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Read T, Winigrad Z, Goliaei A, Liechty C, Grochala C, Damon L, Dickson J, Harris J, Pham C, Rimel J, Rhine C, Simpson D, Martin E, Azofeifa J. Abstract 2755: Identification of novel GPX4 inhibitors using global transcriptional reporters. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-2755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Induction of Ferroptosis is a promising strategy for treating therapy-resistant tumors including mesenchymal tumor types. We performed a phenotypic screen to identify small molecules that induce ferroptosis in mesenchymal cancer cells by screening for compounds whose toxicity could be rescued by the lipophilic antioxidant Ferrostatin-1. To identify compounds that induce GPX4-mediated ferroptosis, we identified several pharmacodynamic biomarkers specific to GPX4 inhibition using our nascent RNA sequencing platform, which allows for time-resolved snapshots of global transcription. We measured the transcriptional changes that occur in the hours following inhibition of GPX4 and identified HMOX1 as a robust biomarker of GPX4i-induced ferroptosis in mesenchymal cancer cell lines. Using HMOX1-induction as a guide, we uncovered a small number of compounds as potential GPX4 inhibitors. One such compound was validated as a bonafide GPX4 inhibitor through a variety of biochemical assays and selected for a hit-to-lead campaign. In addition to standard medicinal chemistry strategies, we are currently employing a newly-developed global transcriptional reporter system to stratify several novel series of GPX4 inhibitors by their transcriptional signatures. This approach represents a unique strategy for determining on- and off- target effects of a compound and for defining structure activity relationships within a chemical series.
Citation Format: Timothy Read, Zoe Winigrad, Ardeshir Goliaei, Cole Liechty, Carter Grochala, Leah Damon, John Dickson, Jason Harris, Casey Pham, Jenna Rimel, Christy Rhine, Dave Simpson, Eric Martin, Joey Azofeifa. Identification of novel GPX4 inhibitors using global transcriptional reporters [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2755.
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Chaudhury A, Zhu X, Chu L, Goliaei A, June CH, Kearns JD, Stein AM. Chimeric Antigen Receptor T Cell Therapies: A Review of Cellular Kinetic-Pharmacodynamic Modeling Approaches. J Clin Pharmacol 2021; 60 Suppl 1:S147-S159. [PMID: 33205434 DOI: 10.1002/jcph.1691] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/13/2020] [Indexed: 12/16/2022]
Abstract
Chimeric antigen receptor T cell (CAR-T cell) therapies have shown significant efficacy in CD19+ leukemias and lymphomas. There remain many challenges and questions for improving next-generation CAR-T cell therapies, and mathematical modeling of CAR-T cells may play a role in supporting further development. In this review, we introduce a mathematical modeling taxonomy for a set of relatively simple cellular kinetic-pharmacodynamic models that describe the in vivo dynamics of CAR-T cell and their interactions with cancer cells. We then discuss potential extensions of this model to include target binding, tumor distribution, cytokine-release syndrome, immunophenotype differentiation, and genotypic heterogeneity.
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Affiliation(s)
- Anwesha Chaudhury
- Pharmacometrics, Novartis Institutes of BioMedical Research, Cambridge, Massachusetts, USA
| | - Xu Zhu
- PK Sciences Oncology, Novartis Institutes of BioMedical Research, Cambridge, Massachusetts, USA
| | - Lulu Chu
- PK Sciences Modeling & Simulation, Novartis Institutes of BioMedical Research, Cambridge, Massachusetts, USA
| | - Ardeshir Goliaei
- PK Sciences Modeling & Simulation, Novartis Institutes of BioMedical Research, Cambridge, Massachusetts, USA
| | - Carl H June
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jeffrey D Kearns
- PK Sciences Modeling & Simulation, Novartis Institutes of BioMedical Research, Cambridge, Massachusetts, USA
| | - Andrew M Stein
- Pharmacometrics, Novartis Institutes of BioMedical Research, Cambridge, Massachusetts, USA
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Goliaei A, Woods HA, Tron AE, Belmonte MA, Secrist JP, Ferguson D, Drew L, Fretland AJ, Aldridge BB, Gibbons FD. Multiscale Model Identifies Improved Schedule for Treatment of Acute Myeloid Leukemia In Vitro With the Mcl-1 Inhibitor AZD5991. CPT Pharmacometrics Syst Pharmacol 2020; 9:561-570. [PMID: 32860732 PMCID: PMC7577016 DOI: 10.1002/psp4.12552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 04/20/2020] [Indexed: 11/06/2022]
Abstract
Anticancer efficacy is driven not only by dose but also by frequency and duration of treatment. We describe a multiscale model combining cell cycle, cellular heterogeneity of B‐cell lymphoma 2 family proteins, and pharmacology of AZD5991, a potent small‐molecule inhibitor of myeloid cell leukemia 1 (Mcl‐1). The model was calibrated using in vitro viability data for the MV‐4‐11 acute myeloid leukemia cell line under continuous incubation for 72 hours at concentrations of 0.03–30 μM. Using a virtual screen, we identified two schedules as having significantly different predicted efficacy and showed experimentally that a “short” schedule (treating cells for 6 of 24 hours) is significantly better able to maintain the rate of cell kill during treatment than a “long” schedule (18 of 24 hours). This work suggests that resistance can be driven by heterogeneity in protein expression of Mcl‐1 alone without requiring mutation or resistant subclones and demonstrates the utility of mathematical models in efficiently identifying regimens for experimental exploration.
