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Ferguson LB, Patil S, Moskowitz BA, Ponomarev I, Harris RA, Mayfield RD, Messing RO. A Pathway-Based Genomic Approach to Identify Medications: Application to Alcohol Use Disorder. Brain Sci 2019; 9:brainsci9120381. [PMID: 31888299 PMCID: PMC6956180 DOI: 10.3390/brainsci9120381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 12/31/2022] Open
Abstract
Chronic, excessive alcohol use alters brain gene expression patterns, which could be important for initiating, maintaining, or progressing the addicted state. It has been proposed that pharmaceuticals with opposing effects on gene expression could treat alcohol use disorder (AUD). Computational strategies comparing gene expression signatures of disease to those of pharmaceuticals show promise for nominating novel treatments. We reasoned that it may be sufficient for a treatment to target the biological pathway rather than lists of individual genes perturbed by AUD. We analyzed published and unpublished transcriptomic data using gene set enrichment of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways to identify biological pathways disrupted in AUD brain and by compounds in the Library of Network-based Cellular Signatures (LINCS L1000) and Connectivity Map (CMap) databases. Several pathways were consistently disrupted in AUD brain, including an up-regulation of genes within the Complement and Coagulation Cascade, Focal Adhesion, Systemic Lupus Erythematosus, and MAPK signaling, and a down-regulation of genes within the Oxidative Phosphorylation pathway, strengthening evidence for their importance in AUD. Over 200 compounds targeted genes within those pathways in an opposing manner, more than twenty of which have already been shown to affect alcohol consumption, providing confidence in our approach. We created a user-friendly web-interface that researchers can use to identify drugs that target pathways of interest or nominate mechanism of action for drugs. This study demonstrates a unique systems pharmacology approach that can nominate pharmaceuticals that target pathways disrupted in disease states such as AUD and identify compounds that could be repurposed for AUD if sufficient evidence is attained in preclinical studies.
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Affiliation(s)
- Laura B. Ferguson
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (L.B.F.); (S.P.); (B.A.M.); (R.A.H.); (R.D.M.)
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Shruti Patil
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (L.B.F.); (S.P.); (B.A.M.); (R.A.H.); (R.D.M.)
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
| | - Bailey A. Moskowitz
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (L.B.F.); (S.P.); (B.A.M.); (R.A.H.); (R.D.M.)
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Igor Ponomarev
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA;
| | - Robert A. Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (L.B.F.); (S.P.); (B.A.M.); (R.A.H.); (R.D.M.)
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
| | - Roy D. Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (L.B.F.); (S.P.); (B.A.M.); (R.A.H.); (R.D.M.)
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
| | - Robert O. Messing
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (L.B.F.); (S.P.); (B.A.M.); (R.A.H.); (R.D.M.)
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
- Correspondence: ; Tel.: +1-512-471-1735
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Temoçin Z, Kim E, Li J, Panzella L, Alfieri ML, Napolitano A, Kelly DL, Bentley WE, Payne GF. The Analgesic Acetaminophen and the Antipsychotic Clozapine Can Each Redox-Cycle with Melanin. ACS Chem Neurosci 2017; 8:2766-2777. [PMID: 28945963 DOI: 10.1021/acschemneuro.7b00310] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Melanins are ubiquitous but their complexity and insolubility has hindered characterization of their structures and functions. We are developing electrochemical reverse engineering methodologies that focus on properties and especially on redox properties. Previous studies have shown that melanins (i) are redox-active and can rapidly and repeatedly exchange electrons with diffusible oxidants and reductants, and (ii) have redox potentials in midregion of the physiological range. These properties suggest the functional activities of melanins will depend on their redox context. The brain has a complex redox context with steep local gradients in O2 that can promote redox-cycling between melanin and diffusible redox-active chemical species. Here, we performed in vitro reverse engineering studies and report that melanins can redox-cycle with two common redox-active drugs. Experimentally, we used two melanin models: a convenient natural melanin derived from cuttlefish (Sepia melanin) and a synthetic cysteinyldopamine-dopamine core-shell model of neuromelanin. One drug, acetaminophen (APAP), has been used clinically for over a century, and recent studies suggest that low doses of APAP can protect the brain from oxidative-stress-induced toxicity and neurodegeneration, while higher doses can have toxic effects in the brain. The second drug, clozapine (CLZ), is a second generation antipsychotic with polypharmacological activities that remain incompletely understood. These in vitro observations suggest that the redox activities of drugs may be relevant to their modes-of-action, and that melanins may interact with drugs in ways that affect their activities, metabolism, and toxicities.
