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Li H, Hardy CD, Reidl CT, Jing Q, Xue F, Cinelli M, Silverman RB, Poulos TL. Crystallographic and Computational Insights into Isoform-Selective Dynamics in Nitric Oxide Synthase. Biochemistry 2024; 63:788-796. [PMID: 38417024 PMCID: PMC10956423 DOI: 10.1021/acs.biochem.3c00601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 03/01/2024]
Abstract
In our efforts to develop inhibitors selective for neuronal nitric oxide synthase (nNOS) over endothelial nitric oxide synthase (eNOS), we found that nNOS can undergo conformational changes in response to inhibitor binding that does not readily occur in eNOS. One change involves movement of a conserved tyrosine, which hydrogen bonds to one of the heme propionates, but in the presence of an inhibitor, changes conformation, enabling part of the inhibitor to hydrogen bond with the heme propionate. This movement does not occur as readily in eNOS and may account for the reason why these inhibitors bind more tightly to nNOS. A second structural change occurs upon the binding of a second inhibitor molecule to nNOS, displacing the pterin cofactor. Binding of this second site inhibitor requires structural changes at the dimer interface, which also occurs more readily in nNOS than in eNOS. Here, we used a combination of crystallography, mutagenesis, and computational methods to better understand the structural basis for these differences in NOS inhibitor binding. Computational results show that a conserved tyrosine near the primary inhibitor binding site is anchored more tightly in eNOS than in nNOS, allowing for less flexibility of this residue. We also find that the inefficiency of eNOS to bind a second inhibitor molecule is likely due to the tighter dimer interface in eNOS compared with nNOS. This study provides a better understanding of how subtle structural differences in NOS isoforms can result in substantial dynamic differences that can be exploited in the development of isoform-selective inhibitors.
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Affiliation(s)
- Huiying Li
- Departments
of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and
Chemistry, University of California, Irvine, California 92697-3900, United
States
| | - Christine D. Hardy
- Departments
of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and
Chemistry, University of California, Irvine, California 92697-3900, United
States
| | - Cory T. Reidl
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry of Life
Processes Institute, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Qing Jing
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry of Life
Processes Institute, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Fengtian Xue
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry of Life
Processes Institute, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Maris Cinelli
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry of Life
Processes Institute, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Richard B. Silverman
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry of Life
Processes Institute, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
- Department
of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
| | - Thomas L. Poulos
- Departments
of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and
Chemistry, University of California, Irvine, California 92697-3900, United
States
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2
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Mittal A, Kakkar R. Nitric Oxide Synthases and Their Inhibitors: A Review. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666190222154457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nitric Oxide (NO), an important biological mediator, is involved in the regulation of the cardiovascular, nervous and immune systems in mammals. Synthesis of NO is catalyzed by its biosynthetic enzyme, Nitric Oxide Synthase (NOS). There are three main isoforms of the enzyme, neuronal NOS, endothelial NOS and inducible NOS, which have very similar structures but differ in their expression and activities. NO is produced in the active site of the enzyme in two distinct cycles from oxidation of the substrate L-arg (L-arginine) in nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reaction. NOS has gained considerable attention of biochemists due to its complexity and unique catalytic mechanism. The review focuses on NOS structure, its function and catalytic reaction mechanism. In particular, the review is concluded with a discussion on the role of all three isoforms of NOS in physiological and pathological conditions and their inhibitors with a focus on the role of computational techniques in their development.
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Affiliation(s)
- Anshika Mittal
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
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3
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Cinelli MA, Li H, Chreifi G, Poulos TL, Silverman RB. Nitrile in the Hole: Discovery of a Small Auxiliary Pocket in Neuronal Nitric Oxide Synthase Leading to the Development of Potent and Selective 2-Aminoquinoline Inhibitors. J Med Chem 2017; 60:3958-3978. [PMID: 28422508 PMCID: PMC5567828 DOI: 10.1021/acs.jmedchem.7b00259] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Neuronal nitric oxide synthase (nNOS) inhibition is a promising strategy to treat neurodegenerative disorders, but the development of nNOS inhibitors is often hindered by poor pharmacokinetics. We previously developed a class of membrane-permeable 2-aminoquinoline inhibitors and later rearranged the scaffold to decrease off-target binding. However, the resulting compounds had decreased permeability, low human nNOS activity, and low selectivity versus human eNOS. In this study, 5-substituted phenyl ether-linked aminoquinolines and derivatives were synthesized and assayed against purified NOS isoforms. 5-Cyano compounds are especially potent and selective rat and human nNOS inhibitors. Activity and selectivity are mediated by the binding of the cyano group to a new auxiliary pocket in nNOS. Potency was enhanced by methylation of the quinoline and by introduction of simple chiral moieties, resulting in a combination of hydrophobic and auxiliary pocket effects that yielded high (∼500-fold) n/e selectivity. Importantly, the Caco-2 assay also revealed improved membrane permeability over previous compounds.
