1
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Ghosh R, Nair RR, Ghosh S, Debnath S, Chatterjee PB. A Water-Soluble Wavy Coordination Polymer of Cu(II) as a Turn-On Luminescent Probe for Histidine and Histidine-Rich Proteins/Peptides. Inorg Chem 2024; 63:8320-8328. [PMID: 38660721 DOI: 10.1021/acs.inorgchem.4c00665] [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: 04/26/2024]
Abstract
Histidine plays an essential role in most biological systems. Changes in the homeostasis of histidine and histidine-rich proteins are connected to several diseases. Herein, we report a water-soluble Cu(II) coordination polymer, labeled CuCP, for the fluorimetric detection of histidine and histidine-rich proteins and peptides. Single-crystal structure determination of CuCP revealed a two-dimensional wavy network structure in which a carboxylate group connects the individual Cu(II) dimer unit in a syn-anti conformation. The weakly luminescent and water-soluble CuCP shows turn-on blue emission in the presence of histidine and histidine-rich peptides and proteins. The polymer can also stain histidine-rich proteins via gel electrophoresis. The limits of quantifications for histidine, glycine-histidine, serine-histidine, human serum albumin (HSA), bovine serum albumin, pepsin, trypsin, and lysozyme were found to be 300, 160, 600, 300, 600, 800, 120, and 290 nM, respectively. Utilizing the fluorescence turn-on property of CuCP, we measured HSA quantitatively in the urine samples. We also validated the present urinary HSA measurement assay with existing analytical techniques. Job's plot, 1H NMR, high-resolution mass spectrometry (HRMS), electron paramagnetic resonance (EPR), fluorescence, and UV-vis studies confirmed the ligand displacement from CuCP in the presence of histidine.
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Affiliation(s)
- Riya Ghosh
- Analytical & Environmental Science Division and Centralized Instrument Facility, CSIR-CSMCRI, G. B. Marg, Bhavnagar 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ratish R Nair
- Analytical & Environmental Science Division and Centralized Instrument Facility, CSIR-CSMCRI, G. B. Marg, Bhavnagar 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shibaji Ghosh
- Analytical & Environmental Science Division and Centralized Instrument Facility, CSIR-CSMCRI, G. B. Marg, Bhavnagar 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Snehasish Debnath
- Analytical & Environmental Science Division and Centralized Instrument Facility, CSIR-CSMCRI, G. B. Marg, Bhavnagar 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pabitra B Chatterjee
- Analytical & Environmental Science Division and Centralized Instrument Facility, CSIR-CSMCRI, G. B. Marg, Bhavnagar 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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2
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Nguyen RC, Stagliano C, Liu A. Structural insights into the half-of-sites reactivity in homodimeric and homotetrameric metalloenzymes. Curr Opin Chem Biol 2023; 75:102332. [PMID: 37269676 PMCID: PMC10528533 DOI: 10.1016/j.cbpa.2023.102332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 04/24/2023] [Accepted: 04/29/2023] [Indexed: 06/05/2023]
Abstract
Half-of-sites reactivity in many homodimeric and homotetrameric metalloenzymes has been known for half a century, yet its benefit remains poorly understood. A recently reported cryo-electron microscopy structure has given some clues on the less optimized reactivity of Escherichia coli ribonucleotide reductase with an asymmetric association of α2β2 subunits during catalysis. Moreover, nonequivalence of enzyme active sites has been reported in many other enzymes, possibly as a means of regulation. They are often induced by substrate binding or caused by a critical component introduced from a neighboring subunit in response to substrate loadings, such as in prostaglandin endoperoxide H synthase, cytidine triphosphate synthase, glyoxalase, tryptophan dioxygenase, and several decarboxylases or dehydrogenases. Overall, half-of-sites reactivity is likely not an act of wasting resources but rather a method devised in nature to accommodate catalytic or regulatory needs.
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Affiliation(s)
- Romie C Nguyen
- Department of Chemistry, University of Texas, San Antonio, TX, 78249, USA
| | - Cassadee Stagliano
- Department of Chemistry, University of Texas, San Antonio, TX, 78249, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas, San Antonio, TX, 78249, USA.
