1
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Abstract
Protein glycation is a disease associated, non-enzymatic, posttranslational modification generated by endogenous dicarbonyl metabolites. Currently, there is a lack of chemical tools capable of studying protein adducts caused by this class of reactive species. Here, we report a chemical biology platform, termed T-DiP (targetable-dicarbonyl precursor), that releases a physiologically relevant dose of bio-orthogonally functionalized dicarbonyl probe upon irradiation with 365 nm light. This approach enables protein glycation to be controlled with spatiotemporal precision within live cells and expands the chemical toolbox needed to elucidate the roles of glycated proteins across various pathologies.
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Affiliation(s)
- Alexander K Hurben
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Peng Ge
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Jacob L Bouchard
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Todd M Doran
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
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2
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Ge P, Yang M, Bouchard JL, Dzamko N, Lewis SJG, Halliday GM, Doran TM. Chemoselective Bioconjugation of Amyloidogenic Protein Antigens to PEGylated Microspheres Enables Detection of α-Synuclein Autoantibodies in Human Plasma. Bioconjug Chem 2022; 33:301-310. [PMID: 35020392 DOI: 10.1021/acs.bioconjchem.1c00530] [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: 11/30/2022]
Abstract
The misfolding and subsequent aggregation of amyloidogenic proteins is a classic pathological hallmark of neurodegenerative diseases. Aggregates of the α-synuclein protein (αS) are implicated in Parkinson's disease (PD) pathogenesis, and naturally occurring autoantibodies to these aggregates are proposed to be potential early-stage biomarkers to facilitate the diagnosis of PD. However, upon misfolding, αS forms a multitude of quaternary structures of varying functions that are unstable ex vivo. Thus, when used as a capture agent in enzyme-linked immunosorbent assays (ELISAs), significant variance among laboratories has prevented the development of these valuable diagnostic tests. We reasoned that those conflicting results arise due to the high nonspecific binding and amyloid nucleation that are typical of ELISA platforms. In this work, we describe a multiplexed, easy-to-operate immunoassay that is generally applicable to quantify the levels of amyloid proteins and their binding partners, named Oxaziridine-Assisted Solid-phase Immunosorbent (OASIS) assay. The assay is built on a hydrophilic poly(ethylene glycol) scaffold that inhibits aggregate nucleation, which we show reduces assay variance when compared to similar ELISA measurements. To validate our OASIS assay in patient-derived samples, we measured the levels of naturally occurring antibodies against the αS monomer and oligomers in a cohort of donor plasma from patients diagnosed with PD. Using OASIS assays, we observed significantly higher titers of immunoglobulin G antibody recognizing αS oligomers in PD patients compared to those in healthy controls, while there was no significant difference in naturally occurring antibodies against the αS monomer. In addition to its development into a blood test to potentially predict or monitor PD, we anticipate that the OASIS assay will be of high utility for studies aimed at understanding protein misfolding, its pathology and symptomology in PD, and other neurodegenerative diseases.
