organisms. Nat Commun 2022; 13:2947. [PMID: 35618717 PMCID: PMC9135737 DOI: 10.1038/s41467-022-30491-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/02/2022] [Indexed: 12/04/2022] Open
Abstract
Dimethylsulfoniopropionate (DMSP) is an important marine anti-stress compound, with key roles in global nutrient cycling, chemotaxis and, potentially, climate regulation. Recently, diverse marine Actinobacteria, α- and γ-proteobacteria were shown to initiate DMSP synthesis via the methionine (Met) S-methyltransferase enzyme (MmtN), generating S-methyl-Met (SMM). Here we characterize a roseobacterial MmtN, providing structural and mechanistic insights into this DMSP synthesis enzyme. We propose that MmtN uses the proximity and desolvation mechanism for Met S-methylation with two adjacent MmtN monomers comprising the Met binding site. We also identify diverse functional MmtN enzymes in potentially symbiotic archaeal Candidatus Woesearchaeota and Candidate Phyla Radiation (CPR) bacteria, and the animalcule Adineta steineri, not anticipated to produce SMM and/or DMSP. These diverse MmtN enzymes, alongside the larger plant MMT enzyme with an N-terminus homologous to MmtN, likely utilize the same proximity and desolvation mechanism. This study provides important insights into the catalytic mechanism of SMM and/or DMSP production, and proposes roles for these compounds in secondary metabolite production, and SMM cycling in diverse organisms and environments. S-methyl methionine (SMM) is a key molecule in production of dimethylsulfoniopropionate (DMSP), an important marine anti-stress compound, with roles in global nutrient cycling. Here, the authors determine the mechanism of SMM synthesis and uncover unexpected roles for SMM in archaea, CPR bacteria and animals.
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5
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Geck RC, Boyle G, Amorosi CJ, Fowler DM, Dunham MJ. Measuring Pharmacogene Variant Function at Scale Using Multiplexed Assays. Annu Rev Pharmacol Toxicol 2021; 62:531-550. [PMID: 34516287 DOI: 10.1146/annurev-pharmtox-032221-085807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As costs of next-generation sequencing decrease, identification of genetic variants has far outpaced our ability to understand their functional consequences. This lack of understanding is a central challenge to a key promise of pharmacogenomics: using genetic information to guide drug selection and dosing. Recently developed multiplexed assays of variant effect enable experimental measurement of the function of thousands of variants simultaneously. Here, we describe multiplexed assays that have been performed on nearly 25,000 variants in eight key pharmacogenes (ADRB2, CYP2C9, CYP2C19, NUDT15, SLCO1B1, TMPT, VKORC1, and the LDLR promoter), discuss advances in experimental design, and explore key challenges that must be overcome to maximize the utility of multiplexed functional data. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Renee C Geck
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Gabriel Boyle
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Clara J Amorosi
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; , .,Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
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Franca R, Braidotti S, Stocco G, Decorti G. Understanding thiopurine methyltransferase polymorphisms for the targeted treatment of hematologic malignancies. Expert Opin Drug Metab Toxicol 2021; 17:1187-1198. [PMID: 34452592 DOI: 10.1080/17425255.2021.1974398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Thiopurine methyltransferase (TPMT) catalyzes the S-methylation of thiopurines (mercaptopurine (MP) and tioguanine (TG)), chemotherapeutic agents used in the treatment of acute lymphoblastic leukemia (ALL). Polymorphisms in TPMT gene encode diminished activity enzyme, enhancing accumulation of active metabolites, and partially explaining the inter-individual differences in patients' clinical response. AREAS COVERED This review gives an overview on TPMT gene and function, and discusses the pharmacogenomic implications of TPMT variants in the prevention of severe thiopurine-induced hematological toxicities and the less known implication on TG-induced sinusoidal obstruction syndrome. Additional genetic and non-genetic factors impairing TPMT activity are considered. Literature search was done in PubMed for English articles published since1990, and on PharmGKB. EXPERT OPINION To titrate thiopurines safely and effectively, achieve the right degree of lymphotoxic effect and avoid excessive myelosuppression, the optimal management will combine a preemptive TPMT genotyping to establish a safe initial dose with a close phenotypic monitoring of TPMT activity and/or of active metabolites during long-term treatment. Compared to current ALL protocols, replacement of TG by MP during reinduction phase in TPMT heterozygotes and novel individualized TG regimens in maintenance for TPMT wild-type subjects could be investigated to improve outcomes while avoiding risk of severe hepatotoxicity.
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Affiliation(s)
- R Franca
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - S Braidotti
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - G Stocco
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - G Decorti
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal & Child Health (I.r.c.c.s) Burlo Garofolo, Trieste, Italy
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7
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Insights into S-adenosyl-l-methionine (SAM)-dependent methyltransferase related diseases and genetic polymorphisms. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108396. [PMID: 34893161 DOI: 10.1016/j.mrrev.2021.108396] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 12/11/2022]
Abstract
Enzymatic methylation catalyzed by methyltransferases has a significant impact on many human biochemical reactions. As the second most ubiquitous cofactor in humans, S-adenosyl-l-methionine (SAM or AdoMet) serves as a methyl donor for SAM-dependent methyltransferases (MTases), which transfer a methyl group to a nucleophilic acceptor such as O, As, N, S, or C as the byproduct. SAM-dependent methyltransferases can be grouped into different types based on the substrates. Here we systematically reviewed eight types of methyltransferases associated with human diseases. Catechol O-methyltransferase (COMT), As(III) S-adenosylmethionine methyltransferase (AS3MT), indolethylamine N-methyltransferase (INMT), phenylethanolamine N-methyltransferase (PNMT), histamine N-methyltransferase (HNMT), nicotinamide N-methyltransferase (NNMT), thiopurine S-methyltransferase (TPMT) and DNA methyltansferase (DNMT) are classic SAM-dependent MTases. Correlations between genotypes and disease susceptibility can be partially explained by genetic polymorphisms. The physiological function, substrate specificity, genetic variants and disease susceptibility associated with these eight SAM-dependent methyltransferases are discussed in this review.