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3
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Newton A, McCann L, Huo L, Liu A. Kynurenine Pathway Regulation at Its Critical Junctions with Fluctuation of Tryptophan. Metabolites 2023; 13:metabo13040500. [PMID: 37110158 PMCID: PMC10143591 DOI: 10.3390/metabo13040500] [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: 02/22/2023] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
The kynurenine pathway (KP) is the primary route for the catabolism of the essential amino acid tryptophan. The central KP metabolites are neurologically active molecules or biosynthetic precursors to critical molecules, such as NAD+. Within this pathway are three enzymes of interest, HAO, ACMSD, and AMSDH, whose substrates and/or products can spontaneously cyclize to form side products such as quinolinic acid (QA or QUIN) and picolinic acid. Due to their unstable nature for spontaneous autocyclization, it might be expected that the levels of these side products would be dependent on tryptophan intake; however, this is not the case in healthy individuals. On top of that, the regulatory mechanisms of the KP remain unknown, even after a deeper understanding of the structure and mechanism of the enzymes that handle these unstable KP metabolic intermediates. Thus, the question arises, how do these enzymes compete with the autocyclization of their substrates, especially amidst increased tryptophan levels? Here, we propose the formation of a transient enzyme complex as a regulatory mechanism for metabolite distribution between enzymatic and non-enzymatic routes during periods of increased metabolic intake. Amid high levels of tryptophan, HAO, ACMSD, and AMSDH may bind together, forming a tunnel to shuttle the metabolites through each enzyme, consequently regulating the autocyclization of their products. Though further research is required to establish the formation of transient complexation as a solution to the regulatory mysteries of the KP, our docking model studies support this new hypothesis.
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Affiliation(s)
- Ashley Newton
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Luree McCann
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Lu Huo
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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4
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Cianci M, Giacchè N, Cialabrini L, Carotti A, Liscio P, Rosatelli E, De Franco F, Gasparrini M, Robertson J, Amici A, Raffaelli N, Pellicciari R. Structural Basis of Human Dimeric α-Amino-β-Carboxymuconate-ε-Semialdehyde Decarboxylase Inhibition With TES-1025. Front Mol Biosci 2022; 9:834700. [PMID: 35463964 PMCID: PMC9021598 DOI: 10.3389/fmolb.2022.834700] [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: 12/13/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Human α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) stands at a branch point of the de novo NAD+ synthesis pathway and plays an important role in maintaining NAD+ homeostasis. It has been recently identified as a novel therapeutic target for a wide range of diseases, including inflammatory, metabolic disorders, and aging. So far, in absence of potent and selective enzyme inhibitors, only a crystal structure of the complex of human dimeric ACMSD with pseudo-substrate dipicolinic acid has been resolved. In this study, we report the crystal structure of the complex of human dimeric ACMSD with TES-1025, the first nanomolar inhibitor of this target, which shows a binding conformation different from the previously published predicted binding mode obtained by docking experiments. The inhibitor has a Ki value of 0.85 ± 0.22 nM and binds in the catalytic site, interacting with the Zn2+ metal ion and with residues belonging to both chains of the dimer. The results provide new structural information about the mechanism of inhibition exerted by a novel class of compounds on the ACMSD enzyme, a novel therapeutic target for liver and kidney diseases.
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Affiliation(s)
- Michele Cianci
- Biochemistry and Structural Biology Laboratory, Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
- *Correspondence: Michele Cianci, ; Nicola Giacchè,
| | - Nicola Giacchè
- TES Pharma S.r.l, Perugia, Italy
- *Correspondence: Michele Cianci, ; Nicola Giacchè,
| | - Lucia Cialabrini
- Biochemistry and Structural Biology Laboratory, Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | | | | | | | - Massimiliano Gasparrini
- Biochemistry and Structural Biology Laboratory, Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | | | - Adolfo Amici
- Department of Clinical Sciences DISCO, Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Nadia Raffaelli
- Biochemistry and Structural Biology Laboratory, Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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5
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Park SJ, Ahn JW, Choi JI. Improved tolerance of recombinant Chlamydomonas rainhardtii with putative 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pyropia yezoensis to nitrogen starvation. J Microbiol 2021; 60:63-69. [PMID: 34964943 DOI: 10.1007/s12275-022-1491-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022]
Abstract
In a previous study, a putative 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (ACMSD) was highly expressed in a mutant strain of Pyropia yezoensis, which exhibited an improved growth rate compared to its wild strain. To investigate the functional role of the putative ACMSD (Pyacmsd) of P. yezoensis, the putative Pyacmsd was cloned and expressed in Chlamydomonas reinhardtii. Recombinant C. reinhardtii cells with Pyacmsd (Cr_Pyacmsd) exhibited enhanced tolerance compared to control C. reinhardtii cells (Cr_control) under nitrogen starvation. Notably, Cr_Pyacmsd cells showed accumulation of lipids in nitrogen-enriched conditions. These results demonstrate the role of Pyacmsd in the generation of acetyl-coenzyme A. Thus, it can be used to enhance the production of biofuel using microalgae such as C. reinhardtii and increase the tolerance of other biological systems to nitrogen-deficient conditions.
