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Xu H, Gan C, Xiang Z, Xiang T, Li J, Huang X, Qin X, Liu T, Sheng J, Wang X. Targeting the TNF-α-TNFR interaction with EGCG to block NF-κB signaling in human synovial fibroblasts. Biomed Pharmacother 2023; 161:114575. [PMID: 36963358 DOI: 10.1016/j.biopha.2023.114575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 03/26/2023] Open
Abstract
The tumor necrosis factor alpha (TNF-α)-TNF-α receptor (TNFR) interaction plays a central role in the pathogenesis of various autoimmune diseases, particularly rheumatoid arthritis, and is therefore considered a key target for drug discovery. However, natural compounds that can specifically block the TNF-α-TNFR interaction are rarely reported. (-)-Epigallocatechin-3-gallate (EGCG) is the most active, abundant, and thoroughly investigated polyphenolic compound in green tea. However, the molecular mechanism by which EGCG ameliorates autoimmune arthritis remains to be elucidated. In the present study, we found that EGCG can directly bind to TNF-α, TNFR1, and TNFR2 with similar μM affinity and disrupt the interactions between TNF-α and TNFR1 and TNFR2, which inhibits TNF-α-induced L929 cell death, blocks TNF-α-induced NF-κB activation in 293-TNF-α response cell line, and eventually leads to inhibition of TNF-α-induced NF-κB signaling pathway in HFLS and MH7A cells. Thus, regular consumption of EGCG in green tea may represent a potential therapeutic agent for the treatment of TNF-α-associated diseases.
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Affiliation(s)
- Huanhuan Xu
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China; College of Science, Yunnan Agricultural University, Kunming 650201, China
| | - Chunxia Gan
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Zemin Xiang
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Ting Xiang
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jin Li
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China; College of Science, Yunnan Agricultural University, Kunming 650201, China
| | - Xueqin Huang
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Xiangdong Qin
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China; College of Science, Yunnan Agricultural University, Kunming 650201, China
| | - Titi Liu
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China; College of Science, Yunnan Agricultural University, Kunming 650201, China.
| | - Jun Sheng
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China; State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming 650201, China.
| | - Xuanjun Wang
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China; State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming 650201, China.
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2
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Dimitrova YN, Gutierrez JA, Huard K. It's ok to be outnumbered - sub-stoichiometric modulation of homomeric protein complexes. RSC Med Chem 2023; 14:22-46. [PMID: 36760737 PMCID: PMC9890894 DOI: 10.1039/d2md00212d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
An arsenal of molecular tools with increasingly diversified mechanisms of action is being developed by the scientific community to enable biological interrogation and pharmaceutical modulation of targets and pathways of ever increasing complexity. While most small molecules interact with the target of interest in a 1 : 1 relationship, a noteworthy number of recent examples were reported to bind in a sub-stoichiometric manner to a homomeric protein complex. This approach requires molecular understanding of the physiologically relevant protein assemblies and in-depth characterization of the compound's mechanism of action. The recent literature examples summarized here were selected to illustrate methods used to identify and characterize molecules with such mechanisms. The concept of one small molecule targeting a homomeric protein assembly is not new but the subject deserves renewed inspection in light of emerging technologies and increasingly diverse target biology, to ensure relevant in vitro systems are used and valuable compounds with potentially novel sub-stoichiometric mechanisms of action aren't overlooked.
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Affiliation(s)
| | | | - Kim Huard
- Genentech 1 DNA Way South San Francisco CA 94080 USA
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3
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Vugler A, O’Connell J, Nguyen MA, Weitz D, Leeuw T, Hickford E, Verbitsky A, Ying X, Rehberg M, Carrington B, Merriman M, Moss A, Nicholas JM, Stanley P, Wright S, Bourne T, Foricher Y, Brookings D, Horsley H, Herrmann M, Rao S, Kohlmann M, Florian P. An orally available small molecule that targets soluble TNF to deliver anti-TNF biologic-like efficacy in rheumatoid arthritis. Front Pharmacol 2022; 13:1037983. [PMID: 36467083 PMCID: PMC9709720 DOI: 10.3389/fphar.2022.1037983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/21/2022] [Indexed: 07/30/2023] Open
Abstract
Tumor necrosis factor (TNF) is a pleiotropic cytokine belonging to a family of trimeric proteins with both proinflammatory and immunoregulatory functions. TNF is a key mediator in autoimmune diseases and during the last couple of decades several biologic drugs have delivered new therapeutic options for patients suffering from chronic autoimmune diseases such as rheumatoid arthritis and chronic inflammatory bowel disease. Attempts to design small molecule therapies directed to this cytokine have not led to approved products yet. Here we report the discovery and development of a potent small molecule inhibitor of TNF that was recently moved into phase 1 clinical trials. The molecule, SAR441566, stabilizes an asymmetrical form of the soluble TNF trimer, compromises downstream signaling and inhibits the functions of TNF in vitro and in vivo. With SAR441566 being studied in healthy volunteers we hope to deliver a more convenient orally bioavailable and effective treatment option for patients suffering with chronic autoimmune diseases compared to established biologic drugs targeting TNF.