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Affiliation(s)
- Peng Ge
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mu Yang
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jacob L Bouchard
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Nicolas Dzamko
- Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Simon J G Lewis
- Parkinson's Disease Research Clinic, Brain and Mind Centre, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Glenda M Halliday
- Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Todd M Doran
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
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3
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Hurben AK, Erber LN, Tretyakova NY, Doran TM. Proteome-Wide Profiling of Cellular Targets Modified by Dopamine Metabolites Using a Bio-Orthogonally Functionalized Catecholamine. ACS Chem Biol 2021; 16:2581-2594. [PMID: 34726906 PMCID: PMC9872492 DOI: 10.1021/acschembio.1c00629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Selective death of midbrain dopaminergic neurons is a hallmark pathology of Parkinson's disease (PD), but the molecular mechanisms that initiate the cascade of events resulting in neurodegeneration in PD remain unclear. Compelling evidence suggests that dysregulation of dopamine (DA) induces neuronal stress and damage responses that are operative processes in striatal degeneration preceding PD-like symptoms. Improper DA sequestration to vesicles raises cytosolic DA levels, which is rapidly converted into electrophilic dopaquinone species (DQs) that react readily with protein nucleophiles forming covalent modifications that alter the native structure and function of proteins. These so-called DA-protein adducts (DPAs) have been reported to play a role in neurotoxicity, and their abundance with respect to neurodegeneration has been linked to clinical and pathological features of PD that suggest that they play a causal role in PD pathogenesis. Therefore, characterizing DPAs is a critical first step in understanding the susceptibility of midbrain dopaminergic neurons during PD. To help achieve this goal, we report here a novel DA-mimetic (DAyne) containing a biorthogonal alkyne handle that exhibits a reactivity profile similar to DA in aqueous buffers. By linking DPAs formed with DAyne to a fluorescent reporter molecule, DPAs were visualized in fixed cells and within lysates. DAyne enabled global mapping of cellular proteins affected by DQ modification and their bioactive pathways through enrichment. Our proteomic profiling of DPAs in neuronal SH-SY5Y cells indicates that proteins susceptible to DPA formation are extant throughout the proteome, potentially influencing several diverse biological pathways involved in PD such as endoplasmic reticulum (ER) stress, cytoskeletal instability, proteotoxicity, and clathrin function. We validated that a protein involved in the ER stress pathway, protein disulfide isomerase 3 (PDIA3), which was enriched in our chemoproteomic analysis, is functionally inhibited by DA, providing evidence that dysregulated cellular DA may induce or exacerbate ER stress. Thus, DAyne provided new mechanistic insights into DA toxicity that may be observed during PD by enabling characterization of DPAs generated reproducibly at physiologically relevant quinone exposures. We anticipate our design and application of this reactivity-based probe will be generally applicable for clarifying mechanisms of metabolic quinone toxicity.
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Affiliation(s)
- Alexander K. Hurben
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Luke N. Erber
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Todd M. Doran
- Department of Medicinal Chemistry and Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
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4
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Doran TM, Nilsson BL. Incorporation of an Azobenzene β-Turn Peptidomimetic into Amyloid-β to Probe Potential Structural Motifs Leading to β-Sheet Self-Assembly. Methods Mol Biol 2018; 1777:387-406. [PMID: 29744850 DOI: 10.1007/978-1-4939-7811-3_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Alzheimer's disease (AD) is characterized by chronic neurodegeneration and the insidious accumulation of senile plaques comprised of the amyloid-β (Aβ) peptide. An important goal in AD research is to characterize the structural basis for how Aβ aggregates exert their noxious effects on neurons. We describe herein synthetic steps to incorporate a light-controlled β-turn mimetic, 3-(3-aminomethylphenylazo)-phenylacetic acid (AMPP), into the backbone of a putative turn region within Aβ. AMPP adopts a rigid β-hairpin turn when azobenzene is in the cis conformation, and can adopt an extended "β-arc" turn in the trans-azobenzene conformation. The long lifetimes of these conformationally stable isomers permit detailed biochemical analyses that help to clarify the controversial role played by these two types of turns during the toxic misfolding pathway of Aβ. Methods to photo-nucleate the cis- or trans-AMPP isomeric turns in aqueous buffer are also described. Finally, we detail selected techniques to characterize the Aβ aggregates derived from these photoisomerized variants.
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Affiliation(s)
- Todd M Doran
- Department of Medicinal Chemistry, Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, NY, USA.
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5
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DiMaio JTM, Doran TM, Ryan DM, Raymond DM, Nilsson BL. Modulating Supramolecular Peptide Hydrogel Viscoelasticity Using Biomolecular Recognition. Biomacromolecules 2017; 18:3591-3599. [PMID: 28872306 DOI: 10.1021/acs.biomac.7b00925] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Self-assembled peptide-based hydrogels are emerging materials that have been exploited for wound healing, drug delivery, tissue engineering, and other applications. In comparison to synthetic polymer hydrogels, supramolecular peptide-based gels have advantages in biocompatibility, biodegradability, and ease of synthesis and modification. Modification of the emergent viscoelasticity of peptide hydrogels in a stimulus responsive fashion is a longstanding goal in the development of next-generation materials. In an effort to selectively modulate hydrogel viscoelasticity, we report herein a method to enhance the elasticity of β-sheet peptide hydrogels using specific molecular recognition events between functionalized hydrogel fibrils and biomolecules. Two distinct biomolecular recognition strategies are demonstrated: oligonucleotide Watson-Crick duplex formation between peptide nucleic acid (PNA) modified fibrils with a bridging oligonucleotide and protein-ligand recognition between mannose modified fibrils with concanavalin A. These methods to modulate hydrogel elasticity should be broadly adaptable in the context of these materials to a wide variety of molecular recognition partners.