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Affiliation(s)
- Zülfikar Temoçin
- Department
of Chemistry, Science and Arts Faculty, Kırıkkale University, Yahs̨ihan,71450 Kırıkkale, Turkey
- Institute
for Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, Maryland 20742, United States
| | - Eunkyoung Kim
- Institute
for Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, Maryland 20742, United States
- Fischell
Department of Bioengineering University of Maryland, College Park, Maryland 20742, United States
| | - Jinyang Li
- Institute
for Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, Maryland 20742, United States
- Fischell
Department of Bioengineering University of Maryland, College Park, Maryland 20742, United States
| | - Lucia Panzella
- Department
of Chemical Sciences, University of Naples Federico II, Via Cintia
4, I-80126 Naples, Italy
| | - Maria Laura Alfieri
- Department
of Chemical Sciences, University of Naples Federico II, Via Cintia
4, I-80126 Naples, Italy
| | - Alessandra Napolitano
- Department
of Chemical Sciences, University of Naples Federico II, Via Cintia
4, I-80126 Naples, Italy
| | - Deanna L. Kelly
- Maryland
Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland 21228, United States
| | - William E. Bentley
- Institute
for Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, Maryland 20742, United States
- Fischell
Department of Bioengineering University of Maryland, College Park, Maryland 20742, United States
| | - Gregory F. Payne
- Institute
for Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, Maryland 20742, United States
- Fischell
Department of Bioengineering University of Maryland, College Park, Maryland 20742, United States
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Schartner J, Nabers A, Budde B, Lange J, Hoeck N, Wiltfang J, Kötting C, Gerwert K. An ATR-FTIR Sensor Unraveling the Drug Intervention of Methylene Blue, Congo Red, and Berberine on Human Tau and Aβ. ACS Med Chem Lett 2017; 8:710-714. [PMID: 28740603 DOI: 10.1021/acsmedchemlett.7b00079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/09/2017] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease affects millions of human beings worldwide. The disease progression is characterized by the formation of plaques and neurofibrillary tangles in the brain, which are based on aggregation processes of the Aβ peptide and tau protein. Today there is no cure and even no in vitro assay available for the identification of drug candidates, which provides direct information concerning the protein secondary structure label-free. Therefore, we developed an attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) sensor, which uses surface bound antibodies to immobilize a desired target protein. The secondary structure of the protein can be evaluated based on the secondary structure sensitive frequency of the amide I band. Direct information about the effect of a drug candidate on the secondary structure distribution of the total target protein fraction within the respective body fluid can be detected by a frequency shift of the amide I band. Thereby, the extent of the amide I shift is indicative for the compound efficiency. The functionality of this approach was demonstrated by the quantification of the effect of the drug candidate methylene blue on the pathogenic misfolded tau protein as extracted from cerebrospinal fluid (CSF). Methylene blue induces a shift from pathogenic folded β-sheet dominated to the healthy monomeric state. A similar effect was observed for congo red on pathogenic Aβ isoforms from CSF. In addition, the effect of berberine on synthetic Aβ1-42 is studied. Berberine seems to decelerate the aggregation process of synthetic Aβ1-42 peptides.
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Affiliation(s)
- Jonas Schartner
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Andreas Nabers
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Brian Budde
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Julia Lange
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Nina Hoeck
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Jens Wiltfang
- Department
of Psychiatry and Psychotherapy, Georg-August-University Göttingen, University Medical
Center, 37099 Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), 37099 Göttingen, Germany
- iBiMED,
Medical Sciences Department, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carsten Kötting
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Klaus Gerwert
- Department
of Biophysics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
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