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Affiliation(s)
- Seo-Jeong Park
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Joon Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Jong-Il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju, 61186, Republic of Korea.
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6
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The effect of 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase gene overexpression in the kynurenine pathway on the expression levels of indoleamine 2,3-dioxygenase 1 and interferon-γ in inflammatory conditions: an in vitro study. Mol Biol Rep 2021; 49:1103-1111. [PMID: 34775574 DOI: 10.1007/s11033-021-06935-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND The kynurenine pathway (KP) can be involved in the pathogenesis of neurodegenerative diseases and excessive neurotoxic metabolite production. This study aimed to evaluate the effects of overexpression of murine 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (Acmsd) gene in inflammatory conditions in RAW 264.7 cell line to present more information about the effect of this gene on inflammatory conditions and the KP cycle. METHODS AND RESULTS The coding sequence of the Acmsd gene was cloned into pCMV6-AC-IRES-GFP expression vector with a green fluorescent protein (GFP) marker. To simulate inflammatory conditions, RAW 264.7 macrophage cells were stimulated by Lipopolysaccharide (LPS) 24 h before transfection, and transfected by Polyethyleneimine (PEI) with constructed plasmids expressing the Acmsd gene. The effect of Acmsd gene expression level on murine Interferon-gamma (Ifn-γ) and murine Indoleamine 2,3-dioxygenase 1 (Ido1) gene expression level was investigated by Real-Time PCR. According to the results of this study, good transfection efficiency was observed 72 h after transfection, and Acmsd expression level increased 29-fold (P < 0.001) in transfected LPS-stimulated cells compared to the control group (LPS-stimulated cells that were not transfected). Additionally, increased Acmsd expression level significantly down-regulated Ifn-γ (P < 0.001) and Ido1 (P < 0.01) expression level in transfected LPS-stimulated cells compared to LPS-stimulated cells. CONCLUSIONS Acmsd gene overexpression in inflammatory conditions can reduce the expression levels of the Ido1 gene, and its regulator, Ifn-γ. Consequently, it may be considered as a novel regulatory factor in the KP balance.
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7
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Yang Y, Borel T, de Azambuja F, Johnson D, Sorrentino JP, Udokwu C, Davis I, Liu A, Altman RA. Diflunisal Derivatives as Modulators of ACMS Decarboxylase Targeting the Tryptophan-Kynurenine Pathway. J Med Chem 2020; 64:797-811. [PMID: 33369426 DOI: 10.1021/acs.jmedchem.0c01762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In the kynurenine pathway for tryptophan degradation, an unstable metabolic intermediate, α-amino-β-carboxymuconate-ε-semialdehyde (ACMS), can nonenzymatically cyclize to form quinolinic acid, the precursor for de novo biosynthesis of nicotinamide adenine dinucleotide (NAD+). In a competing reaction, ACMS is decarboxylated by ACMS decarboxylase (ACMSD) for further metabolism and energy production. Therefore, the inhibition of ACMSD increases NAD+ levels. In this study, an Food and Drug Administration (FDA)-approved drug, diflunisal, was found to competitively inhibit ACMSD. The complex structure of ACMSD with diflunisal revealed a previously unknown ligand-binding mode and was consistent with the results of inhibition assays, as well as a structure-activity relationship (SAR) study. Moreover, two synthesized diflunisal derivatives showed half-maximal inhibitory concentration (IC50) values 1 order of magnitude better than diflunisal at 1.32 ± 0.07 μM (22) and 3.10 ± 0.11 μM (20), respectively. The results suggest that diflunisal derivatives have the potential to modulate NAD+ levels. The ligand-binding mode revealed here provides a new direction for developing inhibitors of ACMSD.
