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Müller M, Germer P, Andexer JN. Biocatalytic One-Carbon Transfer – A Review. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/s-0040-1719884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
AbstractThis review provides an overview of different C1 building blocks as substrates of enzymes, or part of their cofactors, and the resulting functionalized products. There is an emphasis on the broad range of possibilities of biocatalytic one-carbon extensions with C1 sources of different oxidation states. The identification of uncommon biosynthetic strategies, many of which might serve as templates for synthetic or biotechnological applications, towards one-carbon extensions is supported by recent genomic and metabolomic progress and hence we refer principally to literature spanning from 2014 to 2020.1 Introduction2 Methane, Methanol, and Methylamine3 Glycine4 Nitromethane5 SAM and SAM Ylide6 Other C1 Building Blocks7 Formaldehyde and Glyoxylate as Formaldehyde Equivalents8 Cyanide9 Formic Acid10 Formyl-CoA and Oxalyl-CoA11 Carbon Monoxide12 Carbon Dioxide13 Conclusions
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Holdgate GA, Bardelle C, Lanne A, Read J, O'Donovan DH, Smith JM, Selmi N, Sheppard R. Drug discovery for epigenetics targets. Drug Discov Today 2021; 27:1088-1098. [PMID: 34728375 DOI: 10.1016/j.drudis.2021.10.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/19/2021] [Accepted: 10/27/2021] [Indexed: 12/28/2022]
Abstract
Dysregulation of the epigenome is associated with the onset and progression of several diseases, including cancer, autoimmune, cardiovascular, and neurological disorders. Members from the three families of epigenetic proteins (readers, writers, and erasers) have been shown to be druggable using small-molecule inhibitors. Increasing knowledge of the role of epigenetics in disease and the reversibility of these modifications explain why pharmacological intervention is an attractive strategy for tackling epigenetic-based disease. In this review, we provide an overview of epigenetics drug targets, focus on approaches used for initial hit identification, and describe the subsequent role of structure-guided chemistry optimisation of initial hits to clinical candidates. We also highlight current challenges and future potential for epigenetics-based therapies.
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Affiliation(s)
- Geoffrey A Holdgate
- High-throughput Screening, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK.
| | - Catherine Bardelle
- High-throughput Screening, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Alice Lanne
- High-throughput Screening, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Jon Read
- Structure and Biophysics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | | | - Nidhal Selmi
- iLAB, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Robert Sheppard
- Medicinal Chemistry, Cardiovascular, Renal, Metabolism R&D, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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Zhang L, Guo K, Yin S, Peng J, Pang J, Ma N, Zhang X, Xie Y, Chen L, Jiang Y. RNA-Seq Reveals Underlying Transcriptomic Mechanisms of Bone Marrow-Derived Mesenchymal Stem Cells in the Regulation of Microglia-Mediated Neuroinflammation After Subarachnoid Hemorrhage. Stem Cells Dev 2020; 29:562-573. [PMID: 31918626 DOI: 10.1089/scd.2019.0216] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Lifang Zhang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Neurosurgery Clinical Medical Research Center of Sichuan Province, Luzhou, China
| | - Kecheng Guo
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shigang Yin
- Laboratory of Neurological Diseases and Brain Functions, Clinical Medical Research Center, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jianhua Peng
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinwei Pang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Ning Ma
- Inflammation & Allergic Diseases Research Unit, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xianhui Zhang
- Neurosurgery Clinical Medical Research Center of Sichuan Province, Luzhou, China
| | - Yuke Xie
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Ligang Chen
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Neurosurgery Clinical Medical Research Center of Sichuan Province, Luzhou, China
| | - Yong Jiang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Neurosurgery Clinical Medical Research Center of Sichuan Province, Luzhou, China
- Laboratory of Neurological Diseases and Brain Functions, Clinical Medical Research Center, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, China
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Gjoksi B, Ghayor C, Siegenthaler B, Ruangsawasdi N, Zenobi-Wong M, Weber FE. The epigenetically active small chemical N-methyl pyrrolidone (NMP) prevents estrogen depletion induced osteoporosis. Bone 2015; 78:114-21. [PMID: 25959414 DOI: 10.1016/j.bone.2015.05.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/20/2015] [Accepted: 05/02/2015] [Indexed: 12/22/2022]
Abstract
Currently, there are several treatments for osteoporosis however; they all display some sort of limitation and/or side effects making the need for new treatments imperative. We have previously demonstrated that NMP is a bioactive drug which enhances bone regeneration in vivo and acts as an enhancer of bone morphogenetic protein (BMP) in vitro. NMP also inhibits osteoclast differentiation and attenuates bone resorption. In the present study, we tested NMP as a bromodomain inhibitor and for osteoporosis prevention on ovariectomized (OVX) induced rats while treated systemically with NMP. Female Sprague-Dawley rats were ovariectomized and weekly NMP treatment was administrated 1 week after surgery for 15 weeks. Bone parameters and related serum biomarkers were analyzed. 15 weeks of NMP treatment decreased ovariectomy-induced gained weight in average by 43% and improved bone mineral density (BMD) and bone volume over total volume (BV/TV) in rat femur on average by 25% and 41% respectively. Moreover, mineral apposition rate and bone biomarkers of bone turnover in the treatment group were at similar levels with those of the Sham group. Due to the function of NMP as a low affinity bromodomain inhibitor and its mechanism of action involving osteoblasts/osteoclasts balance and inhibitory effect on inflammatory cytokines, NMP is a promising therapeutic compound for the prevention of osteoporosis.