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Affiliation(s)
- Ardeshir Goliaei
- Drug Metabolism and Pharmacokinetics (DMPK), Oncology R&D, AstraZeneca, Waltham, Massachusetts, USA.,Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Haley A Woods
- Bioscience, Oncology R&D, AstraZeneca, Waltham, Massachusetts, USA
| | - Adriana E Tron
- Bioscience, Oncology R&D, AstraZeneca, Waltham, Massachusetts, USA.,Agios Pharmaceuticals, Cambridge, Massachusetts, USA
| | | | - J Paul Secrist
- Bioscience, Oncology R&D, AstraZeneca, Waltham, Massachusetts, USA
| | - Douglas Ferguson
- Drug Metabolism and Pharmacokinetics (DMPK), Oncology R&D, AstraZeneca, Waltham, Massachusetts, USA
| | - Lisa Drew
- Bioscience, Oncology R&D, AstraZeneca, Waltham, Massachusetts, USA
| | - Adrian J Fretland
- Drug Metabolism and Pharmacokinetics (DMPK), Oncology R&D, AstraZeneca, Waltham, Massachusetts, USA
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA.,Department of Biomedical Engineering, Tufts University, Medford, Massachusetts, USA
| | - Francis D Gibbons
- Drug Metabolism and Pharmacokinetics (DMPK), Oncology R&D, AstraZeneca, Waltham, Massachusetts, USA
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Sarker M, Goliaei A, Golesi F, Poggi M, Cook A, Khan MAI, Temple BR, Stefanini L, Canault M, Bergmeier W, Campbell SL. Subcellular localization of Rap1 GTPase activator CalDAG-GEFI is orchestrated by interaction of its atypical C1 domain with membrane phosphoinositides. J Thromb Haemost 2020; 18:693-705. [PMID: 31758832 PMCID: PMC7050387 DOI: 10.1111/jth.14687] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/17/2019] [Accepted: 11/14/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND The small GTPase Rap1 and its guanine nucleotide exchange factor, CalDAG-GEFI (CDGI), are critical for platelet function and hemostatic plug formation. CDGI function is regulated by a calcium binding EF hand regulatory domain and an atypical C1 domain with unknown function. OBJECTIVE Here, we investigated whether the C1 domain controls CDGI subcellular localization, both in vitro and in vivo. METHODS CDGI interaction with phosphoinositides was studied by lipid co-sedimentation assays and molecular dynamics simulations. Cellular localization of CDGI was studied in heterologous cells by immunofluorescence and subcellular fractionation assays. RESULTS Lipid co-sedimentation studies demonstrated that the CDGI C1 domain associates with membranes through exclusive recognition of phosphoinositides, phosphatidylinositol (4,5)-biphosphate (PIP2) and phosphatidylinositol (3,4,5)-triphosphate (PIP3). Molecular dynamics simulations identified a phospholipid recognition motif consisting of residues exclusive to the CDGI C1 domain. Mutation of those residues abolished co-sedimentation of the C1 domain with lipid vesicles and impaired membrane localization of CDGI in heterologous cells. CONCLUSION Our studies identify a novel interaction between an atypical C1 domain and phosphatidylinositol (4,5)-biphosphate and phosphatidylinositol (3,4,5)-triphosphate in cellular membranes, which is critical for Rap1 signaling in health and disease.