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8
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Methylation of selenocysteine catalysed by thiopurine S-methyltransferase. Biochim Biophys Acta Gen Subj 2018; 1863:182-190. [PMID: 30308221 DOI: 10.1016/j.bbagen.2018.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/25/2018] [Accepted: 10/02/2018] [Indexed: 12/16/2022]
Abstract
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. METHODS To address the role of TPMT in methylation of selenium compounds, we established the research on saturation transfer difference (STD) and 77Se NMR spectroscopy, fluorescence measurements, as well as computational molecular docking simulations. RESULTS Using STD NMR spectroscopy and fluorescence measurements of tryptophan residues in TPMT, we determined the binding of selenocysteine (Sec) to human recombinant TPMT. By comparing binding characteristics of Sec in the absence and in the presence of methyl donor, we confirmed S-adenosylmethionine (SAM)-induced conformational changes in TPMT. Molecular docking analysis positioned Sec into the active site of TPMT with orientation relevant for methylation reaction. Se-methylselenocysteine (MeSec), produced in the enzymatic reaction, was detected by 77Se NMR spectroscopy. A direct interaction between Sec and SAM in the active site of rTPMT and the formation of both products, MeSec and S-adenosylhomocysteine, was demonstrated using NMR spectroscopy. CONCLUSIONS The present study provides evidence on in vitro methylation of Sec by rTPMT in a SAM-dependant manner. GENERAL SIGNIFICANCE Our results suggest novel role of TPMT and demonstrate new insights into enzymatic modifications of the 21st amino acid.
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9
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Matreyek KA, Starita LM, Stephany JJ, Martin B, Chiasson MA, Gray VE, Kircher M, Khechaduri A, Dines JN, Hause RJ, Bhatia S, Evans WE, Relling MV, Yang W, Shendure J, Fowler DM. Multiplex assessment of protein variant abundance by massively parallel sequencing. Nat Genet 2018; 50:874-882. [PMID: 29785012 PMCID: PMC5980760 DOI: 10.1038/s41588-018-0122-z] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/29/2018] [Indexed: 11/09/2022]
Abstract
Determining the pathogenicity of genetic variants is a critical challenge, and functional assessment is often the only option. Experimentally characterizing millions of possible missense variants in thousands of clinically important genes requires generalizable, scalable assays. We describe variant abundance by massively parallel sequencing (VAMP-seq), which measures the effects of thousands of missense variants of a protein on intracellular abundance simultaneously. We apply VAMP-seq to quantify the abundance of 7,801 single-amino-acid variants of PTEN and TPMT, proteins in which functional variants are clinically actionable. We identify 1,138 PTEN and 777 TPMT variants that result in low protein abundance, and may be pathogenic or alter drug metabolism, respectively. We observe selection for low-abundance PTEN variants in cancer, and show that p.Pro38Ser, which accounts for ~10% of PTEN missense variants in melanoma, functions via a dominant-negative mechanism. Finally, we demonstrate that VAMP-seq is applicable to other genes, highlighting its generalizability.
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Affiliation(s)
- Kenneth A Matreyek
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jason J Stephany
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Melissa A Chiasson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Vanessa E Gray
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Arineh Khechaduri
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jennifer N Dines
- Department of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Ronald J Hause
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Smita Bhatia
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Genetic Networks Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada.
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10
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Wennerstrand P, Blissing A, Mårtensson LG. In Vitro Protein Stability of Two Naturally Occurring Thiopurine S-Methyltransferase Variants: Biophysical Characterization of TPMT*6 and TPMT*8. ACS OMEGA 2017; 2:4991-4999. [PMID: 30023734 PMCID: PMC6044926 DOI: 10.1021/acsomega.7b00801] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/18/2017] [Indexed: 06/02/2023]
Abstract
Thiopurine S-methyltransferase (TPMT) is a polymorphic enzyme involved in the metabolism and inactivation of thiopurine substances administered as immunosuppressants in the treatment of malignancies and autoimmune diseases. In this study, the naturally occurring variants, TPMT*6 (Y180F) and TPMT*8 (R215H), have been biophysically characterized. Despite being classified as low and intermediate in vivo enzyme activity variants, respectively, our results demonstrate a discrepancy because both TPMT*6 and TPMT*8 were found to exhibit normal functionality in vitro. While TPMT*8 exhibited biophysical properties almost indistinguishable from those of TPMTwt, the TPMT*6 variant was found to be destabilized. Furthermore, the contributions of the cofactor S-adenosylmethionine (SAM) to the thermodynamic stability of TPMT were investigated, but only a modest stabilizing effect was observed. Also presented herein is a new method for studies of the biophysical characteristics of TPMT and its variants using the extrinsic fluorescent probe 8-anilinonaphthalene-1-sulfonic acid (ANS). ANS was found to bind strongly to all investigated TPMT variants with a Kd of approximately 0.2 μM and a 1:1 binding ratio as determined by isothermal titration calorimetry (ITC). Circular dichroism and fluorescence measurements showed that ANS binds exclusively to the native state of TPMT, and binding to the active site was confirmed by molecular modeling and simulated docking as well as ITC measurements. The strong binding of the probe to native TPMT and the conformity of the obtained results demonstrate the advantages of using ANS binding characteristics in studies of this protein and its variants.
