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DeBalsi KL, Newman JH, Sommerville LJ, Phillips JA, Hamid R, Cogan J, Fessel JP, Evans AM, Network UD, Kennedy AD. A Case Study of Dysfunctional Nicotinamide Metabolism in a 20-Year-Old Male. Metabolites 2023; 13:399. [PMID: 36984839 PMCID: PMC10055858 DOI: 10.3390/metabo13030399] [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: 01/31/2023] [Revised: 02/24/2023] [Accepted: 03/04/2023] [Indexed: 03/10/2023] Open
Abstract
We present a case study of a 20-year-old male with an unknown neurodegenerative disease who was referred to the Undiagnosed Diseases Network Vanderbilt Medical Center site. A previous metabolic panel showed that the patient had a critical deficiency in nicotinamide intermediates that are generated during the biosynthesis of NAD(H). We followed up on these findings by evaluating the patient's ability to metabolize nicotinamide. We performed a global metabolic profiling analysis of plasma samples that were collected: (1) under normal fed conditions (baseline), (2) after the patient had fasted, and (3) after he was challenged with a 500 mg nasogastric tube bolus of nicotinamide following the fast. Our findings showed that the patient's nicotinamide N-methyltransferase (NNMT), a key enzyme in NAD(H) biosynthesis and methionine metabolism, was not functional under normal fed or fasting conditions but was restored in response to the nicotinamide challenge. Altered levels of metabolites situated downstream of NNMT and in neighboring biochemical pathways provided further evidence of a baseline defect in NNMT activity. To date, this is the only report of a critical defect in NNMT activity manifesting in adulthood and leading to neurodegenerative disease. Altogether, this study serves as an important reference in the rare disease literature and also demonstrates the utility of metabolomics as a diagnostic tool for uncharacterized metabolic diseases.
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Affiliation(s)
| | - John H. Newman
- Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | | | | | - Rizwan Hamid
- Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Joy Cogan
- Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Joshua P. Fessel
- National Institutes of Health, National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
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Wang D, Zhou L, Zhou H, Hou G. Chemical composition and anti-inflammatory activity of n-butanol extract of Piper sarmentosum Roxb. In the intestinal porcine epithelial cells (IPEC-J2). JOURNAL OF ETHNOPHARMACOLOGY 2021; 269:113723. [PMID: 33358857 DOI: 10.1016/j.jep.2020.113723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Piper sarmentosum Roxb. (PS) is a terrestrial herb primarily distributed in tropical and subtropical regions of Asia. It is widely used in folk medicine in certain countries of Southeast Asia for the treatment of fever, toothache, coughing and pleurisy, which showed the anti-inflammatory activity of PS. AIM OF THE STUDY This study aimed to investigate the chemical constituents and the molecular mechanism and related metabolic pathway by which n-butanol extract of PS (PSE-NB) exerts its anti-inflammatory effects. MATERIALS AND METHODS Chemical constituents of PSE-NB was analyzed using ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) technique. Anti-inflammatory effects of PSE-NB were investigated in lipopolysaccharide (LPS)-induced IPEC-J2 cells. RESULTS In total, 218 compounds, including 94 alkaloids and 26 phenolics were tentatively identified, which indicating alkaloids and phenolics were the main constituents of PSE-NB. In addition, the current cell experiment in vitro showed that PSE-NB (10-500 μg/mL) pre-treatment before LPS stimulation significantly decreased mRNA expression of IL-1β, IL-6 and TNF-α in IPEC-J2 cells compared with LPS treatment (p < 0.05). PSE-NB improved mRNA expression of tight junction proteins (ZO-1 and Occludin) and NHE3, which were reduced by LPS stimulation (p < 0.05). Moreover, PSE-NB (10 μg/mL) alleviated LPS-induced protein expression of p65 and p-p65 (p < 0.05), and reduced p65 translocation into the nucleus induced by LPS. At the same time, metabolic pathway analysis indicated that PSE-NB exerts anti-inflammatory effects mainly via augmentation of methionine metabolism in IPEC-J2 cells. CONCLUSIONS Taken together, the results suggested that alkaloids and phenolics were the main constituents in PSE-NB. PSE-NB might attenuate LPS-induced inflammatory responses in IPEC-J2 cells by regulating NF-κB signaling pathway and intracellular metabolic pattern.