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Affiliation(s)
- Muzaddid Sarker
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ardeshir Goliaei
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Marjorie Poggi
- Aix Marseille University, INSERM, INRA, Marseille, France
| | - Aaron Cook
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mohammad A. I. Khan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brenda R. Temple
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- RL Juliano Structural Bioinformatics Core, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lucia Stefanini
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Rome, Italy
| | | | - Wolfgang Bergmeier
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sharon L. Campbell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Goliaei A, Lau EY, Adhikari U, Schwegler E, Berkowitz ML. Behavior of P85 and P188 Poloxamer Molecules: Computer Simulations Using United-Atom Force-Field. J Phys Chem B 2016; 120:8631-41. [PMID: 27232763 DOI: 10.1021/acs.jpcb.6b03030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To study the interaction between poloxamer molecules and lipid bilayers using molecular dynamics simulation technique with the united-atom resolution, we augmented the GROMOS force-field to include poloxamers. We validated the force-field by calculating the radii of gyration of two poloxamers, P85 and P188, solvated in water and by considering the poloxamer density distributions at the air/water interface. The emphasis of our simulations was on the study of the interaction between poloxamers and lipid bilayer. At the water/lipid bilayer interface, we observed that both poloxamers studied, P85 and P188, behaved like surfactants: the hydrophilic blocks of poloxamers became adsorbed at the polar interface, while their hydrophobic block penetrated the interface into the aliphatic tail region of the lipid bilayer. We also observed that when P85 and P188 poloxamers interacted with damaged membranes that contained pores, the hydrophobic blocks of copolymers penetrated into the membrane in the vicinity of the pore and compressed the membrane. Due to this compression, water molecules were evacuated from the pore.
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Affiliation(s)
| | - Edmond Y Lau
- Lawrence Livermore National Laboratory , 7000 East Avenue, Livermore, California 94550, United States
| | | | - Eric Schwegler
- Lawrence Livermore National Laboratory , 7000 East Avenue, Livermore, California 94550, United States
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Adhikari U, Goliaei A, Berkowitz ML. Interaction of Poloxamers with Lipid Bilayer: Molecular Dynamics Simulations using United Atom and Coarse-Grained Force Fields. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Adhikari U, Goliaei A, Tsereteli L, Berkowitz ML. Properties of Poloxamer Molecules and Poloxamer Micelles Dissolved in Water and Next to Lipid Bilayers: Results from Computer Simulations. J Phys Chem B 2016; 120:5823-30. [PMID: 26719970 DOI: 10.1021/acs.jpcb.5b11448] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To study the properties of poloxamer molecules P85 and P188 and micelles containing these poloxamers in bulk water and also next to lipid bilayers, we performed coarse-grained molecular dynamics computer simulations. We used MARTINI force-field and adjusted Lennard-Jones nonbonded interaction strength parameters for poloxamer beads to take into account the presence of polarizable water. Simulations of systems containing poloxamer molecules or micelles solvated in bulk water showed that structural properties, such as radii of gyration of the molecules and micelles, agree with the ones inferred from experiments. We observed that P85 micelle is almost spherical in shape, whereas the P188 micelle is distorted from being spherical. Simulations containing systems with the water-lipid bilayer interface showed that hydrophilic blocks of poloxamers interact with lipid headgroups of the bilayer and remain at the interface, whereas hydrophobic blocks prefer to insert into the central hydrophobic region of the bilayer. Simulations containing poloxamer micelles next to lipid bilayer showed no permeation of these micelles into the bilayer. To study the "healing" properties of P188 poloxamer, we performed simulations on a system containing a P188 micelle next to "damaged" lipid bilayer containing a pore. We observed that hydrophobic chains of poloxamers got inserted into the bilayer through the pore region, ultimately closing the pore.
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Affiliation(s)
- Upendra Adhikari
- Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Ardeshir Goliaei
- Department of Biochemistry and Biophysics and Program in Molecular and Cellular Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Levan Tsereteli
- Theory and Bio-Systems, Max Planck Institute for Colloids and Interfaces , 14424 Potsdam, Germany
| | - Max L Berkowitz
- Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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Abstract
Shock wave induced cavitation denaturates blood–brain barrier tight junction proteins; this may result in various neurological complications.
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Affiliation(s)
- Upendra Adhikari
- Department of Chemistry
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
| | - Ardeshir Goliaei
- Department of Biochemistry and Biophysics and Program in Molecular and Cellular Biophysics
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
| | - Max L. Berkowitz
- Department of Chemistry
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
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Goliaei A, Adhikari U, Berkowitz ML. Opening of the blood-brain barrier tight junction due to shock wave induced bubble collapse: a molecular dynamics simulation study. ACS Chem Neurosci 2015; 6:1296-301. [PMID: 26075566 DOI: 10.1021/acschemneuro.5b00116] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Passage of a shock wave across living organisms may produce bubbles in the blood vessels and capillaries. It was suggested that collapse of these bubbles imposed by an impinging shock wave can be responsible for the damage or even destruction of the blood-brain barrier. To check this possibility, we performed molecular dynamics computer simulations on systems that contained a model of tight junction from the blood-brain barrier. In our model, we represent the tight junction by two pairs of interacting proteins, claudin-15. Some of the simulations were done in the absence of a nanobubble, some in its presence. Our simulations show that when no bubble is present in the system, no damage to tight junction is observed when the shock wave propagates across it. In the presence of a nanobubble, even when the impulse of the shock wave is relatively low, the implosion of the bubble causes serious damage to our model tight junction.