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11
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One amino acid makes a difference-Characterization of a new TPMT allele and the influence of SAM on TPMT stability. Sci Rep 2017; 7:46428. [PMID: 28462921 PMCID: PMC5411961 DOI: 10.1038/srep46428] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/16/2017] [Indexed: 12/28/2022] Open
Abstract
Thiopurine induced toxicity is associated with defects in the thiopurine methyltransferase (TPMT) gene. TPMT is a polymorphic enzyme, with most of the single nucleotide polymorphisms (SNPs) causing an amino acid change, altering the enzymatic activity of the TPMT protein. In this study, we characterize a novel patient allele c.719A > C, named TPMT*41, together with the more common variant *3C c.719A > G, resulting in an amino acid shift at tyrosine 240 to serine, p.Y240S and cysteine, p.Y240C respectively. We show that the patient heterozygote for c.719A > C has intermediate enzymatic activity in red blood cells. Furthermore, in vitro studies, using recombinant protein, show that TPMT p.Y240S is less stable than both TPMTwt and TPMT p.Y240C. The addition of SAM increases the stability and, in agreement with Isothermal Titration Calorimetry (ITC) data, higher molar excess of SAM is needed in order to stabilize TPMT p.Y240C and TPMT p.Y240S compared to TPMTwt. Molecular dynamics simulations show that the loss of interactions is most severe for Y240S, which agrees with the thermal stability of the mutations. In conclusion, our study shows that SAM increases the stability of TPMT and that changing only one amino acid can have a dramatic effect on TPMT stability and activity.
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12
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Leucine 208 in human histamine N-methyltransferase emerges as a hotspot for protein stability rationalizing the role of the L208P variant in intellectual disability. Biochim Biophys Acta Mol Basis Dis 2017; 1863:188-199. [DOI: 10.1016/j.bbadis.2016.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/20/2016] [Accepted: 10/11/2016] [Indexed: 11/19/2022]
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13
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Fazel-Najafabadi E, Vahdat Ahar E, Fattahpour S, Sedghi M. Structural and functional impact of missense mutations in TPMT: An integrated computational approach. Comput Biol Chem 2015; 59 Pt A:48-55. [PMID: 26410243 DOI: 10.1016/j.compbiolchem.2015.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 08/17/2015] [Accepted: 09/06/2015] [Indexed: 11/26/2022]
Abstract
BACKGROUND Thiopurine S-methyltransferase (TPMT) detoxifies thiopurine drugs which are used for treatment of various diseases including inflammatory bowel disease (IBD), and hematological malignancies. Individual variation in TPMT activity results from mutations in TPMT gene. In this study, the effects of all the known missense mutations in TPMT enzyme were studied at the sequence and structural level METHODS A broad set of bioinformatic tools was used to assess all the known missense mutations affecting enzyme activity. The effects of these mutations on protein stability, aggregation propensity, and residue interaction network were analyzed. RESULTS Our results indicate that the missense mutations have diverse effects on TPMT structure and function. Stability and aggregation propensities are affected by various mutations. Several mutations also affect residues in ligand binding site. CONCLUSIONS In vitro study of missense mutation is laborious and time-consuming. However, computational methods can be used to obtain information about effects of missense mutations on protein structure. In this study, the effects of most of the mutations on enzyme activity could be explained by computational methods. Thus, the present approach can be used for understanding the protein structure-function relationships.
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Affiliation(s)
- Esmat Fazel-Najafabadi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Vahdat Ahar
- Institute of Biochemistry and Biophysics, University of Tehran, Iran
| | - Shirin Fattahpour
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Sedghi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable disease, Isfahan University of Medical Sciences, Isfahan, Iran.
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14
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Niklasson M, Ahlner A, Andresen C, Marsh JA, Lundström P. Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches. PLoS Comput Biol 2015; 11:e1004022. [PMID: 25569628 PMCID: PMC4288728 DOI: 10.1371/journal.pcbi.1004022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/03/2014] [Indexed: 11/26/2022] Open
Abstract
The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.
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Affiliation(s)
- Markus Niklasson
- Division of Biomolecular Technology, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Alexandra Ahlner
- Division of Biomolecular Technology, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Cecilia Andresen
- Division of Biomolecular Technology, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Joseph A. Marsh
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Patrik Lundström
- Division of Biomolecular Technology, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
- * E-mail:
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15
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Methotrexate binds to recombinant thiopurine S-methyltransferase and inhibits enzyme activity after high-dose infusions in childhood leukaemia. Eur J Clin Pharmacol 2013; 69:1641-9. [PMID: 23660772 DOI: 10.1007/s00228-013-1521-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/19/2013] [Indexed: 01/04/2023]
Abstract
PURPOSE Important drugs in the treatment of childhood acute lymphoblastic leukaemia (ALL) are 6-mercaptopurine (6-MP) and methotrexate (MTX). Thiopurine methyltransferase (TPMT) is a polymorphic enzyme causing variability in 6-MP response and toxicity. The aim of this study was to investigate the fluctuation in TPMT enzyme activity over time and the effect of high-dose MTX infusions on TPMT enzyme activity and 6-MP metabolites in paediatric ALL patients. METHODS Fifty-three children with ALL treated according to the NOPHO-ALL 2000 protocol were included in the study. TPMT enzyme activity was measured at six different times starting from diagnosis until after the end of maintenance treatment. TPMT and 6-MP metabolites were measured before the initiation of high-dose MTX (HD-MTX) infusions and at 66 h post-infusion. The interaction between MTX and TPMT was investigated in vitro using recombinant TPMT protein and a leukaemic cell line. RESULTS Forty percent of TPMT wild-type individuals had deceptively low TPMT enzyme activity according to genotype at the time of diagnosis. TPMT activity had decreased significantly 66 h after the start of HD-MTX infusions (-9.2 %; p = 0.013). MTX bound to recombinant TPMT protein severely inhibiting TPMT enzyme activity (remaining activity 16 %). CONCLUSIONS Our results show that TPMT genotyping should be performed in children with ALL, since 40 % of the children in our study who carried the wild-type TPMT gene were at risk of initial underdosing of 6-MP in cases where only TPMT enzyme activity was determined. MTX inhibits the TPMT enzyme activity after HD-MTX infusions due to protein binding.