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Affiliation(s)
- John T M DiMaio
- University of Rochester , Department of Chemistry, Rochester, New York 14627, United States
| | - Todd M Doran
- University of Rochester , Department of Chemistry, Rochester, New York 14627, United States
| | - Derek M Ryan
- University of Rochester , Department of Chemistry, Rochester, New York 14627, United States
| | - Danielle M Raymond
- University of Rochester , Department of Chemistry, Rochester, New York 14627, United States
| | - Bradley L Nilsson
- University of Rochester , Department of Chemistry, Rochester, New York 14627, United States
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6
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Abstract
Methods to monitor and manipulate the immune system are of enormous clinical interest. For example, the development of vaccines represents one of the earliest and greatest accomplishments of the biomedical research enterprise. More recently, drugs capable of "reawakening" the immune system to cancer have generated enormous excitement. But, much remains to be done. All drugs available today that manipulate the immune system cannot distinguish between "good" and "bad" immune responses and thus drive general and systemic immune suppression or activation. Indeed, with the notable exception of vaccines, our ability to monitor and manipulate antigen-specific immune responses is in its infancy. Achieving this finer level of control would be highly desirable. For example, it might allow the pharmacological editing of pathogenic immune responses without restricting the ability of the immune system to defend against infection. On the diagnostic side, a method to comprehensively monitor the circulating, antigen-specific antibody population could provide a treasure trove of clinically useful biomarkers, since many diseases expose the immune system to characteristic molecules that are deemed foreign and elicit the production of antibodies against them. This Perspective will discuss the state-of-the-art of this area with a focus on what we consider seminal opportunities for the chemistry community to contribute to this important field.
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Affiliation(s)
- Todd M. Doran
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Mohosin Sarkar
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Thomas Kodadek
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
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7
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Doran TM, Morimoto J, Simanski S, Koesema EJ, Clark LF, Pels K, Stoops SL, Pugliese A, Skyler JS, Kodadek T. Discovery of Phosphorylated Peripherin as a Major Humoral Autoantigen in Type 1 Diabetes Mellitus. Cell Chem Biol 2016; 23:618-628. [PMID: 27185639 DOI: 10.1016/j.chembiol.2016.04.006] [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] [Received: 12/02/2015] [Revised: 04/03/2016] [Accepted: 04/07/2016] [Indexed: 12/21/2022]
Abstract
A major goal in understanding autoimmune diseases is to define the antigens that elicit a self-destructive immune response, but this is a difficult endeavor. In an effort to discover autoantigens associated with type 1 diabetes (T1D), we used epitope surrogate technology that screens combinatorial libraries of synthetic molecules for compounds that could recognize disease-linked autoantibodies and enrich them from serum. Autoantibodies from one patient revealed a highly phosphorylated form of peripherin, a neuroendocrine filament protein, as a candidate T1D antigen. Peripherin antibodies were detected in 72% of donor patient sera. Further analysis revealed that the T1D-associated antibodies only recognized a dimeric conformation of peripherin. These data explain why peripherin was dismissed as an important T1D antigen previously. The discovery of this novel autoantigen would not have been possible using standard methods, such as hybridizing serum antibodies to recombinant protein arrays, highlighting the power of epitope surrogate technology for probing the mechanism of autoimmune diseases.