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Affiliation(s)
- Maris A. Cinelli
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Huiying Li
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Georges Chreifi
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Thomas L. Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Richard B. Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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4
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Holden JK, Dejam D, Lewis MC, Huang H, Kang S, Jing Q, Xue F, Silverman RB, Poulos TL. Inhibitor Bound Crystal Structures of Bacterial Nitric Oxide Synthase. Biochemistry 2015; 54:4075-82. [PMID: 26062720 DOI: 10.1021/acs.biochem.5b00431] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitric oxide generated by bacterial nitric oxide synthase (NOS) increases the susceptibility of Gram-positive pathogens Staphylococcus aureus and Bacillus anthracis to oxidative stress, including antibiotic-induced oxidative stress. Not surprisingly, NOS inhibitors also improve the effectiveness of antimicrobials. Development of potent and selective bacterial NOS inhibitors is complicated by the high active site sequence and structural conservation shared with the mammalian NOS isoforms. To exploit bacterial NOS for the development of new therapeutics, recognition of alternative NOS surfaces and pharmacophores suitable for drug binding is required. Here, we report on a wide number of inhibitor-bound bacterial NOS crystal structures to identify several compounds that interact with surfaces unique to the bacterial NOS. Although binding studies indicate that these inhibitors weakly interact with the NOS active site, many of the inhibitors reported here provide a revised structural framework for the development of new antimicrobials that target bacterial NOS. In addition, mutagenesis studies reveal several key residues that unlock access to bacterial NOS surfaces that could provide the selectivity required to develop potent bacterial NOS inhibitors.
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Affiliation(s)
- Jeffrey K Holden
- Departments of †Molecular Biology and Biochemistry, ‡Pharmaceutical Sciences, and §Chemistry, University of California, Irvine, California 92697-3900, United States.,∥Departments of Chemistry and Molecular Biosciences, ⊥Chemistry of Life Processes Institute, #Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Dillon Dejam
- Departments of †Molecular Biology and Biochemistry, ‡Pharmaceutical Sciences, and §Chemistry, University of California, Irvine, California 92697-3900, United States.,∥Departments of Chemistry and Molecular Biosciences, ⊥Chemistry of Life Processes Institute, #Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Matthew C Lewis
- Departments of †Molecular Biology and Biochemistry, ‡Pharmaceutical Sciences, and §Chemistry, University of California, Irvine, California 92697-3900, United States.,∥Departments of Chemistry and Molecular Biosciences, ⊥Chemistry of Life Processes Institute, #Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - He Huang
- Departments of †Molecular Biology and Biochemistry, ‡Pharmaceutical Sciences, and §Chemistry, University of California, Irvine, California 92697-3900, United States.,∥Departments of Chemistry and Molecular Biosciences, ⊥Chemistry of Life Processes Institute, #Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Soosung Kang
- Departments of †Molecular Biology and Biochemistry, ‡Pharmaceutical Sciences, and §Chemistry, University of California, Irvine, California 92697-3900, United States.,∥Departments of Chemistry and Molecular Biosciences, ⊥Chemistry of Life Processes Institute, #Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Qing Jing
- Departments of †Molecular Biology and Biochemistry, ‡Pharmaceutical Sciences, and §Chemistry, University of California, Irvine, California 92697-3900, United States.,∥Departments of Chemistry and Molecular Biosciences, ⊥Chemistry of Life Processes Institute, #Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Fengtian Xue
- Departments of †Molecular Biology and Biochemistry, ‡Pharmaceutical Sciences, and §Chemistry, University of California, Irvine, California 92697-3900, United States.,∥Departments of Chemistry and Molecular Biosciences, ⊥Chemistry of Life Processes Institute, #Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Richard B Silverman
- Departments of †Molecular Biology and Biochemistry, ‡Pharmaceutical Sciences, and §Chemistry, University of California, Irvine, California 92697-3900, United States.,∥Departments of Chemistry and Molecular Biosciences, ⊥Chemistry of Life Processes Institute, #Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Thomas L Poulos
- Departments of †Molecular Biology and Biochemistry, ‡Pharmaceutical Sciences, and §Chemistry, University of California, Irvine, California 92697-3900, United States.,∥Departments of Chemistry and Molecular Biosciences, ⊥Chemistry of Life Processes Institute, #Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
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5
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Mukherjee P, Cinelli MA, Kang S, Silverman RB. Development of nitric oxide synthase inhibitors for neurodegeneration and neuropathic pain. Chem Soc Rev 2014; 43:6814-38. [PMID: 24549364 PMCID: PMC4138306 DOI: 10.1039/c3cs60467e] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule in the human body, playing a crucial role in cell and neuronal communication, regulation of blood pressure, and in immune activation. However, overproduction of NO by the neuronal isoform of nitric oxide synthase (nNOS) is one of the fundamental causes underlying neurodegenerative disorders and neuropathic pain. Therefore, developing small molecules for selective inhibition of nNOS over related isoforms (eNOS and iNOS) is therapeutically desirable. The aims of this review focus on the regulation and dysregulation of NO signaling, the role of NO in neurodegeneration and pain, the structure and mechanism of nNOS, and the use of this information to design selective inhibitors of this enzyme. Structure-based drug design, the bioavailability and pharmacokinetics of these inhibitors, and extensive target validation through animal studies are addressed.