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16
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Larif S, Ben Salem C, Soua Z, Hmouda H, Bouraoui K. Insight into TPMT(∗)23 mutation mis-folding using molecular dynamics simulation and protein structure analysis. J Biomol Struct Dyn 2012; 31:1066-76. [PMID: 23025308 DOI: 10.1080/07391102.2012.721495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Thiopurine S-methyltransferase (TPMT) is an important enzyme that metabolizes thiopurine drugs. This enzyme exhibits a large number of interindividual polymorphism. TPMT(∗)23 polymorphism has been reported in a few cases in the world in co-dominance with TPMT(∗)3A. The phenotype has been reported to affect enzyme activity in vivo and in vitro. Its underlying structural basis is not clarified yet. In our study, the wild type (WT) protein structure was analyzed and the amino acids bordering water channels in thiopurine sites were identified. Molecular dynamics of both the WT and TPMT(∗)23 mutation was carried out. In addition, the effects of this mutation, especially on the thiopurine site which is closed with a pincer like mechanism, were investigated. We focused on explaining how a locally occurred A167G substitution propagated through hydrogen bonds alteration to induce structural modification which affects both thiopurine and S-adenosylmethionine receptors. Finally, a genetic prediction of mutation functional consequences has been conducted confirming altered activity. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:20.
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Affiliation(s)
- Sofiene Larif
- a Faculty of Medicine of Sousse, Metabolic Biophysics and Applied Pharmacology Laboratory, Department of Biophysics , Avenue Mohamed Karoui , Sousse , 4002 , Tunisia
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17
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Wennerstrand P, Dametto P, Hennig J, Klingstedt T, Skoglund K, Lindqvist Appell M, Mårtensson LG. Structural Characteristics Determine the Cause of the Low Enzyme Activity of Two Thiopurine S-Methyltransferase Allelic Variants: A Biophysical Characterization of TPMT*2 and TPMT*5. Biochemistry 2012; 51:5912-20. [DOI: 10.1021/bi300377d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Patricia Wennerstrand
- Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Paolo Dametto
- Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Janosch Hennig
- Division of Molecular Biotechnology, Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Therése Klingstedt
- Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Karin Skoglund
- Division of Drug Research/Clinical Pharmacology, Department of Medical
and Health Sciences, Faculty of Health Sciences, Linköping University, SE-581 83 Linköping, Sweden
| | - Malin Lindqvist Appell
- Division of Drug Research/Clinical Pharmacology, Department of Medical
and Health Sciences, Faculty of Health Sciences, Linköping University, SE-581 83 Linköping, Sweden
| | - Lars-Göran Mårtensson
- Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
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18
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Lahti JL, Tang GW, Capriotti E, Liu T, Altman RB. Bioinformatics and variability in drug response: a protein structural perspective. J R Soc Interface 2012; 9:1409-37. [PMID: 22552919 DOI: 10.1098/rsif.2011.0843] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Marketed drugs frequently perform worse in clinical practice than in the clinical trials on which their approval is based. Many therapeutic compounds are ineffective for a large subpopulation of patients to whom they are prescribed; worse, a significant fraction of patients experience adverse effects more severe than anticipated. The unacceptable risk-benefit profile for many drugs mandates a paradigm shift towards personalized medicine. However, prior to adoption of patient-specific approaches, it is useful to understand the molecular details underlying variable drug response among diverse patient populations. Over the past decade, progress in structural genomics led to an explosion of available three-dimensional structures of drug target proteins while efforts in pharmacogenetics offered insights into polymorphisms correlated with differential therapeutic outcomes. Together these advances provide the opportunity to examine how altered protein structures arising from genetic differences affect protein-drug interactions and, ultimately, drug response. In this review, we first summarize structural characteristics of protein targets and common mechanisms of drug interactions. Next, we describe the impact of coding mutations on protein structures and drug response. Finally, we highlight tools for analysing protein structures and protein-drug interactions and discuss their application for understanding altered drug responses associated with protein structural variants.
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Affiliation(s)
- Jennifer L Lahti
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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19
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Pan XL, Cui FC, Liu JY. Quantum mechanical/molecular mechanical molecular dynamics and free energy simulations of the thiopurine S-methyltransferase reaction with 6-mercaptopurine. J Phys Chem B 2011; 115:8033-7. [PMID: 21615136 DOI: 10.1021/jp2027516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations were performed to investigate the methylation of 6-mercaptopurine catalyzed by thiopurine S-methyltransferase. Several setups with different tautomeric forms and orientations of the substrate were considered. It is found that, with the orientation in chain A of the X-ray structure, the substrate can form an ideal near-attack configuration for the methylation reaction, which may take place after the deprotonation of the substrate by the conserved residue Asp23 through a water chain. The potential of mean force (PMF) of the methyl-transfer step for the most favorable pathway is 19.6 kcal/mol, which is in good agreement with the available experimental rate constant data.