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Affiliation(s)
- Todd M Doran
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jumpei Morimoto
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Scott Simanski
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Eric J Koesema
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Lorraine F Clark
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Kevin Pels
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Sydney L Stoops
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Alberto Pugliese
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33101, USA; Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| | - Jay S Skyler
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| | - Thomas Kodadek
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
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8
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Doran TM, Gao Y, Simanski S, McEnaney P, Kodadek T. High affinity binding of conformationally constrained synthetic oligomers to an antigen-specific antibody: Discovery of a diagnostically useful synthetic ligand for murine Type 1 diabetes autoantibodies. Bioorg Med Chem Lett 2015; 25:4910-4917. [PMID: 26067174 PMCID: PMC4607566 DOI: 10.1016/j.bmcl.2015.05.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 04/06/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
Abstract
'Antigen surrogates' are synthetic, non-natural molecules that recognize the antigen-binding sites of antibodies. These molecules are of interest as replacements for native antigens as antibody 'capture agents' in ELISA-like assays of potential diagnostic utility, for example when the antibody is indicative of a disease state. Antigen surrogates for disease-related antibodies can be mined from one-bead one-compound (OBOC) libraries by first denuding the library of ligands for antibodies present in the serum of control patients or animals, followed by screening the remainder of the library against serum from individuals with a particular disease of interest. Most of the work in this area has been done with peptoids (oligomers of N-alkylated glycine), which provide antibody ligands with only modest affinity and selectivity. Here, we explore the hypothesis that this is due to the 'floppiness' of the peptoid backbone by creating libraries of peptoid-like molecules that have conformation-restricting structural elements inserted into their backbones. Indeed, we show here that these libraries can provide high affinity and selectivity antigen surrogates and that this much-improved binding is completely dependent on conformational restriction of the oligomer chain.
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Affiliation(s)
- Todd M Doran
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Yu Gao
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Scott Simanski
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Patrick McEnaney
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Thomas Kodadek
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States.
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9
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Doran TM, Morimoto J, Simanski S, McEnaney PJ, Kodadek T. Reliable diagnosis of murine type 1 diabetes using a panel of autoantigens and "antigen surrogates" mounted onto a liquid array. Mol Biosyst 2015; 11:3156-63. [PMID: 26390856 PMCID: PMC4605892 DOI: 10.1039/c5mb00521c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Autoantibodies raised against β cell antigens are the most reliable preclinical biomarkers for predicting the imminent onset of type 1 diabetes mellitus (T1DM). The most current detection platforms are technically challenging or are run on clinically esoteric equipment. Here, we present a straightforward approach to detect autoantibody biomarkers that employs highly PEGylated microspheres onto which are mounted various capture agents that include affinity-tagged antigens or small molecule "antigen surrogates." After incubation with small quantities of serum, the bound autoantibodies can be measured using a standard flow cytometer. By multiplexing this assay, we show that a panel of antigen and antigen surrogates reliably predicts hyperglycemia in a mouse model of diabetes without false positives.
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Affiliation(s)
- Todd M Doran
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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10
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Doran TM, Simanski S, Kodadek T. Discovery of native autoantigens via antigen surrogate technology: application to type 1 diabetes. ACS Chem Biol 2015; 10:401-12. [PMID: 25474415 PMCID: PMC4339956 DOI: 10.1021/cb5007618] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/04/2014] [Indexed: 01/23/2023]
Abstract
A fundamental goal in understanding the mechanisms of autoimmune disease is the characterization of autoantigens that are targeted by autoreactive antibodies and T cells. Unfortunately, the identification of autoantigens is a difficult problem. We have begun to explore a novel route to the discovery of autoantibody/autoantigen pairs that involves comparative screening of combinatorial libraries of unnatural, synthetic molecules for compounds that bind antibodies present at much higher levels in the serum of individuals with a given autoimmune disease than in the serum of control individuals. We have shown that this approach can yield "antigen surrogates" capable of capturing disease-specific autoantibodies from serum. In this report, we demonstrate that the synthetic antigen surrogates can be used to affinity purify the autoantibodies from serum and that these antibodies can then be used to identify their cognate autoantigen in an appropriate tissue lysate. Specifically, we report the discovery of a peptoid able to bind autoantibodies present in about one-third of nonobese diabetic (NOD) mice. The peptoid-binding autoantibodies were highly enriched through peptoid affinity chromatography and employed to probe mouse pancreatic and brain lysates. This resulted in identification of murine GAD65 as the native autoantigen. GAD65 is a known humoral autoantigen in human type 1 diabetes mellitus (T1DM), but its existence in mice had been controversial. This study demonstrates the potential of this chemical approach for the unbiased identification of autoantigen/autoantibody complexes.
