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Scaletti ER, Unterlass JE, Almlöf I, Koolmeister T, Vallin KS, Kapsitidou D, Tsuber V, Helleday T, Stenmark P, Jemth AS. Kinetic and structural characterization of NUDT15 and NUDT18 as catalysts of isoprene pyrophosphate hydrolysis. FEBS J 2024. [PMID: 38944687 DOI: 10.1111/febs.17202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/19/2024] [Accepted: 06/06/2024] [Indexed: 07/01/2024]
Abstract
Isoprene pyrophosphates play a crucial role in the synthesis of a diverse array of essential nonsterol and sterol biomolecules and serve as substrates for posttranslational isoprenylation of proteins, enabling specific anchoring to cellular membranes. Hydrolysis of isoprene pyrophosphates would be a means to modulate their levels, downstream products, and protein isoprenylation. While NUDIX hydrolases from plants have been described to catalyze the hydrolysis of isoprene pyrophosphates, homologous enzymes with this function in animals have not yet been reported. In this study, we screened an extensive panel of human NUDIX hydrolases for activity in hydrolyzing isoprene pyrophosphates. We found that human nucleotide triphosphate diphosphatase NUDT15 and 8-oxo-dGDP phosphatase NUDT18 efficiently catalyze the hydrolysis of several physiologically relevant isoprene pyrophosphates. Notably, we demonstrate that geranyl pyrophosphate is an excellent substrate for NUDT18, with a catalytic efficiency of 2.1 × 105 m-1·s-1, thus making it the best substrate identified for NUDT18 to date. Similarly, geranyl pyrophosphate proved to be the best isoprene pyrophosphate substrate for NUDT15, with a catalytic efficiency of 4.0 × 104 M-1·s-1. LC-MS analysis of NUDT15 and NUDT18 catalyzed isoprene pyrophosphate hydrolysis revealed the generation of the corresponding monophosphates and inorganic phosphate. Furthermore, we solved the crystal structure of NUDT15 in complex with the hydrolysis product geranyl phosphate at a resolution of 1.70 Å. This structure revealed that the active site nicely accommodates the hydrophobic isoprenoid moiety and helped identify key binding residues. Our findings imply that isoprene pyrophosphates are endogenous substrates of NUDT15 and NUDT18, suggesting they are involved in animal isoprene pyrophosphate metabolism.
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Affiliation(s)
- Emma R Scaletti
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Judith E Unterlass
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Ingrid Almlöf
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Tobias Koolmeister
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Karl S Vallin
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Despina Kapsitidou
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Viktoriia Tsuber
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Thomas Helleday
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Ann-Sofie Jemth
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
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2
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Wong DD, Ho SA, Domazetovska A, Yong MK, Rawlinson WD. Evidence supporting the use of therapeutic drug monitoring of ganciclovir in transplantation. Curr Opin Infect Dis 2023; 36:505-513. [PMID: 37729654 DOI: 10.1097/qco.0000000000000965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
PURPOSE OF REVIEW This review describes current knowledge of ganciclovir (GCV) and valganciclovir (ValGCV) pharmacokinetic/pharmacodynamic characteristics, highlighting the likely contribution from host genetic factors to interpatient variability. The evidence and challenges surrounding optimization of drug dosing through therapeutic drug monitoring (TDM) are examined, with recommendations made. RECENT FINDINGS Pharmacokinetic studies of current dosing guidelines have shown high interindividual and intraindividual variability of GCV concentrations. This is sometimes associated with a slow decline in cytomegalovirus (CMV) viral load in some transplant recipients. A high incidence of GCV-associated myelosuppression has limited the use of this drug in the transplant setting. Patient groups identified to benefit from GCV TDM include pediatric patients, cystic fibrosis with lung transplantation, obese with kidney transplantation, and patients with fluctuating renal function or on hemodialysis. The emergence of refractory resistant CMV, particularly in immune compromised patients, highlights the importance of appropriate dosing of these antivirals. Host genetic factors need to be considered where recently, two host genes were shown to account for interpatient variation during ganciclovir therapy. Therapeutic Drug Monitoring has been shown to improve target antiviral-level attainment. The use of TDM may guide concentration-based dose adjustment, potentially improving virological and clinical outcomes. However, evidence supporting the use of TDM in clinical practice remains limited and further study is needed in the transplant cohort. SUMMARY Further studies examining novel biomarkers are needed to guide target concentrations in prophylaxis and treatment. The use of TDM in transplant recipients is likely to improve the clinical efficacy of current antivirals and optimize outcomes in transplant recipients.