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Affiliation(s)
- Yu Yang
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Timothy Borel
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | | | - David Johnson
- Computational Chemical Biology Core and Molecular Graphics and Modeling Laboratory, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Jacob P Sorrentino
- Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Chinedum Udokwu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Ian Davis
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Ryan A Altman
- Department of Medicinal Chemistry and Molecular Pharmacology and Department of Chemistry, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
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8
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Wang Y, Liu KF, Yang Y, Davis I, Liu A. Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens. Proc Natl Acad Sci U S A 2020; 117:19720-19730. [PMID: 32732435 PMCID: PMC7443976 DOI: 10.1073/pnas.2005327117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The synthesis of quinolinic acid from tryptophan is a critical step in the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD+) in mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4-dioxygenase responsible for quinolinic acid production was studied by performing time-resolved in crystallo reactions monitored by UV-vis microspectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and X-ray crystallography. Seven catalytic intermediates were kinetically and structurally resolved in the crystalline state, and each accompanies protein conformational changes at the active site. Among them, a monooxygenated, seven-membered lactone intermediate as a monodentate ligand of the iron center at 1.59-Å resolution was captured, which presumably corresponds to a substrate-based radical species observed by EPR using a slurry of small-sized single crystals. Other structural snapshots determined at around 2.0-Å resolution include monodentate and subsequently bidentate coordinated substrate, superoxo, alkylperoxo, and two metal-bound enol tautomers of the unstable dioxygenase product. These results reveal a detailed stepwise O-atom transfer dioxygenase mechanism along with potential isomerization activity that fine-tunes product profiling and affects the production of quinolinic acid at a junction of the metabolic pathway.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Yu Yang
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Ian Davis
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249;
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9
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Yang Y, Davis I, Matsui T, Rubalcava I, Liu A. Quaternary structure of α-amino-β-carboxymuconate-ϵ-semialdehyde decarboxylase (ACMSD) controls its activity. J Biol Chem 2019; 294:11609-11621. [PMID: 31189654 PMCID: PMC6663868 DOI: 10.1074/jbc.ra119.009035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/10/2019] [Indexed: 01/07/2023] Open
Abstract
α-Amino-β-carboxymuconate-ϵ-semialdehyde decarboxylase (ACMSD) plays an important role in l-tryptophan degradation via the kynurenine pathway. ACMSD forms a homodimer and is functionally inactive as a monomer because its catalytic assembly requires an arginine residue from a neighboring subunit. However, how the oligomeric state and self-association of ACMSD are controlled in solution remains unexplored. Here, we demonstrate that ACMSD from Pseudomonas fluorescens can self-assemble into homodimer, tetramer, and higher-order structures. Using size-exclusion chromatography coupled with small-angle X-ray scattering (SEC-SAXS) analysis, we investigated the ACMSD tetramer structure, and fitting the SAXS data with X-ray crystal structures of the monomeric component, we could generate a pseudo-atomic structure of the tetramer. This analysis revealed a tetramer model of ACMSD as a head-on dimer of dimers. We observed that the tetramer is catalytically more active than the dimer and is in equilibrium with the monomer and dimer. Substituting a critical residue of the dimer-dimer interface, His-110, altered the tetramer dissociation profile by increasing the higher-order oligomer portion in solution without changing the X-ray crystal structure. ACMSD self-association was affected by pH, ionic strength, and other electrostatic interactions. Alignment of ACMSD sequences revealed that His-110 is highly conserved in a few bacteria that utilize nitrobenzoic acid as a sole source of carbon and energy, suggesting a dedicated functional role of ACMSD's self-assembly into the tetrameric and higher-order structures. These results indicate that the dynamic oligomerization status potentially regulates ACMSD activity and that SEC-SAXS coupled with X-ray crystallography is a powerful tool for studying protein self-association.
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Affiliation(s)
- Yu Yang
- Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Ian Davis
- Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025
| | - Ivan Rubalcava
- Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Aimin Liu
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, To whom correspondence should be addressed. Tel.:
210-458-7062; E-mail:
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10
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Wang L, Li NN, Lu ZJ, Li JY, Peng JX, Duan LR, Peng R. Association of three candidate genetic variants in ACMSD/TMEM163, GPNMB and BCKDK /STX1B with sporadic Parkinson's disease in Han Chinese. Neurosci Lett 2019; 703:45-48. [PMID: 30880162 DOI: 10.1016/j.neulet.2019.03.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/18/2019] [Accepted: 03/12/2019] [Indexed: 02/05/2023]
Abstract
Large-scale meta-analyses of genome-wide association studies have identified that polymorphisms ACMSD/TMEM163 rs6430538, GPNMB rs199347 and BCKDK /STX1B rs14235 to be the risk loci for Parkinson's disease (PD) in a Caucasian population. However, the role of these three polymorphisms in a Han Chinese population from mainland China still remains to be clarified. We conducted a large sample study to examine genetic associations of rs6430538, rs199347 and rs14235 with PD in a Han Chinese population of 989 sporadic PD patients and 1058 healthy controls. All subjects were genotyped for these loci using the Sequenom iPLEX Assay. In addition, we conducted further stratified analysis according to age at onset and compared the clinical characteristics between minor allele carriers and non-carriers for each locus. However, no significant differences were found in genotype and allele frequency distribution between PD patients and controls for the three loci, even after being stratified by age at onset. Moreover, we demonstrated that minor allele carriers cannot be distinguished from non-carriers based on their clinical features. Our study is the first to demonstrate that ACMSD/TMEM163 rs6430538, GPNMB rs199347 and BCKDK /STX1B rs14235 do not confer a significant risk for sporadic PD in mainland China. Therefore, more replication studies in additional Chinese population and other cohorts and functional studies are warranted to further clarify the role of the three loci in PD susceptibility.