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Affiliation(s)
- Todd M. Doran
- Departments
of Chemistry
& Cancer Biology, The Scripps Research
Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
| | - Scott Simanski
- Departments
of Chemistry
& Cancer Biology, The Scripps Research
Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments
of Chemistry
& Cancer Biology, The Scripps Research
Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
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11
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Doran TM, Gao Y, Mendes K, Dean S, Simanski S, Kodadek T. Utility of redundant combinatorial libraries in distinguishing high and low quality screening hits. ACS Comb Sci 2014; 16:259-70. [PMID: 24749624 PMCID: PMC4053090 DOI: 10.1021/co500030f] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Large
one-bead one-compound (OBOC) combinatorial libraries can
be constructed relatively easily by solid-phase split and pool synthesis.
The use of resins with hydrophilic surfaces, such as TentaGel, allows
the beads to be used directly in screens for compounds that bind selectively
to labeled proteins, nucleic acids, or other biomolecules. However,
we have found that this method, while useful, has a high false positive
rate. In other words, beads that are scored as hits often display
compounds that prove to be poor ligands for the target of interest
when they are resynthesized and carried through validation trials.
This results in a significant waste of time and resources in cases
where putative hits cannot be validated without resynthesis. Here,
we report that this problem can be largely eliminated through the
use of redundant OBOC libraries, where more than one bead displaying
the same compound is present in the screen. We show that compounds
isolated more than once are likely to be high quality ligands for
the target of interest, whereas compounds isolated only once have
a much higher likelihood of being poor ligands. While the use of redundant
libraries does limit the number of unique compounds that can be screened
at one time in this format, the overall savings in time, effort, and
materials makes this a more efficient route to the isolation of useful
ligands for biomolecules.
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Affiliation(s)
- Todd M. Doran
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Yu Gao
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Kimberly Mendes
- OPKO Health, Inc., 555 Heritage
Drive, Jupiter, Florida 33458, United States
| | - Sonja Dean
- OPKO Health, Inc., 555 Heritage
Drive, Jupiter, Florida 33458, United States
| | - Scott Simanski
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
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12
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Abstract
Synthetic molecule microarrays, consisting of many different compounds spotted onto a planar surface such as modified glass or cellulose, have proven to be useful tools for the multiplexed analysis of small molecule- and peptide-protein interactions. However, these arrays are technically difficult to manufacture and use with high reproducibility and require specialized equipment. Here we report a more convenient alternative composed of color-encoded beads that display a small molecule protein ligand on the surface. Quantitative, multiplexed assay of protein binding to up to 24 different ligands can be achieved using a common flow cytometer for the readout. This technology should be useful for evaluating hits from library screening efforts, the determination of structure activity relationships, and certain types of serological analyses.
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Affiliation(s)
- Todd M Doran
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida , 130 Scripps Way, Jupiter , Florida 33458, United States
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13
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Abstract
Peptide hydrogels are promising biomaterials for applications ranging from drug delivery to tissue engineering.