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Affiliation(s)
- Paramita Mukherjee
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA.
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6
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Jing Q, Li H, Roman LJ, Martásek P, Poulos TL, Silverman RB. Combination of chiral linkers with thiophenecarboximidamide heads to improve the selectivity of inhibitors of neuronal nitric oxide synthase. Bioorg Med Chem Lett 2014; 24:4504-4510. [PMID: 25149509 PMCID: PMC4204799 DOI: 10.1016/j.bmcl.2014.07.079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 07/25/2014] [Accepted: 07/29/2014] [Indexed: 11/18/2022]
Abstract
To develop potent and selective nNOS inhibitors, a new series of double-headed molecules with chiral linkers that derive from natural amino acid derivatives have been designed and synthesized. The new structures integrate a thiophenecarboximidamide head with two types of chiral linkers, presenting easy synthesis and good inhibitory properties. Inhibitor (S)-9b exhibits a potency of 14.7 nM against nNOS and is 1134 and 322-fold more selective for nNOS over eNOS and iNOS, respectively. Crystal structures show that the additional binding between the aminomethyl moiety of 9b and propionate A on the heme and tetrahydrobiopterin (H4B) in nNOS, but not eNOS, contributes to its high selectivity. This work demonstrates the advantage of integrating known structures into structure optimization, and it should be possible to more readily develop compounds that incorporate bioavailability with these advanced features. Moreover, this integrative strategy is a general approach in new drug discovery.
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Affiliation(s)
- Qing Jing
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA; Department of Molecular Biosciences, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA; Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA; Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
| | - Huiying Li
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA; Department of Pharmaceutical Chemistry, University of California, Irvine, CA 92697, USA; Department of Chemistry, University of California, Irvine, CA 92697, USA
| | - Linda J Roman
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78384-7760, USA
| | - Pavel Martásek
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78384-7760, USA; Department of Pediatrics and Center for Applied Genomics, 1st School of Medicine, Charles University, Prague, Czech Republic
| | - Thomas L Poulos
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA; Department of Pharmaceutical Chemistry, University of California, Irvine, CA 92697, USA; Department of Chemistry, University of California, Irvine, CA 92697, USA.
| | - Richard B Silverman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA; Department of Molecular Biosciences, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA; Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA; Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA.
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7
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Jing Q, Li H, Roman LJ, Martásek P, Poulos TL, Silverman RB. An Accessible Chiral Linker to Enhance Potency and Selectivity of Neuronal Nitric Oxide Synthase Inhibitors. ACS Med Chem Lett 2014; 5:56-60. [PMID: 24660051 DOI: 10.1021/ml400381s] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The three important mammalian isozymes of nitric oxide synthase (NOS) are neuronal NOS (nNOS), endothelial NOS (eNOS), and inducible NOS (iNOS). Inhibitors of nNOS show promise as treatments for neurodegenerative diseases. Eight easily-synthesized compounds containing either one (20a,b) or two (9a-d; 15a,b) 2-amino-4-methylpyridine groups with a chiral pyrrolidine linker were designed as selective nNOS inhibitors. Inhibitor 9c is the best of these compounds, having a potency of 9.7 nM and dual selectivity of 693 and 295 against eNOS and iNOS, respectively. Crystal structures of nNOS complexed with either 9a or 9c show a double-headed binding mode, where each 2-aminopyridine head group interacts with either a nNOS active site Glu residue or a heme propionate. In addition, the pyrrolidine nitrogen of 9c contributes additional hydrogen bonds to the heme propionate, resulting in a unique binding orientation. In contrast, the lack of hydrogen bonds from the pyrrolidine of 9a to the heme propionate allows the inhibitor to adopt two different binding orientations. Both 9a and 9c bind to eNOS in a single-headed mode, which is the structural basis for the isozyme selectivity.
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Affiliation(s)
- Qing Jing
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry
of Life Processes Institute, Center for Molecular Innovation and Drug
Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Huiying Li
- Departments
of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and
Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Linda J. Roman
- Department
of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas 78384-7760, United States
| | - Pavel Martásek
- Department
of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas 78384-7760, United States
- Department
of Pediatrics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Thomas L. Poulos
- Departments
of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and
Chemistry, University of California, Irvine, California 92697-3900, United States
| | - Richard B. Silverman
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry
of Life Processes Institute, Center for Molecular Innovation and Drug
Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
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8
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Structural and biological studies on bacterial nitric oxide synthase inhibitors. Proc Natl Acad Sci U S A 2013; 110:18127-31. [PMID: 24145412 DOI: 10.1073/pnas.1314080110] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitric oxide (NO) produced by bacterial NOS functions as a cytoprotective agent against oxidative stress in Staphylococcus aureus, Bacillus anthracis, and Bacillus subtilis. The screening of several NOS-selective inhibitors uncovered two inhibitors with potential antimicrobial properties. These two compounds impede the growth of B. subtilis under oxidative stress, and crystal structures show that each compound exhibits a unique binding mode. Both compounds serve as excellent leads for the future development of antimicrobials against bacterial NOS-containing bacteria.
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