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Affiliation(s)
- Ling Wang
- Department of Neurology, West China Hospital, Sichuan University, Sichuan, China
| | - Nan-Nan Li
- Department of Neurology, West China Hospital, Sichuan University, Sichuan, China
| | - Zhong-Jiao Lu
- Department of Neurology, West China Hospital, Sichuan University, Sichuan, China
| | - Jun-Ying Li
- Department of Neurology, West China Hospital, Sichuan University, Sichuan, China
| | - Jia-Xin Peng
- Department of Neurology, West China Hospital, Sichuan University, Sichuan, China
| | - Li-Ren Duan
- Department of Neurology, West China Hospital, Sichuan University, Sichuan, China
| | - Rong Peng
- Department of Neurology, West China Hospital, Sichuan University, Sichuan, China.
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11
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Sharif T, Martell E, Dai C, Ghassemi-Rad MS, Kennedy BE, Lee PWK, Gujar S. Regulation of Cancer and Cancer-Related Genes via NAD . Antioxid Redox Signal 2019; 30:906-923. [PMID: 29334761 DOI: 10.1089/ars.2017.7478] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
SIGNIFICANCE NAD+ is an essential redox cofactor in cellular metabolism and has emerged as an important regulator of a wide spectrum of disease conditions, most notably, cancers. As such, various strategies targeting NAD+ synthesis in cancers are in clinical trials. Recent Advances: Being a substrate required for the activity of various enzyme families, especially sirtuins and poly(adenosine diphosphate [ADP]-ribose) polymerases, NAD+-mediated signaling plays an important role in gene expression, calcium release, cell cycle progression, DNA repair, and cell proliferation. Many strategies exploring the potential of interfering with NAD+ metabolism to sensitize cancer cells to achieve anticancer benefits are highly promising, and are being pursued. CRITICAL ISSUES With the multifaceted roles of NAD+ in cancer, it is important to understand how cellular processes are reliant on NAD+. This review summarizes how NAD+ metabolism regulates various pathophysiological processes in cancer, and how this knowledge can be exploited to devise effective anticancer therapies in clinical settings. FUTURE DIRECTIONS In line with the redundant pathways that facilitate NAD+ metabolism, further studies should comprehensively understand the roles of the various NAD+-synthesizing as well as NAD+-utilizing biomolecules to understand its true potential in cancer treatment.