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Affiliation(s)
- Dingfa Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China
| | - Luli Zhou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China
| | - Hanlin Zhou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China.
| | - Guanyu Hou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China
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Tanemura KA, Das S, Merz KM. AutoGraph: Autonomous Graph-Based Clustering of Small-Molecule Conformations. J Chem Inf Model 2021; 61:1647-1656. [PMID: 33780248 DOI: 10.1021/acs.jcim.0c01492] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While accurately modeling the conformational ensemble is required for predicting properties of flexible molecules, the optimal method of obtaining the conformational ensemble appears as varied as their applications. Ensemble structures have been modeled by generation, refinement, and clustering of conformations with a sufficient number of samples. We present a conformational clustering algorithm intended to automate the conformational clustering step through the Louvain algorithm, which requires minimal hyperparameters and importantly no predefined number of clusters or threshold values. The conformational graphs produced by this method for O-succinyl-l-homoserine, oxidized nicotinamide adenine dinucleotide, and 200 representative metabolites each preserved the geometric/energetic correlation expected for points on the potential energy surface. Clustering based on these graphs provides partitions informed by the potential energy surface. Automating conformational clustering in a workflow with AutoGraph may mitigate human biases introduced by guess and check over hyperparameter selection while allowing flexibility to the result by not imposing predefined criteria other than optimizing the model's loss function. Associated codes are available at https://github.com/TanemuraKiyoto/AutoGraph.
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Affiliation(s)
- Kiyoto Aramis Tanemura
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Susanta Das
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
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Wilk A, Hayat F, Cunningham R, Li J, Garavaglia S, Zamani L, Ferraris DM, Sykora P, Andrews J, Clark J, Davis A, Chaloin L, Rizzi M, Migaud M, Sobol RW. Extracellular NAD + enhances PARP-dependent DNA repair capacity independently of CD73 activity. Sci Rep 2020; 10:651. [PMID: 31959836 PMCID: PMC6971268 DOI: 10.1038/s41598-020-57506-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/29/2019] [Indexed: 02/06/2023] Open
Abstract
Changes in nicotinamide adenine dinucleotide (NAD+) levels that compromise mitochondrial function trigger release of DNA damaging reactive oxygen species. NAD+ levels also affect DNA repair capacity as NAD+ is a substrate for PARP-enzymes (mono/poly-ADP-ribosylation) and sirtuins (deacetylation). The ecto-5′-nucleotidase CD73, an ectoenzyme highly expressed in cancer, is suggested to regulate intracellular NAD+ levels by processing NAD+ and its bio-precursor, nicotinamide mononucleotide (NMN), from tumor microenvironments, thereby enhancing tumor DNA repair capacity and chemotherapy resistance. We therefore investigated whether expression of CD73 impacts intracellular NAD+ content and NAD+-dependent DNA repair capacity. Reduced intracellular NAD+ levels suppressed recruitment of the DNA repair protein XRCC1 to sites of genomic DNA damage and impacted the amount of accumulated DNA damage. Further, decreased NAD+ reduced the capacity to repair DNA damage induced by DNA alkylating agents. Overall, reversal of these outcomes through NAD+ or NMN supplementation was independent of CD73. In opposition to its proposed role in extracellular NAD+ bioprocessing, we found that recombinant human CD73 only poorly processes NMN but not NAD+. A positive correlation between CD73 expression and intracellular NAD+ content could not be made as CD73 knockout human cells were efficient in generating intracellular NAD+ when supplemented with NAD+ or NMN.
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Affiliation(s)
- Anna Wilk
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Faisal Hayat
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Richard Cunningham
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Silvia Garavaglia
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
| | - Leila Zamani
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Davide M Ferraris
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
| | - Peter Sykora
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Amelia Technologies, 14676 Rothgeb Drive, Rockville, MD, 20850, USA
| | - Joel Andrews
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Jennifer Clark
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Amanda Davis
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Laurent Chaloin
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, 34293, Montpellier, France
| | - Menico Rizzi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
| | - Marie Migaud
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA. .,Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA.