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Affiliation(s)
- Todd M. Doran
- Department of Chemistry
- University of Rochester
- Rochester
- USA
| | - Derek M. Ryan
- Department of Chemistry
- University of Rochester
- Rochester
- USA
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14
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Doran TM, Anderson EA, Latchney SE, Opanashuk LA, Nilsson BL. Correction to An Azobenzene Photoswitch Sheds Light on Turn Nucleation in Amyloid-β Self-Assembly. ACS Chem Neurosci 2012. [DOI: 10.1021/cn300032g] [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: 11/29/2022] Open
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15
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Doran TM, Anderson EA, Latchney SE, Opanashuk LA, Nilsson BL. An azobenzene photoswitch sheds light on turn nucleation in amyloid-β self-assembly. ACS Chem Neurosci 2012; 3:211-20. [PMID: 22860190 DOI: 10.1021/cn2001188] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [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: 11/25/2011] [Revised: 01/09/2012] [Indexed: 11/30/2022] Open
Abstract
Amyloid-β (Aβ) self-assembly into cross-β amyloid fibrils is implicated in a causative role in Alzheimer's disease pathology. Uncertainties persist regarding the mechanisms of amyloid self-assembly and the role of metastable prefibrillar aggregates. Aβ fibrils feature a sheet-turn-sheet motif in the constituent β-strands; as such, turn nucleation has been proposed as a rate-limiting step in the self-assembly pathway. Herein, we report the use of an azobenzene β-hairpin mimetic to study the role turn nucleation plays on Aβ self-assembly. [3-(3-Aminomethyl)phenylazo]phenylacetic acid (AMPP) was incorporated into the putative turn region of Aβ42 to elicit temporal control over Aβ42 turn nucleation; it was hypothesized that self-assembly would be favored in the cis-AMPP conformation if β-hairpin formation occurs during Aβ self-assembly and that the trans-AMPP conformer would display attenuated fibrillization propensity. It was unexpectedly observed that the trans-AMPP Aβ42 conformer forms fibrillar constructs that are similar in almost all characteristics, including cytotoxicity, to wild-type Aβ42. Conversely, the cis-AMPP Aβ42 congeners formed nonfibrillar, amorphous aggregates that exhibited no cytotoxicity. Additionally, cis-trans photoisomerization resulted in rapid formation of native-like amyloid fibrils and trans-cis conversion in the fibril state reduced the population of native-like fibrils. Thus, temporal photocontrol over Aβ turn conformation provides significant insight into Aβ self-assembly. Specifically, Aβ mutants that adopt stable β-turns form aggregate structures that are unable to enter folding pathways leading to cross-β fibrils and cytotoxic prefibrillar intermediates.
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Affiliation(s)
- Todd M. Doran
- Department of Chemistry, University of Rochester, Rochester, New York 14627,
United States
| | - Elizabeth A. Anderson
- Department of Chemistry, University of Rochester, Rochester, New York 14627,
United States
| | - Sarah E. Latchney
- Department
of Environmental
Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | - Lisa A. Opanashuk
- Department
of Environmental
Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | - Bradley L. Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627,
United States
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Olsen JS, DiMaio JTM, Doran TM, Brown C, Nilsson BL, Dewhurst S. Seminal plasma accelerates semen-derived enhancer of viral infection (SEVI) fibril formation by the prostatic acid phosphatase (PAP248-286) peptide. J Biol Chem 2012; 287:11842-9. [PMID: 22354963 PMCID: PMC3320932 DOI: 10.1074/jbc.m111.314336] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Amyloid fibrils contained in semen, known as SEVI, or semen-derived enhancer of viral infection, have been shown to increase the infectivity of HIV dramatically. However, previous work with these fibrils has suggested that extensive time and nonphysiologic levels of agitation are necessary to induce amyloid formation from the precursor peptide (a proteolytic cleavage product of prostatic acid phosphatase, PAP248–286). Here, we show that fibril formation by PAP248–286 is accelerated dramatically in the presence of seminal plasma (SP) and that agitation is not required for fibrillization in this setting. Analysis of the effects of specific SP components on fibril formation by PAP248–286 revealed that this effect is primarily due to the anionic buffer components of SP (notably inorganic phosphate and sodium bicarbonate). Divalent cations present in SP had little effect on the kinetics of fibril formation, but physiologic levels of Zn2+ strongly protected SEVI fibrils from degradation by seminal proteases. Taken together, these data suggest that in the in vivo environment, PAP248–286 is likely to form fibrils efficiently, thus providing an explanation for the presence of SEVI in human semen.