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Affiliation(s)
- Ardeshir Goliaei
- Department of Biochemistry
and Biophysics and Program
in Molecular and Cellular Biophysics, and ‡Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Upendra Adhikari
- Department of Biochemistry
and Biophysics and Program
in Molecular and Cellular Biophysics, and ‡Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Max L. Berkowitz
- Department of Biochemistry
and Biophysics and Program
in Molecular and Cellular Biophysics, and ‡Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Adhikari U, Goliaei A, Berkowitz ML. Mechanism of Membrane Poration by Shock Wave Induced Nanobubble Collapse: A Molecular Dynamics Study. J Phys Chem B 2015; 119:6225-34. [DOI: 10.1021/acs.jpcb.5b02218] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Upendra Adhikari
- Department
of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ardeshir Goliaei
- Department
of Biochemistry and Biophysics and Program in Molecular and Cellular
Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Max L. Berkowitz
- Department
of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Goliaei A, Santo KP, Berkowitz ML. Local pressure changes in lipid bilayers due to adsorption of melittin and magainin-h2 antimicrobial peptides: results from computer simulations. J Phys Chem B 2014; 118:12673-9. [PMID: 25299589 DOI: 10.1021/jp507919p] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We performed a series of coarse-grained computer simulations in order to study how the placement of melittin and magainin-h2 antimicrobial peptides on the surface of the bilayer changes the local pressure profiles in the bilayer. The simulations were done using the NPT ensemble when the total stress on the bilayer was zero and also using the NP(z)AT ensemble, with a nonzero total stress. In the NPT ensemble, although the total stress was zero, each leaflet of the bilayer experienced a nonzero stress, and the stresses are equal by magnitude, but opposite in their direction. The observed stresses acting on the monolayers may cause the rupture of the monolayers to release the stress. Our simulations were done at different peptide to lipid ratio (P/L). When the P/L ratio was 1/50 there was no large difference in the local pressure profile for bilayers with melittin versus bilayers with magainin-h2. When simulations were performed in the NP(z)AT ensemble at P/L = 3/100 we observed a large difference in the pressure profiles in the bilayers with melittin peptides compared to the bilayer with magainin-h2. The observed in this case difference in stress may explain the difference in actions of melittin and magainin at high P/L.
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Affiliation(s)
- Ardeshir Goliaei
- Department of Biochemistry and Biophysics and Program in Molecular and Cellular Biophysics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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Payabvash S, Ghahremani MH, Goliaei A, Mandegary A, Shafaroodi H, Amanlou M, Dehpour AR. Nitric oxide modulates glutathione synthesis during endotoxemia. Free Radic Biol Med 2006; 41:1817-28. [PMID: 17157184 DOI: 10.1016/j.freeradbiomed.2006.09.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Revised: 08/16/2006] [Accepted: 09/09/2006] [Indexed: 11/22/2022]
Abstract
Nitric oxide is known to modulate intracellular glutathione levels, but the relationship between nitric oxide synthesis and glutathione metabolism during endotoxemia is unknown. The present study was designed to examine the effects of increased nitric oxide formation on hepatic glutathione synthesis and antioxidant defense in endotoxemic mice. Our results demonstrate that hepatic glutathione synthesis is decreased for 24 h following injection of lipopolysaccharide (LPS). Administration of the cysteine precursor, L-2-oxothiazolidine-4-carboxylic acid (OTZ), failed to normalize hepatic glutathione concentration, and suggests that decreased gamma-glutamylcysteine ligase activity is primarily responsible for the decrease in hepatic glutathione levels during endotoxemia. Inhibition of nitric oxide synthesis prevented the endotoxin-induced changes in hepatic and plasma glutathione status and up-regulated liver glutathione and cysteine synthesis pathways at the level of gene expression. Furthermore, whereas the activity of glutathione peroxidase and glutathione S-transferase decreased during endotoxemia, both of these changes were prevented by inhibition of nitric oxide synthesis. In conclusion, increased nitric oxide synthesis during endotoxemia causes marked changes in glutathione flux and defenses against oxidative stress in the liver.
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Affiliation(s)
- Seyedmehdi Payabvash
- Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, PO Box 13145-784, Tehran, Iran
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