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Affiliation(s)
- Xiao-Liang Pan
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
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20
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Characterization of a novel sequence variant, TPMT*28, in the human thiopurine methyltransferase gene. Pharmacogenet Genomics 2011; 20:700-7. [PMID: 20881512 DOI: 10.1097/fpc.0b013e3283402ee4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND The activity of the human enzyme thiopurine methyltransferase (TPMT) varies greatly between individuals because of genetic polymorphism. TPMT is involved in the detoxification and activation of thiopurines such as 6-mercaptopurine, 6-thioguanine, and azathioprine. These drugs are used in the treatment of acute lymphoblastic leukemia and inflammatory bowel disease. A total of 29 sequence variants have been identified so far in the TPMT gene. However, most of these variants are rare and not fully characterized. METHODS AND RESULTS In this study, we describe the identification and characterization of a novel TPMT sequence variant, originally found in a Swedish man of Italian origin. Sequencing of the variable number tandem repeats region of the TPMT promoter and exons III-X revealed a T-to-C transition at nucleotide 611, causing an amino acid substitution from isoleucine to threonine at amino acid 204, positioned in an α-helix, approximately 16 Å from the active site. This new variant was found in the patient and in his son. Both had intermediate enzyme activity (8.1 U/ml packed red blood cells and 8.8 U/ml packed red blood cells, respectively) and neither carried other variants in the coding region of the gene. To be able to study this variant in more detail, the TPMT*28 variant was expressed in Escherichia coli, and an in-vitro characterization of the variant revealed that the protein was destabilized and showed a stronger tendency towards degradation at 37°C than the wild-type protein. The individuals carrying the TPMT*28 variant had less TPMT protein and lower TPMT activity in both red and white blood cells compared with a wild-type control. CONCLUSIONS We present a detailed in-vivo and in-vitro characterization of a novel TPMT sequence variant (TPMT*28) causing decreased TPMT activity. Individuals carrying TPMT*28 might have an increased risk for developing severe side effects if treated with conventional doses of thiopurines.
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21
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Cakici O, Sikorski M, Stepkowski T, Bujacz G, Jaskolski M. Crystal structures of NodS N-methyltransferase from Bradyrhizobium japonicum in ligand-free form and as SAH complex. J Mol Biol 2010; 404:874-89. [PMID: 20970431 DOI: 10.1016/j.jmb.2010.10.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 10/12/2010] [Accepted: 10/13/2010] [Indexed: 11/30/2022]
Abstract
NodS is an S-adenosyl-L-methionine (SAM)-dependent N-methyltransferase that is involved in the biosynthesis of Nod factor (NF) in rhizobia, which are bacterial symbionts of legume plants. NF is a modified chitooligosaccharide (COS) signal molecule that is recognized by the legume host, where it initiates symbiotic processes leading to atmospheric nitrogen fixation. We report the crystal structure of recombinant NodS protein from Bradyrhizobium japonicum, which infects lupine and serradella legumes. Two crystal forms--ligand-free NodS and NodS in complex with S-adenosyl-L-homocysteine, which is a by-product of the methylation reaction--were obtained, and their structures were refined to resolutions of 2.43 Å and 1.85 Å, respectively. Although the overall fold (consisting of a seven-stranded β-sheet flanked by layers of helices) is similar to those of other SAM-dependent methyltransferases, NodS has specific features reflecting the unique character of its oligosaccharide substrate. In particular, the N-terminal helix and its connecting loop get ordered upon SAM binding, thereby closing the methyl donor cavity and shaping a long surface canyon that is clearly the binding site for the acceptor molecule. Comparison of the two structural forms of NodS suggests that there are also other conformational changes taking place upon the binding of the donor substrate. As an enzyme that methylates a COS substrate, NodS is the first example among all SAM-dependent methyltransferases to have its three-dimensional structure elucidated. Gaining insight about how NodS binds its donor and acceptor substrates helps to better understand the mechanism of NodS activity and the basis of its functional difference in various rhizobia.
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Affiliation(s)
- Ozgur Cakici
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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22
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Lee BWK, Sun HG, Zang T, Kim BJ, Alfaro JF, Zhou ZS. Enzyme-catalyzed transfer of a ketone group from an S-adenosylmethionine analogue: a tool for the functional analysis of methyltransferases. J Am Chem Soc 2010; 132:3642-3. [PMID: 20196537 DOI: 10.1021/ja908995p] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
S-adenosylmethionine (AdoMet or SAM)-dependent methyltransferases belong to a large and diverse family of group-transfer enzymes that perform vital biological functions on a host of substrates. Despite the progress in genomics, structural proteomics, and computational biology, functional annotation of methyltransferases remains a challenge. Herein, we report the synthesis and activity of a new AdoMet analogue functionalized with a ketone group. Using catechol O-methyltransferase (COMT, EC 2.1.1.6) and thiopurine S-methyltransferase (TPMT, EC 2.1.1.67) as model enzymes, this robust and readily accessible analogue displays kinetic parameters that are comparable to AdoMet and exhibits multiple turnovers with enzyme. More importantly, this AdoMet surrogate displays the same substrate specificity as the natural methyl donor. Incorporation of the ketone group allows for subsequent modification via bio-orthogonal labeling strategies and sensitive detection of the tagged ketone products. Hence, this AdoMet analogue expands the toolbox available to interrogate the biochemical functions of methyltransferases.