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Affiliation(s)
- Bebeka Gjoksi
- University Hospital, Division of Cranio-Maxillofacial and Oral Surgery and University of Zurich, Center of Dental Medicine, Oral Biotechnology & Bioengineering, Plattenstrasse 11, 8032 Zürich, Switzerland; Cartilage Engineering+Regeneration Laboratory, ETH Zurich, Zurich, Switzerland
| | - Chafik Ghayor
- University Hospital, Division of Cranio-Maxillofacial and Oral Surgery and University of Zurich, Center of Dental Medicine, Oral Biotechnology & Bioengineering, Plattenstrasse 11, 8032 Zürich, Switzerland
| | - Barbara Siegenthaler
- University Hospital, Division of Cranio-Maxillofacial and Oral Surgery and University of Zurich, Center of Dental Medicine, Oral Biotechnology & Bioengineering, Plattenstrasse 11, 8032 Zürich, Switzerland; Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Switzerland
| | - Nisarat Ruangsawasdi
- University Hospital, Division of Cranio-Maxillofacial and Oral Surgery and University of Zurich, Center of Dental Medicine, Oral Biotechnology & Bioengineering, Plattenstrasse 11, 8032 Zürich, Switzerland
| | - Marcy Zenobi-Wong
- Cartilage Engineering+Regeneration Laboratory, ETH Zurich, Zurich, Switzerland
| | - Franz E Weber
- University Hospital, Division of Cranio-Maxillofacial and Oral Surgery and University of Zurich, Center of Dental Medicine, Oral Biotechnology & Bioengineering, Plattenstrasse 11, 8032 Zürich, Switzerland; Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Switzerland; CABMM, Center for Applied Biotechnology and Molecular Medicine, University of Zurich, Zurich, Switzerland.
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Glant TT, Mikecz K, Rauch TA. Epigenetics in the pathogenesis of rheumatoid arthritis. BMC Med 2014; 12:35. [PMID: 24568138 PMCID: PMC3936819 DOI: 10.1186/1741-7015-12-35] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 02/03/2014] [Indexed: 01/05/2023] Open
Abstract
An increasing number of studies show that besides the inherited genetic architecture (that is, genomic DNA), various environmental factors significantly contribute to the etiology of rheumatoid arthritis. Epigenetic factors react to external stimuli and form bridges between the environment and the genetic information-harboring DNA. Epigenetic mechanisms are implicated in the final interpretation of the encoded genetic information by regulating gene expression, and alterations in their profile influence the activity of the immune system. Overall, epigenetic mechanisms further increase the well-known complexity of rheumatoid arthritis by providing additional subtle contributions to rheumatoid arthritis susceptibility. Although there are controversies regarding the involvement of epigenetic and genetic factors in rheumatoid arthritis etiology, it is becoming obvious that the two systems (genetic and epigenetic) interact with each other and are ultimately responsible for rheumatoid arthritis development. Here, epigenetic factors and mechanisms involved in rheumatoid arthritis are reviewed and new, potential therapeutic targets are discussed.
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Affiliation(s)
- Tibor T Glant
- Section of Molecular Medicine, Department of Orthopedic Surgery, Rush University Medical Center, 1735 West Harrison Street, Chicago, IL 60612, USA.
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Sang Y, Brichalli W, Rowland RRR, Blecha F. Genome-wide analysis of antiviral signature genes in porcine macrophages at different activation statuses. PLoS One 2014; 9:e87613. [PMID: 24505295 PMCID: PMC3914820 DOI: 10.1371/journal.pone.0087613] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 12/20/2013] [Indexed: 12/24/2022] Open
Abstract
Macrophages (MФs) can be polarized to various activation statuses, including classical (M1), alternative (M2), and antiviral states. To study the antiviral activation status of porcine MФs during porcine reproductive and respiratory syndrome virus (PRRSV) infection, we used RNA Sequencing (RNA-Seq) for transcriptomic analysis of differentially expressed genes (DEGs). Sequencing assessment and quality evaluation showed that our RNA-Seq data met the criteria for genome-wide transcriptomic analysis. Comparisons of any two activation statuses revealed more than 20,000 DEGs that were normalized to filter out 153–5,303 significant DEGs [false discovery rate (FDR) ≤0.001, fold change ≥2] in each comparison. The highest 5,303 significant DEGs were found between lipopolysaccharide- (LPS) and interferon (IFN)γ-stimulated M1 cells, whereas only 153 significant DEGs were detected between interleukin (IL)-10-polarized M2 cells and control mock-activated cells. To identify signature genes for antiviral regulation pertaining to each activation status, we identified a set of DEGs that showed significant up-regulation in only one activation state. In addition, pathway analyses defined the top 20–50 significantly regulated pathways at each activation status, and we further analyzed DEGs pertinent to pathways mediated by AMP kinase (AMPK) and epigenetic mechanisms. For the first time in porcine macrophages, our transcriptomic analyses not only compared family-wide differential expression of most known immune genes at different activation statuses, but also revealed transcription evidence of multiple gene families. These findings show that using RNA-Seq transcriptomic analyses in virus-infected and status-synchronized macrophages effectively profiled signature genes and gene response pathways for antiviral regulation, which may provide a framework for optimizing antiviral immunity and immune homeostasis.
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Affiliation(s)
- Yongming Sang
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail: (YS); (FB)
| | - Wyatt Brichalli
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Raymond R. R. Rowland
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Frank Blecha
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail: (YS); (FB)
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