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Kwolek-Mirek M, Maslanka R, Molon M. Disorders in NADPH generation via pentose phosphate pathway influence the reproductive potential of the Saccharomyces cerevisiae yeast due to changes in redox status. J Cell Biochem 2019; 120:8521-8533. [PMID: 30474881 DOI: 10.1002/jcb.28140] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/31/2018] [Indexed: 01/24/2023]
Abstract
Intermediary metabolites have a crucial impact on basic cell functions. There is a relationship between cellular metabolism and redox balance. To maintain redox homoeostasis, the cooperation of both glutathione and nicotine adenine dinucleotides is necessary. Availability of nicotinamide adenine dinucleotide phosphate (NADPH) as a major electron donor is critical for many intracellular redox reactions. The activity of glucose-6-phosphate dehydrogenase (Zwf1p) and 6-phosphogluconate dehydrogenase (Gnd1p and Gnd2p) is responsible for NADPH formation in a pentose phosphate (PP) pathway. In this study, we examine the impact of redox homoeostasis on cellular physiology and proliferation. We have noted that the Δzwf1 mutant lacking the rate-limiting enzyme of the PP pathway shows changes in the cellular redox status caused by disorders in NADPH generation. This leads to a decrease in reproductive potential but without affecting the total lifespan of the cell. The results presented in this paper show that nicotine adenine dinucleotides play a central role in cellular physiology.
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Affiliation(s)
- Magdalena Kwolek-Mirek
- Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszow, Rzeszow, Poland
| | - Roman Maslanka
- Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszow, Rzeszow, Poland
| | - Mateusz Molon
- Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszow, Rzeszow, Poland
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Abstract
Zinc(II) ions are redox-inert in biology. Yet, their interaction with sulfur of cysteine in cellular proteins can confer ligand-centered redox activity on zinc coordination sites, control protein functions, and generate signalling zinc ions as potent effectors of many cellular processes. The specificity and relative high affinity of binding sites for zinc allow regulation in redox biology, free radical biology, and the biology of reactive species. Understanding the role of zinc in these areas of biology requires an understanding of how cellular Zn2+ is homeostatically controlled and can serve as a regulatory ion in addition to Ca2+, albeit at much lower concentrations. A rather complex system of dozens of transporters and metallothioneins buffer the relatively high (hundreds of micromolar) total cellular zinc concentrations in such a way that the available zinc ion concentrations are only picomolar but can fluctuate in signalling. The proteins targeted by Zn2+ transients include enzymes controlling phosphorylation and redox signalling pathways. Networks of regulatory functions of zinc integrate gene expression and metabolic and signalling pathways at several hierarchical levels. They affect enzymatic catalysis, protein structure and protein-protein/biomolecular interactions and add to the already impressive number of catalytic and structural functions of zinc in an estimated three thousand human zinc proteins. The effects of zinc on redox biology have adduced evidence that zinc is an antioxidant. Without further qualifications, this notion is misleading and prevents a true understanding of the roles of zinc in biology. Its antioxidant-like effects are indirect and expressed only in certain conditions because a lack of zinc and too much zinc have pro-oxidant effects. Teasing apart these functions based on quantitative considerations of homeostatic control of cellular zinc is critical because opposite consequences are observed depending on the concentrations of zinc: pro- or anti-apoptotic, pro- or anti-inflammatory and cytoprotective or cytotoxic. The article provides a biochemical basis for the links between redox and zinc biology and discusses why zinc has pleiotropic functions. Perturbation of zinc metabolism is a consequence of conditions of redox stress. Zinc deficiency, either nutritional or conditioned, and cellular zinc overload cause oxidative stress. Thus, there is causation in the relationship between zinc metabolism and the many diseases associated with oxidative stress.
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Affiliation(s)
- Wolfgang Maret
- Metal Metabolism Group, Department of Nutritional Sciences, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.
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