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Affiliation(s)
- Bobby W K Lee
- The Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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23
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Rutherford K, Daggett V. Polymorphisms and disease: hotspots of inactivation in methyltransferases. Trends Biochem Sci 2010; 35:531-8. [PMID: 20382027 DOI: 10.1016/j.tibs.2010.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 03/10/2010] [Accepted: 03/10/2010] [Indexed: 01/13/2023]
Abstract
Methyltransferases catalyze the methylation processes essential for protein/DNA repair, transcriptional regulation, and drug metabolism in vivo. More than 500 human methyltransferase polymorphisms have been identified, many of which are linked to disease. We mapped all available coding polymorphisms of seven methyltransferases onto their structures to address their structural significance, and identified a polymorphic hotspot ∼20Å from the active site in four of the proteins. Molecular dynamics simulations of these proteins reveal a common mechanism of destabilization: the mutations alter important side-chain contacts within the polymorphic site that are propagated through the protein, thereby distorting the active site. We propose that this hotspot might have arisen to modulate enzymatic activity, with decreased activity actually conferring an advantage in three of the four methyltransferases.
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Affiliation(s)
- Karen Rutherford
- Department of Biochemistry, Box 355013, University of Washington, Seattle WA 98195-5013, USA
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24
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Feng Q, Vannaprasaht S, Peng Y, Angsuthum S, Avihingsanon Y, Yee VC, Tassaneeyakul W, Weinshilboum RM. Thiopurine S-methyltransferase pharmacogenetics: functional characterization of a novel rapidly degraded variant allozyme. Biochem Pharmacol 2009; 79:1053-61. [PMID: 19945438 DOI: 10.1016/j.bcp.2009.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 11/13/2009] [Accepted: 11/20/2009] [Indexed: 11/25/2022]
Abstract
A novel human thiopurine S-methyltransferase (TPMT) variant allele, (319 T>G, 107Tyr>Asp, *27), was identified in a Thai renal transplantation recipient with reduced erythrocyte TPMT activity. The TPMT*27 variant allozyme showed a striking decrease in both immunoreactive protein level and enzyme activity after transient expression in a mammalian cell line. We set out to explore the mechanism(s) responsible for decreased expression of this novel variant of an important drug-metabolizing enzyme. We observed accelerated degradation of TPMT*27 protein in a rabbit reticulocyte lysate. TPMT*27 degradation was slowed by proteasome inhibition and involved chaperone proteins-similar to observations with regard to the degradation of the common TPMT*3A variant allozyme. TPMT*27 aggresome formation was also observed in transfected mammalian cells after proteasome inhibition. Inhibition of autophagy also decreased TPMT*27 degradation. Finally, structural analysis and molecular dynamics simulation indicated that TPMT*27 was less stable than was the wild type TPMT allozyme. In summary, TPMT*27 serves to illustrate the potential importance of protein degradation - both proteasome and autophagy-mediated degradation - for the pharmacogenetic effects of nonsynonymous SNPs.
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Affiliation(s)
- Qiping Feng
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic-Mayo Medical School, 200 First Street SW, Rochester, MN 55905, United States
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25
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Mokmak W, Tongsima S, Jenwitheesuk E. Molecular dynamics simulation of a human thiopurine S-methyltransferase complexed with 6-mercaptopurine model. Bioinformation 2009; 4:59-62. [PMID: 20198169 PMCID: PMC2823381 DOI: 10.6026/97320630004059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2009] [Revised: 04/21/2009] [Accepted: 07/18/2009] [Indexed: 11/23/2022] Open
Abstract
Human thiopurine S-methyltransferase (TPMT) is an essential protein in 6-mercaptopurine (6MP) drug metabolism. To understand the
pharmacogenetics of TPMT and 6MP, X-ray co-crystal structures of TPMT complexes with S-adenosyl-L-methionine (AdoMet) and 6MP
are required. However, the co-crystal structure of this complex has not been reported because 6MP is poorly water soluble. We used
molecular dynamics (MD) simulation to predict the structure of the complex of human TPMT-AdoHcy(CH2)6MP, where the sulfur atoms of
AdoHcy and 6MP were linked by a CH2 group. After 1300 picoseconds of MD simulation, the trajectory showed that 6MP was stabilized in
the TPMT active site by formation of non-bonded interactions between 6MP and Phe40, Pro196 and Arg226 side chains of TPMT. The
intersulfur distance between AdoHcy and 6MP as well as the binding modes and the interactions of our TPMT-AdoHcy model are
consistent with those observed in the X-ray crystal structure of murine TPMT-AdoHcy-6MP complex. The predicted binding modes of
AdoHcy and 6MP in our model are consistent with those observed in murine TPMT X-ray crystal structures, which provides structural
insights into the interactions of TPMT, AdoHcy, and 6MP at the atomic level and may be used as a starting point for further study of
thiopurine drug pharmacogenetics.
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Affiliation(s)
- Wanwimon Mokmak
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klongluang, Pathumthani 12120, Thailand
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26
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Milek M, Karas Kuzelicki N, Smid A, Mlinaric-Rascan I. S-adenosylmethionine regulates thiopurine methyltransferase activity and decreases 6-mercaptopurine cytotoxicity in MOLT lymphoblasts. Biochem Pharmacol 2009; 77:1845-53. [PMID: 19428339 DOI: 10.1016/j.bcp.2009.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2009] [Revised: 02/27/2009] [Accepted: 03/04/2009] [Indexed: 11/30/2022]
Abstract
Six-mercaptopurine (6-MP) is a pro-drug widely used in treatment of various diseases, including acute lymphoblastic leukaemia (ALL). Side-effects of thiopurine therapy have been correlated with thiopurine methyltransferase (TPMT) activity. We propose a novel TPMT-mediated mechanism of S-adenosylmethionine (SAM)-specific effects on 6-mercaptopurine (6-MP) induced cytotoxicity in a model cell line for acute lymphoblastic leukemia (MOLT). Our results show that exogenous SAM (10-50microM) rescues cells from the toxic effects of 6-MP (5microM) by delaying the onset of apoptosis. We prove that the extent of methylthioinosine monophosphate (MeTIMP) induced inhibition of de novo purine synthesis (DNPS) determines the concentrations of intracellular ATP, and consequently SAM, which acts as a positive modulator of TPMT activity. This leads to a greater conversion of 6-MP to inactive 6-methylmercaptopurine, and thus lower availability of thioinosine monophosphate for the biotransformation to cytotoxic thioguanine nucleotides (TGNs) and MeTIMP. We further show that the addition of exogenous SAM to 6-MP treated cells maintains intracellular SAM levels, TPMT activity and protein levels, all of which are diminished in cells incubated with 6-MP. Since TPMT mRNA levels remained unaltered, the effect of SAM appears to be restricted to protein stabilisation rather than an increase of TPMT expression. We thus propose that SAM reverses the extent of 6-MP cytotoxicity, by acting as a TPMT-stabilizing factor. This study provides new insights into the pharmacogenetics of thiopurine drugs. Identification of SAM as critical modulator of TPMT activity and consequently thiopurine toxicity may set novel grounds for the rationalization of thiopurine therapy.