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Affiliation(s)
- Diana D Wong
- National Measurement Institute, Lindfield, Sydney, New South Wales
| | - Su Ann Ho
- Peter MacCallum Cancer Centre
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria
| | - Ana Domazetovska
- Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales
| | - Michelle K Yong
- Peter MacCallum Cancer Centre
- Department Infectious Diseases, Royal Melbourne Hospital
- National Centre for Infections in Cancer, Parkville
| | - William D Rawlinson
- Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales
- Schools of Biomedical Sciences, Biotechnology and Biomolecular Sciences, Clinical Sciences, University of NSW, Sydney New South Wales, Australia
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Lukaszewicz M, Ferenc-Mrozek A, Kokosza J, Stefaniuk A, Stepinski J, Bojarska E, Darzynkiewicz E. Mammalian Nudt15 hydrolytic and binding activity on methylated guanosine mononucleotides. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:487-495. [PMID: 37644211 PMCID: PMC10618335 DOI: 10.1007/s00249-023-01678-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/06/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
The Nudt15 enzyme of the NUDIX protein family is the subject of extensive study due to its action on thiopurine drugs used in the treatment of cancer and inflammatory diseases. In addition to thiopurines, Nudt15 is enzymatically active in vitro on several nucleotide substrates. It has also been suggested that this enzyme may play a role in 5'RNA turnover by hydrolyzing m7GDP, a product of mRNA decapping. However, no detailed studies on this substrate with Nudt15 are available. Here, we analyzed the enzymatic activity of Nudt15 with m7GDP, its triphosphate form m7GTP, and the trimethylated counterparts (m32,2,7GDP and m32,2,7GTP). Kinetic data revealed a moderate activity of Nudt15 toward these methylated mononucleotides compared to the dGTP substrate. However m7GDP and m32,2,7GDP showed a distinct stabilization of Nudt15 upon ligand binding, in the same range as dGTP, and thus these two mononucleotides may be used as leading structures in the design of small molecule binders of Nudt15.
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Affiliation(s)
- Maciej Lukaszewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.
| | - Aleksandra Ferenc-Mrozek
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Julia Kokosza
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Anna Stefaniuk
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Janusz Stepinski
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Elzbieta Bojarska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Edward Darzynkiewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
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4
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Scott ER, Yang Y, Botton MR, Seki Y, Hoshitsuki K, Harting J, Baybayan P, Cody N, Nicoletti P, Moriyama T, Chakraborty S, Yang JJ, Edelmann L, Schadt EE, Korlach J, Scott SA. Long-read HiFi sequencing of NUDT15: Phased full-gene haplotyping and pharmacogenomic allele discovery. Hum Mutat 2022; 43:1557-1566. [PMID: 36057977 PMCID: PMC9875722 DOI: 10.1002/humu.24457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 01/27/2023]
Abstract
To determine the phase of NUDT15 sequence variants for more comprehensive star (*) allele diplotyping, we developed a novel long-read single-molecule real-time HiFi amplicon sequencing method. A 10.5 kb NUDT15 amplicon assay was validated using reference material positive controls and additional samples for specimen type and blinded accuracy assessment. Triplicate NUDT15 HiFi sequencing of two reference material samples had nonreference genotype concordances of >99.9%, indicating that the assay is robust. Notably, short-read genome sequencing of a subset of samples was unable to determine the phase of star (*) allele-defining NUDT15 variants, resulting in ambiguous diplotype results. In contrast, long-read HiFi sequencing phased all variants across the NUDT15 amplicons, including a *2/*9 diplotype that previously was characterized as *1/*2 in the 1000 Genomes Project v3 data set. Assay throughput was also tested using 8.5 kb amplicons from 100 Ashkenazi Jewish individuals, which identified a novel NUDT15 *1 suballele (c.-121G>A) and a rare likely deleterious coding variant (p.Pro129Arg). Both novel alleles were Sanger confirmed and assigned as *1.007 and *20, respectively, by the PharmVar Consortium. Taken together, NUDT15 HiFi amplicon sequencing is an innovative method for phased full-gene characterization and novel allele discovery, which could improve NUDT15 pharmacogenomic testing and subsequent phenotype prediction.