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Affiliation(s)
- Joanna S Olsen
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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Doran TM, Anderson EA, Latchney SE, Opanashuk LA, Nilsson BL. Turn nucleation perturbs amyloid β self-assembly and cytotoxicity. J Mol Biol 2012; 421:315-28. [PMID: 22326870 DOI: 10.1016/j.jmb.2012.01.055] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 01/27/2012] [Accepted: 01/31/2012] [Indexed: 10/14/2022]
Abstract
The accumulation of senile plaques composed of amyloid β (Aβ) fibrils is a hallmark of Alzheimer's disease, although prefibrillar oligomeric species are believed to be the primary neurotoxic congeners in the pathogenesis of Alzheimer's disease. Uncertainty regarding the mechanistic relationship between Aβ oligomer and fibril formation and the cytotoxicity of these aggregate species persists. β-Turn formation has been proposed to be a potential rate-limiting step during Aβ fibrillogenesis. The effect of turn nucleation on Aβ self-assembly was probed by systematically replacing amino acid pairs in the putative turn region of Aβ (residues 24-27) with d-ProGly ((D)PG), an effective turn-nucleating motif. The kinetic, thermodynamic, and cytotoxic effects of these mutations were characterized. It was found that turn formation dramatically accelerated Aβ fibril self-assembly dependent on the site of turn nucleation. The cytotoxicity of the three (D)PG-containing Aβ variants was significantly lower than that of wild-type Aβ40, presumably due to decreased oligomer populations as a function of a more rapid progression to mature fibrils; oligomer populations were not eliminated, however, suggesting that turn formation is also a feature of oligomer structures. These results indicate that turn nucleation is a critical step in Aβ40 fibril formation.
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Affiliation(s)
- Todd M Doran
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
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Doran TM, Kamens AJ, Byrnes NK, Nilsson BL. Role of amino acid hydrophobicity, aromaticity, and molecular volume on IAPP(20-29) amyloid self-assembly. Proteins 2012; 80:1053-65. [DOI: 10.1002/prot.24007] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 11/12/2011] [Accepted: 11/18/2011] [Indexed: 01/22/2023]
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Abstract
Noncovalent self-assembled materials inspired by amyloid architectures are useful for biomedical applications ranging from regenerative medicine to drug delivery. The selective coassembly of complementary monomeric units to provide ordered multicomponent fibrils is a possible strategy for enhancing the sophistication of these noncovalent materials. Herein we report that complementary π-π interactions can be exploited to promote the coassembly of phenylalanine (Phe) derivatives that possess complementary aromatic side-chain functionality. Specifically, equimolar mixtures of Fmoc-Phe and Fmoc-F(5)-Phe, which possess side-chain groups with complementary quadrupole electronics, readily coassemble to form two-component fibrils and hydrogels under conditions where Fmoc-Phe alone fails to self-assemble. In addition, it was found that equimolar mixtures of Fmoc-Phe with monohalogenated (F, Cl, and Br) Fmoc-Phe derivatives also coassembled into two-component fibrils. These results collectively indicate that face-to-face quadrupole stacking between benzyl side-chain groups does not account for the molecular recognition between Phe and halogenated Phe derivatives that promote cofibrillization but that coassembly is mediated by more subtle π-π effects arising from the halogenation of the benzyl side chain. The use of complementary π-π interactions to promote the coassembly of two distinct monomeric units into ordered two-component fibrils dramatically expands the repertoire of noncovalent interactions that can be used in the development of sophisticated noncovalent materials.