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Affiliation(s)
- Tanveer Sharif
- 1 Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
| | - Emma Martell
- 2 Department of Pathology, Dalhousie University, Halifax, Canada
| | - Cathleen Dai
- 1 Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
| | | | - Barry E Kennedy
- 1 Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
| | - Patrick W K Lee
- 1 Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada.,2 Department of Pathology, Dalhousie University, Halifax, Canada
| | - Shashi Gujar
- 1 Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada.,2 Department of Pathology, Dalhousie University, Halifax, Canada.,3 Department of Biology, Dalhousie University, Halifax, Canada.,4 Centre for Innovative and Collaborative Health Systems Research, IWK Health Centre, Halifax, Canada
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12
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Patent highlights June-July 2018. Pharm Pat Anal 2019; 7:241-248. [PMID: 30632451 DOI: 10.4155/ppa-2018-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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13
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Hogancamp TN, Mabanglo MF, Raushel FM. Structure and Reaction Mechanism of the LigJ Hydratase: An Enzyme Critical for the Bacterial Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway. Biochemistry 2018; 57:5841-5850. [PMID: 30207699 DOI: 10.1021/acs.biochem.8b00713] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
LigJ from the soil bacterium Sphingobium sp. SYK-6 catalyzes the reversible hydration of (3 Z)-2-keto-4-carboxy-3-hexenedioate (KCH) to 4-carboxy-4-hydroxy-2-oxoadipate (CHA) in the degradation of lignin in the protocatechuate 4,5-cleavage pathway. LigJ is a member of the amidohydrolase superfamily and an enzyme in cog2159. The three-dimensional crystal structure of wild-type LigJ was determined in the presence [Protein Data Bank (PDB) entry 6DXQ ] and absence of the product CHA (PDB entry 6DWV ). The protein folds as a distorted (β/α)8-barrel, and a single zinc ion is bound in the active site at the C-terminal end of the central β-barrel. The product CHA is ligated to the zinc ion in the active site via the displacement of a single water molecule from the coordination shell of the metal center in LigJ. The product-bound structure reveals that the enzyme catalyzes the hydration of KCH with the formation of a chiral center at C4 with S stereochemistry. The E284Q mutant was unable to catalyze the hydration of KCH to CHA, and the structure of this mutant was determined in the presence of the substrate KCH (PDB entry 6DXS ). On the basis of the structure of LigJ in the presence of KCH and CHA, it is proposed that the side chain carboxylate of Glu-284 functions as a general base in the abstraction of a proton from a bound water molecule for nucleophilic attack at C4 of the substrate. The reaction is facilitated by the delocalization of the negative charge to the metal center via the carbonyl group at C2 of the substrate. C3 of the substrate is subsequently protonated by Glu-284 functioning as a general acid. The overall reaction occurs by the syn addition of water to the double bond between C4 and C3 of the substrate KCH. The kinetic constants for the hydration of KCH to CHA by LigJ at pH 8.0 are 25 s-1 ( kcat) and 2.6 × 106 M-1 s-1 ( kcat/ Km).
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Affiliation(s)
- Tessily N Hogancamp
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Mark F Mabanglo
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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Davis I, Yang Y, Wherritt D, Liu A. Reassignment of the human aldehyde dehydrogenase ALDH8A1 (ALDH12) to the kynurenine pathway in tryptophan catabolism. J Biol Chem 2018; 293:9594-9603. [PMID: 29703752 DOI: 10.1074/jbc.ra118.003320] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/25/2018] [Indexed: 12/17/2022] Open
Abstract
The kynurenine pathway is the primary route for l-tryptophan degradation in mammals. Intermediates and side products of this pathway are involved in immune response and neurodegenerative diseases. This makes the study of enzymes, especially those from mammalian sources, of the kynurenine pathway worthwhile. Recent studies on a bacterial version of an enzyme of this pathway, 2-aminomuconate semialdehyde (2-AMS) dehydrogenase (AMSDH), have provided a detailed understanding of the catalytic mechanism and identified residues conserved for muconate semialdehyde recognition and activation. Findings from the bacterial enzyme have prompted the reconsideration of the function of a previously identified human aldehyde dehydrogenase, ALDH8A1 (or ALDH12), which was annotated as a retinal dehydrogenase based on its ability to preferentially oxidize 9-cis-retinal over trans-retinal. Here, we provide compelling bioinformatics and experimental evidence that human ALDH8A1 should be reassigned to the missing 2-AMS dehydrogenase of the kynurenine metabolic pathway. For the first time, the product of the semialdehyde oxidation by AMSDH is also revealed by NMR and high-resolution MS. We found that ALDH8A1 catalyzes the NAD+-dependent oxidation of 2-AMS with a catalytic efficiency equivalent to that of AMSDH from the bacterium Pseudomonas fluorescens Substitution of active-site residues required for substrate recognition, binding, and isomerization in the bacterial enzyme resulted in human ALDH8A1 variants with 160-fold increased Km or no detectable activity. In conclusion, this molecular study establishes an additional enzymatic step in an important human pathway for tryptophan catabolism.