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Affiliation(s)
- Erick R Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yao Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mariana R Botton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Yoshinori Seki
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Keito Hoshitsuki
- School of Pharmacy, University of Pittsburgh, Pennsylvania, Pittsburgh, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - John Harting
- Pacific Biosciences, Menlo Park, California, USA
| | | | - Neal Cody
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Paola Nicoletti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Takaya Moriyama
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | | | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
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5
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Jemth AS, Scaletti ER, Homan E, Stenmark P, Helleday T, Michel M. Nudix hydrolase 18 catalyzes the hydrolysis of active triphosphate metabolites of the antivirals remdesivir, ribavirin, and molnupiravir. J Biol Chem 2022; 298:102169. [PMID: 35732208 PMCID: PMC9212496 DOI: 10.1016/j.jbc.2022.102169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/28/2022] Open
Abstract
Remdesivir and molnupiravir have gained considerable interest because of their demonstrated activity against SARS-CoV-2. These antivirals are converted intracellularly to their active triphosphate forms remdesivir-TP and molnupiravir-TP. Cellular hydrolysis of these active metabolites would consequently decrease the efficiency of these drugs; however, whether endogenous enzymes that can catalyze this hydrolysis exist is unknown. Here, we tested remdesivir-TP as a substrate against a panel of human hydrolases and found that only Nudix hydrolase (NUDT) 18 catalyzed the hydrolysis of remdesivir-TP with notable activity. The kcat/Km value of NUDT18 for remdesivir-TP was determined to be 17,700 s-1M-1, suggesting that NUDT18-catalyzed hydrolysis of remdesivir-TP may occur in cells. Moreover, we demonstrate that the triphosphates of the antivirals ribavirin and molnupiravir are also hydrolyzed by NUDT18, albeit with lower efficiency than Remdesivir-TP. Low activity was also observed with the triphosphate forms of sofosbuvir and aciclovir. This is the first report showing that NUDT18 hydrolyzes triphosphates of nucleoside analogs of exogenous origin, suggesting that NUDT18 can act as a cellular sanitizer of modified nucleotides and may influence the antiviral efficacy of remdesivir, molnupiravir, and ribavirin. As NUDT18 is expressed in respiratory epithelial cells, it may limit the antiviral efficacy of remdesivir and molnupiravir against SARS-CoV-2 replication by decreasing the intracellular concentration of their active metabolites at their intended site of action.
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Affiliation(s)
- Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
| | - Emma Rose Scaletti
- Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden
| | - Evert Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Pål Stenmark
- Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden; Weston Park Cancer Centre, Department of Oncology & Metabolism, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Maurice Michel
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
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Maillard M, Gong L, Nishii R, Yang JJ, Whirl-Carrillo M, Klein TE. PharmGKB summary: acyclovir/ganciclovir pathway. Pharmacogenet Genomics 2022; 32:201-208. [PMID: 35665708 PMCID: PMC9179945 DOI: 10.1097/fpc.0000000000000474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Maud Maillard
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Li Gong
- Departments of Biomedical Data Science
| | - Rina Nishii
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Teri E Klein
- Departments of Biomedical Data Science
- Medicine (BMIR), Stanford University, Stanford, California, USA
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7
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Shingare A, Dhope N, Bahadur MM. Novel risk factor for valganciclovir toxicity-NUDT15 genetic variant. Transpl Infect Dis 2022; 24:e13799. [PMID: 35064735 DOI: 10.1111/tid.13799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Ashay Shingare
- Department of Nephrology and Transplantation, Jaslok Hospital and Research Centre, Mumbai, India
| | - Nikhil Dhope
- Department of Nephrology and Transplantation, Jaslok Hospital and Research Centre, Mumbai, India
| | - Madan M Bahadur
- Department of Nephrology and Transplantation, Jaslok Hospital and Research Centre, Mumbai, India
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