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Affiliation(s)
- Derek M Ryan
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
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Ryan DM, Doran TM, Anderson SB, Nilsson BL. Effect of C-terminal modification on the self-assembly and hydrogelation of fluorinated Fmoc-Phe derivatives. Langmuir 2011; 27:4029-4039. [PMID: 21401045 DOI: 10.1021/la1048375] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The development of hydrogels resulting from the self-assembly of low molecular weight (LMW) hydrogelators is a rapidly expanding area of study. Fluorenylmethoxycarbonyl (Fmoc) protected aromatic amino acids derived from phenylalanine (Phe) have been shown to be highly effective LMW hydrogelators. It has been found that side chain functionalization of Fmoc-Phe exerts a significant effect on the self-assembly and hydrogelation behavior of these molecules; fluorinated derivatives, including pentafluorophenylalanine (F(5)-Phe) and 3-F-phenylalanine (3-F-Phe), spontaneously self-assemble into fibrils that form a hydrogel network upon dissolution into water. In this study, Fmoc-F(5)-Phe-OH and Fmoc-3-F-Phe-OH were used to characterize the role of the C-terminal carboxylic acid on the self-assembly and hydrogelation of these derivatives. The C-terminal carboxylic acid moieties of Fmoc-F(5)-Phe-OH and Fmoc-3-F-Phe-OH were converted to C-terminal amide and methyl ester groups in order to perturb the hydrophobicity and hydrogen bond capacity of the C-terminus. Self-assembly and hydrogelation of these derivatives was investigated in comparison to the parent carboxylic acid compounds at neutral and acidic pH. It was found that hydrogelation of the C-terminal acids was highly sensitive to solvent pH, which influences the charge state of the terminal group. Rigid hydrogels form at pH 3.5, but at pH 7 hydrogel rigidity is dramatically weakened. C-terminal esters self-assembled into fibrils only slowly and failed to form hydrogels due to the higher hydrophobicity of these derivatives. C-terminal amide derivatives assembled much more rapidly than the parent carboxylic acids at both acidic and neutral pH, but the resultant hydrogels were unstable to shear stress as a function of the lower water solubility of the amide functionality. Co-assembly of acid and amide functionalized monomers was also explored in order to characterize the properties of hybrid hydrogels; these gels were rigid in unbuffered water but significantly weaker in phosphate buffered saline. These results highlight the complex nature of monomer/solvent interactions and their ultimate influence on self-assembly and hydrogelation, and provide insight that will facilitate the development of optimal amino acid LMW hydrogelators for gelation of complex buffered media.
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Affiliation(s)
- Derek M Ryan
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
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Senguen FT, Doran TM, Anderson EA, Nilsson BL. Clarifying the influence of core amino acid hydrophobicity, secondary structure propensity, and molecular volume on amyloid-β 16–22 self-assembly. ACTA ACUST UNITED AC 2011; 7:497-510. [DOI: 10.1039/c0mb00210k] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ryan DM, Doran TM, Nilsson BL. Stabilizing self-assembled Fmoc–F5–Phe hydrogels by co-assembly with PEG-functionalized monomers. Chem Commun (Camb) 2011; 47:475-7. [DOI: 10.1039/c0cc02217a] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Senguen FT, Lee NR, Gu X, Ryan DM, Doran TM, Anderson EA, Nilsson BL. Probing aromatic, hydrophobic, and steric effects on the self-assembly of an amyloid-β fragment peptide. ACTA ACUST UNITED AC 2011; 7:486-96. [DOI: 10.1039/c0mb00080a] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Olsen JS, Brown C, Capule CC, Rubinshtein M, Doran TM, Srivastava RK, Feng C, Nilsson BL, Yang J, Dewhurst S. Amyloid-binding small molecules efficiently block SEVI (semen-derived enhancer of virus infection)- and semen-mediated enhancement of HIV-1 infection. J Biol Chem 2010; 285:35488-96. [PMID: 20833717 PMCID: PMC2975173 DOI: 10.1074/jbc.m110.163659] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Semen was recently shown to contain amyloid fibrils formed from a self-assembling peptide fragment of the protein prostatic acid phosphatase. These amyloid fibrils, termed semen-derived enhancer of virus infection, or SEVI, have been shown to strongly enhance HIV infectivity and may play an important role in sexual transmission of HIV, making them a potential microbicide target. One novel approach to target these fibrils is the use of small molecules known to intercalate into the structure of amyloid fibrils, such as derivatives of thioflavin-T. Here, we show that the amyloid-binding small molecule BTA-EG6 (the hexa(ethylene glycol) derivative of benzothiazole aniline) is able to bind SEVI fibrils and effectively inhibit both SEVI-mediated and semen-mediated enhancement of HIV infection. BTA-EG6 also blocks the interactions of SEVI with HIV-1 virions and HIV-1 target cells but does not cause any inflammation or toxicity to cervical epithelial cells. These results suggest that an amyloid-binding small molecule may have utility as a microbicide, or microbicidal supplement, for HIV-1.
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Affiliation(s)
- Joanna S Olsen
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York 14627, USA
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Moreno AJ, Sanders LR, Battafarano NJ, Doran TM, Turnbull GL. Non-Hodgkin's lymphoma. Clin Nucl Med 1986; 11:801-2. [PMID: 3466732 DOI: 10.1097/00003072-198611000-00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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