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Affiliation(s)
- Miha Milek
- University of Ljubljana, Faculty of Pharmacy, Ljubljana, Slovenia
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Mani S, Ghalib M, Chaudhary I, Goel S. Alterations of chemotherapeutic pharmacokinetic profiles by drug-drug interactions. Expert Opin Drug Metab Toxicol 2009; 5:109-30. [PMID: 19239394 PMCID: PMC3533254 DOI: 10.1517/17425250902753212] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Drug interactions in oncology are common place and largely ignored as we tolerate high thresholds of 'toxic' drug responses in these patients. However, in the era of 'targeted' or seemingly 'less toxic' therapy, these interactions are more commonly flagged and contribute significantly towards poor 'quality of life' and medical fatalities. OBJECTIVE This review and opinion article focuses on alteration of chemotherapeutic pharmacokinetic profiles by drug interactions in the setting of polypharmacy. The assumption is that the drugs, with changes in their pharmacokinetics, will contribute towards changes in their pharmacodynamics. METHODS The examples cited for such drug-drug interactions are culled from published literature with an emphasis on those interactions that have been well characterized at the molecular level. RESULTS Although very few drug interaction studies have been performed on approved oncology based drugs, it is clear that drugs whose pharmacokinetics profiles are closely related to their pharmacodynamics will indeed result in clinically important drug interactions. Some newer mechanisms are described that involve interactions at the level of gene transcription, whereby, drug metabolism is significantly altered. However, for any given drug interaction, there does not seem to be a comprehensive model describing interactions. CONCLUSIONS Mechanisms based drug interactions are plentiful in oncology; however, there is an absolute lack of a comprehensive model that would predict drug-drug interactions.
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Affiliation(s)
- Sridhar Mani
- Associate Professor: Medicine, Oncology and Molecular Genetics, 1300 Morris Park Ave, Chanin 302D-1, NY 10461, Bronx, USA, Tel: +1 718 430 2871; Fax: +1 718 904 2830
| | - Mohammed Ghalib
- Medicine, Oncology and Molecular Genetics, 1300 Morris Park Ave, Chanin 302D-1, NY 10461, Bronx, USA, Tel: +1 718 430 2871; Fax: +1 718 904 2830
| | - Imran Chaudhary
- Medicine, Oncology and Molecular Genetics, 1300 Morris Park Ave, Chanin 302D-1, NY 10461, Bronx, USA, Tel: +1 718 430 2871; Fax: +1 718 904 2830
| | - Sanjay Goel
- Associate Professor, Medicine, Oncology and Molecular Genetics, 1300 Morris Park Ave, Chanin 302D-1, NY 10461, Bronx, USA, Tel: +1 718 430 2871; Fax: +1 718 904 2830
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Functional characterization of 23 allelic variants of thiopurine S-methyltransferase gene (TPMT*2 - *24). Pharmacogenet Genomics 2008; 18:887-93. [PMID: 18708949 DOI: 10.1097/fpc.0b013e3283097328] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Thiopurine S-methyltransferase (TPMT) is an enzyme responsible for the detoxification of the widely used thiopurine drugs. TPMT is genetically polymorphic and is associated with large interindividual variations in thiopurine drug toxicity and therapeutic efficacy. In this study, we performed an in-vitro analysis of TPMT variant alleles, namely, TPMT*2, *3A, *3B, *3C, *5, *6, *7, *8, *9, *10, *11, *12, *13, *14, *16, *17, *18, *19, *20, *21, *22, *23, and *24. METHODS The wild-type TPMT proteins, TPMT.1 and 23 variants were heterologously expressed in COS-7 cells, and the kinetic parameters Km, Vmax, and intrinsic clearance (Vmax/Km) of 6-thioguanine S-methylation were determined. RESULTS The expression levels of TPMT.2, TPMT.3A, TPMT.5, TPMT.12, TPMT.14, and TPMT.22 were considerably lower than that of TPMT.1 (P<0.005), and that of TPMT.18 was slightly reduced (P<0.05). The kinetic parameters of TPMT.3A, TPMT.3B, TPMT.5, TPMT.14, TPMT.18, TPMT.21, and TPMT.22 could not be accurately established because of no activity in 6-thioguanine S-methylation. The Vmax/Km values of TPMT.2, TPMT.7, TPMT.17, and TPMT.24 were displayed less than 10% of the wild-type. CONCLUSION This functional analysis with respect to TPMT variants could provide useful information for individualization of thiopurine drugs therapy.