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Affiliation(s)
- Ian Davis
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Yu Yang
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Daniel Wherritt
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Aimin Liu
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249
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15
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Singh N, Dalal V, Kumar P. Structure based mimicking of Phthalic acid esters (PAEs) and inhibition of hACMSD, an important enzyme of the tryptophan kynurenine metabolism pathway. Int J Biol Macromol 2018; 108:214-224. [DOI: 10.1016/j.ijbiomac.2017.12.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/01/2017] [Accepted: 12/03/2017] [Indexed: 10/18/2022]
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16
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Pellicciari R, Liscio P, Giacchè N, De Franco F, Carotti A, Robertson J, Cialabrini L, Katsyuba E, Raffaelli N, Auwerx J. α-Amino-β-carboxymuconate-ε-semialdehyde Decarboxylase (ACMSD) Inhibitors as Novel Modulators of De Novo Nicotinamide Adenine Dinucleotide (NAD +) Biosynthesis. J Med Chem 2018; 61:745-759. [PMID: 29345930 DOI: 10.1021/acs.jmedchem.7b01254] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
NAD+ has a central function in linking cellular metabolism to major cell-signaling and gene-regulation pathways. Defects in NAD+ homeostasis underpin a wide range of diseases, including cancer, metabolic disorders, and aging. Although the beneficial effects of boosting NAD+ on mitochondrial fitness, metabolism, and lifespan are well established, to date, no therapeutic enhancers of de novo NAD+ biosynthesis have been reported. Herein we report the discovery of 3-[[[5-cyano-1,6-dihydro-6-oxo-4-(2-thienyl)-2-pyrimidinyl]thio]methyl]phenylacetic acid (TES-1025, 22), the first potent and selective inhibitor of human ACMSD (IC50 = 0.013 μM) that increases NAD+ levels in cellular systems. The results of physicochemical-property, ADME, and safety profiling, coupled with in vivo target-engagement studies, support the hypothesis that ACMSD inhibition increases de novo NAD+ biosynthesis and position 22 as a first-class molecule for the evaluation of the therapeutic potential of ACMSD inhibition in treating disorders with perturbed NAD+ supply or homeostasis.
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Affiliation(s)
| | - Paride Liscio
- TES Pharma S.r.l. , IT-06073 Corciano, Perugia, Italy
| | | | | | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia , IT-06123 Perugia, Italy
| | | | - Lucia Cialabrini
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche , IT-60131 Ancona, Italy
| | - Elena Katsyuba
- Laboratory of Integrative and Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne CH-1015 Lausanne, Switzerland
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche , IT-60131 Ancona, Italy
| | - Johan Auwerx
- Laboratory of Integrative and Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne CH-1015 Lausanne, Switzerland
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17
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Thirtamara-Rajamani K, Li P, Escobar Galvis ML, Labrie V, Brundin P, Brundin L. Is the Enzyme ACMSD a Novel Therapeutic Target in Parkinson's Disease? JOURNAL OF PARKINSON'S DISEASE 2017; 7:577-587. [PMID: 29103054 PMCID: PMC5676848 DOI: 10.3233/jpd-171240] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/13/2017] [Indexed: 02/07/2023]
Abstract
Several large genome wide association studies have identified a locus in close proximity to the gene encoding the enzyme aminocarboxymuconate-semialdehyde-decarboxylase (ACMSD) to be associated with the risk for Parkinson's disease (PD), tentatively suggesting that this enzyme might influence PD pathogenesis. Further support for this comes from the recent identification of a disease-segregating stop codon mutation in ACMSD in a family with Parkinsonism, and a missense mutation in the ACMSD gene predicted to disrupt enzyme function in an individual with typical PD. ACMSD is part of the kynurenine pathway, responsible for the catalytic breakdown of tryptophan into NAD+, generating several neuroactive metabolites in the process. The enzyme is located at a key branch-point of the pathway, limiting the production of the neurotoxin quinolinic acid, which has excitotoxic and inflammatory properties. In this review, we discuss the genetic findings in light of the functions of ACMSD and its potential involvement in PD pathogenesis.