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Rutherford K, Daggett V. Four human thiopurine s-methyltransferase alleles severely affect protein structure and dynamics. J Mol Biol 2008; 379:803-14. [PMID: 18482735 PMCID: PMC2518407 DOI: 10.1016/j.jmb.2008.04.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 03/29/2008] [Accepted: 04/11/2008] [Indexed: 10/22/2022]
Abstract
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 alpha3 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 beta-strand 9, distant from the active site. Side-chain contacts between residue 240 and helix alpha8 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.
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Affiliation(s)
- Karen Rutherford
- Department of Biochemistry, University of Washington, Seattle WA 98195-5013
| | - Valerie Daggett
- Department of Biochemistry, University of Washington, Seattle WA 98195-5013
- Department of Bioengineering, University of Washington, Seattle WA 98195-5013
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Rutherford K, Le Trong I, Stenkamp R, Parson W. Crystal Structures of Human 108V and 108M Catechol O-Methyltransferase. J Mol Biol 2008; 380:120-30. [DOI: 10.1016/j.jmb.2008.04.040] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Revised: 04/14/2008] [Accepted: 04/16/2008] [Indexed: 11/29/2022]
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Garat A, Cauffiez C, Renault N, Lo-Guidice JM, Allorge D, Chevalier D, Houdret N, Chavatte P, Loriot MA, Gala JL, Broly F. Characterisation of novel defective thiopurine S-methyltransferase allelic variants. Biochem Pharmacol 2008; 76:404-15. [PMID: 18602085 DOI: 10.1016/j.bcp.2008.05.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Revised: 04/29/2008] [Accepted: 05/01/2008] [Indexed: 10/22/2022]
Abstract
Human thiopurine S-methyltransferase (TPMT, EC 2.1.1.67) is a key enzyme in the detoxification of thiopurine drugs widely used in the treatment of various diseases, such as inflammatory bowel diseases, acute lymphoblastic leukaemia and rheumatic diseases. The TPMT gene is genetically polymorphic and the inverse relationship between TPMT activity and the risk of developing severe hematopoietic toxicity is well known. In this study, the entire coding sequence of TPMT, together with its 5'-flanking promoter region, was analysed in patients with an intermediate phenotype for thiopurine drug methylation. Four polymorphisms were identified, two previously described, c.356A>C (p.Lys(119)Thr, TPMT*9) and c.205C>G (p.Leu(69)Val, TPMT*21), and two novel missense mutations, c.537G>T (p.Gln(179)His, TPMT*24) and c.634T>C (p.Cys(212)Arg, TPMT*25). Structural investigations, using molecular modeling, were undertaken in an attempt to explain the potential impact of the amino acid substitutions on the structure and activity of the variant proteins. Additionally, in order to determine kinetic parameters (K(m) and V(max)) of 6-thioguanine (6-TG) methylation, the four variants were expressed in a recombinant yeast expression system. Assays were performed by HPLC and the results were compared with those of wild-type TPMT. The p.Leu(69)Val and the p.Cys(212)Arg substitutions encode recombinant enzymes with a significantly decreased intrinsic clearance compared to that of the wild-type protein, and, consequently, characterise non-functional alleles of TPMT. The p.Lys(119)Thr and the p.Gln(179)His substitutions do not affect significantly the catalytic activity of the corresponding variant proteins, which prevents to unambiguously describe these latter alleles as defective TPMT variants.
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Affiliation(s)
- A Garat
- Equipe d'accueil 2679, Faculté de Médecine de Lille, Pôle Recherche, Lille, France
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Peng Y, Feng Q, Wilk D, Adjei AA, Salavaggione OE, Weinshilboum RM, Yee VC. Structural basis of substrate recognition in thiopurine s-methyltransferase. Biochemistry 2008; 47:6216-25. [PMID: 18484748 DOI: 10.1021/bi800102x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Yi Peng
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Egle R, Milek M, Mlinarič-Raščan I, Fahr A, Kristl J. A novel gene delivery system for stable transfection of thiopurine-S-methyltransferase gene in versatile cell types. Eur J Pharm Biopharm 2008; 69:23-30. [DOI: 10.1016/j.ejpb.2007.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2007] [Revised: 09/11/2007] [Accepted: 10/03/2007] [Indexed: 10/22/2022]
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Lindqvist M, Skoglund K, Karlgren A, Söderkvist P, Peterson C, Kidhall I, Almer S. Explaining TPMT genotype/phenotype discrepancy by haplotyping of TPMT*3A and identification of a novel sequence variant, TPMT*23. Pharmacogenet Genomics 2007; 17:891-5. [PMID: 17885628 DOI: 10.1097/fpc.0b013e3282ef642b] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Thiopurine methyltransferase (TPMT) is a polymorphic enzyme involved in the metabolism of thiopurine drugs. Owing to polymorphisms in the TPMT gene (TPMT*2-*22), the enzyme activity varies interindividually. Patients with reduced TPMT activity may develop adverse reactions when treated with standard doses of thiopurines. This work focuses on a TPMT genotype/phenotype discrepancy found in a patient during routine testing. The patient displayed very low TPMT enzyme activity and she was genotyped by pyrosequencing as being heterozygous for the 460G>A and 719A>G polymorphisms (TPMT*3A). Complete sequencing in combination with haplotyping of the TPMT gene revealed a novel sequence variant, 500C>G, on one allele and TPMT*3A on the other allele, giving rise to the novel genotype TPMT*3A/*23. When investigating the patient's relatives, they too had the TPMT*3A/*23 genotype in combination with low enzyme activity. We conclude that this novel variant allele affects enzyme activity, as the individuals carrying it had almost undetectable TPMT activity.
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Affiliation(s)
- Malin Lindqvist
- Division of Clinical Pharmacology, Department of Medicine and Care, Faculty of Health Sciences, Linköping, Sweden.
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