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Affiliation(s)
| | - Peipei Li
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | | | - Viviane Labrie
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Patrik Brundin
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Lena Brundin
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
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18
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Yang Y, Davis I, Ha U, Wang Y, Shin I, Liu A. A Pitcher-and-Catcher Mechanism Drives Endogenous Substrate Isomerization by a Dehydrogenase in Kynurenine Metabolism. J Biol Chem 2016; 291:26252-26261. [PMID: 27810899 DOI: 10.1074/jbc.m116.759712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 10/18/2016] [Indexed: 11/06/2022] Open
Abstract
Aldehyde dehydrogenase typically performs oxidation of aldehydes to their corresponding carboxylic acid while reducing NAD(P)+ to NAD(P)H via covalent catalysis mediated by an active-site cysteine residue. One member of this superfamily, the enzyme 2-aminomuconate-6-semialdehyde dehydrogenase (AMSDH), is a component of the kynurenine pathway, which catabolizes tryptophan in mammals and certain bacteria. AMSDH catalyzes the NAD+-dependent oxidation of 2-aminomuconate semialdehyde to 2-aminomuconate. We recently determined the first crystal structure of AMSDH and several catalytic cycle intermediates. A conserved asparagine in the oxyanion hole, Asn-169, is found to be H-bonded to substrate-derived intermediates in the active site of AMSDH during catalysis, including both the covalently bound thiohemiacetal and thioacyl intermediates. To better interrogate the significance of the hydrogen bond provided by Asn-169 to the reaction mechanism of AMSDH, we created Ala, Ser, Asp, and Gln mutants and studied them using biochemical, kinetic, crystallographic, and computational studies. The in crystallo chemical reaction of the primary substrate with the co-crystalized complex of the N169D mutant and NAD+ led to the successful trapping of a new catalytic intermediate that was not previously seen. The structural and computational data are consistent with a substrate imine/enol tautomer intermediate being formed prior to the formation of the covalent bond between the substrate and the active-site cysteine. Thus, AMSDH surprisingly includes an isomerization process within its known catalytic mechanism. These data establish a hidden intrinsic isomerization activity of the dehydrogenase and allow us to propose a pitcher-catcher type of catalytic mechanism for the isomerization.
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Affiliation(s)
- Yu Yang
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and
| | - Ian Davis
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and.,the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Uyen Ha
- the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Yifan Wang
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and
| | - Inchul Shin
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and
| | - Aimin Liu
- From the Department of Chemistry, University of Texas, San Antonio, Texas 78249 and .,the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
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19
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Davis I, Liu A. What is the tryptophan kynurenine pathway and why is it important to neurotherapeutics? Expert Rev Neurother 2015; 15:719-21. [PMID: 26004930 DOI: 10.1586/14737175.2015.1049999] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The kynurenine pathway has received increasing attention as its connection to inflammation, the immune system and neurological conditions has become more apparent. It is the primary route for tryptophan catabolism in the liver and the starting point for the synthesis of nicotinamide adenine dinucleotide in mammals. Dysregulation or overactivation of this pathway can lead to immune system activation and accumulation of potentially neurotoxic compounds. These aspects make the kynurenine pathway a promising target for therapeutic development to treat inflammation and disease with neurological aspects, especially in cancer patients undergoing chemotherapy.
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Affiliation(s)
- Ian Davis
- Department of Chemistry, Atlanta, GA 30303, USA
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20
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Liu F, Geng J, Gumpper RH, Barman A, Davis I, Ozarowski A, Hamelberg D, Liu A. An Iron Reservoir to the Catalytic Metal: THE RUBREDOXIN IRON IN AN EXTRADIOL DIOXYGENASE. J Biol Chem 2015; 290:15621-15634. [PMID: 25918158 DOI: 10.1074/jbc.m115.650259] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Indexed: 01/06/2023] Open
Abstract
The rubredoxin motif is present in over 74,000 protein sequences and 2,000 structures, but few have known functions. A secondary, non-catalytic, rubredoxin-like iron site is conserved in 3-hydroxyanthranilate 3,4-dioxygenase (HAO), from single cellular sources but not multicellular sources. Through the population of the two metal binding sites with various metals in bacterial HAO, the structural and functional relationship of the rubredoxin-like site was investigated using kinetic, spectroscopic, crystallographic, and computational approaches. It is shown that the first metal presented preferentially binds to the catalytic site rather than the rubredoxin-like site, which selectively binds iron when the catalytic site is occupied. Furthermore, an iron ion bound to the rubredoxin-like site is readily delivered to an empty catalytic site of metal-free HAO via an intermolecular transfer mechanism. Through the use of metal analysis and catalytic activity measurements, we show that a downstream metabolic intermediate can selectively remove the catalytic iron. As the prokaryotic HAO is often crucial for cell survival, there is a need for ensuring its activity. These results suggest that the rubredoxin-like site is a possible auxiliary iron source to the catalytic center when it is lost during catalysis in a pathway with metabolic intermediates of metal-chelating properties. A spare tire concept is proposed based on this biochemical study, and this concept opens up a potentially new functional paradigm for iron-sulfur centers in iron-dependent enzymes as transient iron binding and shuttling sites to ensure full metal loading of the catalytic site.
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Affiliation(s)
- Fange Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303.
| | - Jiafeng Geng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303; Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303.
| | - Ryan H Gumpper
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Arghya Barman
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Ian Davis
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303; Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303; Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303
| | - Aimin Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303; Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303.
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