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Affiliation(s)
- Alexander Vugler
- Immunology Therapeutic Area, PV Early Solutions, UCB Pharma, Slough, United Kingdom
| | - James O’Connell
- Discovery Sciences, PV Early Solutions, UCB Pharma, Slough, United Kingdom
| | - Mai Anh Nguyen
- Sanofi R&D, TMED Pharmacokinetics Dynamics and Metabolism, Frankfurt am Main, Germany
| | - Dietmar Weitz
- Sanofi R&D, Drug Metabolism and Pharmacokinetics, Frankfurt am Main, Germany
| | - Thomas Leeuw
- Sanofi R&D, Type 1/17 Immunology, Immunology & Inflammation Research TA, Frankfurt, Germany
| | - Elizabeth Hickford
- Development Science, PV Early Solutions, UCB Pharma, Slough, United Kingdom
| | | | - Xiaoyou Ying
- Sanofi R&D, Translation In vivo Models, Cambridge, MA, United States
| | - Markus Rehberg
- Sanofi R&D, Translational Disease Modelling, Frankfurt am Main, Germany
| | - Bruce Carrington
- Discovery Sciences, PV Early Solutions, UCB Pharma, Slough, United Kingdom
| | - Mark Merriman
- Immunology Therapeutic Area, PV Early Solutions, UCB Pharma, Slough, United Kingdom
| | - Andrew Moss
- Translational Medicine Immunology, PV Early Solutions, UCB Pharma, Slough, United Kingdom
| | - Jean-Marie Nicholas
- Development Science, Drug Metabolism and Pharmacokinetics, UCB Pharma, Braine-I’Alleud, Belgium
| | - Phil Stanley
- Immunology Therapeutic Area, PV Early Solutions, UCB Pharma, Slough, United Kingdom
| | - Sara Wright
- Early PV Missions, PV Early Solutions, UCB Pharma, Slough, United Kingdom
| | - Tim Bourne
- Milvuswood Consultancy, Penn, United Kingdom
| | - Yann Foricher
- Sanofi R&D, Integrated Drug Discovery, Medicinal Chemistry, Therapeutic Area Immunology & Inflammation, Vitry-sur-Seine, France
| | - Daniel Brookings
- Global Chemistry, Discovery Sciences, PV Early Solutions, UCB Pharma, Slough, United Kingdom
| | - Helen Horsley
- Global Chemistry, Discovery Sciences, PV Early Solutions, UCB Pharma, Slough, United Kingdom
| | - Matthias Herrmann
- Sanofi R&D, Type 1/17 Immunology, Immunology & Inflammation Research TA, Frankfurt, Germany
| | - Srinivas Rao
- Sanofi R&D, Translation In vivo Models, Cambridge, MA, United States
| | - Markus Kohlmann
- Sanofi R&D, Early Clinical Development, Therapeutic Area Immunology and Inflammation, Frankfurt am Main, Germany
| | - Peter Florian
- Sanofi R&D, Type 1/17 Immunology, Immunology & Inflammation Research TA, Frankfurt, Germany
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4
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De Vita S, Finamore C, Chini MG, Saviano G, De Felice V, De Marino S, Lauro G, Casapullo A, Fantasma F, Trombetta F, Bifulco G, Iorizzi M. Phytochemical Analysis of the Methanolic Extract and Essential Oil from Leaves of Industrial Hemp Futura 75 Cultivar: Isolation of a New Cannabinoid Derivative and Biological Profile Using Computational Approaches. PLANTS 2022; 11:plants11131671. [PMID: 35807623 PMCID: PMC9269227 DOI: 10.3390/plants11131671] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022]
Abstract
Cannabis sativa L. is a plant belonging to the Cannabaceae family, cultivated for its psychoactive cannabinoid (Δ9-THC) concentration or for its fiber and nutrient content in industrial use. Industrial hemp shows a low Δ9-THC level and is a valuable source of phytochemicals, mainly represented by cannabinoids, flavones, terpenes, and alkaloids, with health-promoting effects. In the present study, we investigated the phytochemical composition of leaves of the industrial hemp cultivar Futura 75, a monoecious cultivar commercially used for food preparations or cosmetic purposes. Leaves are generally discarded, and represent waste products. We analyzed the methanol extract of Futura 75 leaves by HPLC and NMR spectroscopy and the essential oil by GC-MS. In addition, in order to compare the chemical constituents, we prepared the water infusion. One new cannabinoid derivative (1) and seven known components, namely, cannabidiol (2), cannabidiolic acid (3), β-cannabispirol (4), β-cannabispirol (5), canniprene (6), cannabiripsol (7), and cannflavin B (8) were identified. The content of CBD was highest in all preparations. In addition, we present the outcomes of a computational study focused on elucidating the role of 2α-hydroxy-Δ3,7-cannabitriol (1), CBD (2), and CBDA (3) in inflammation and thrombogenesis.
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Affiliation(s)
- Simona De Vita
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Salerno, Italy; (S.D.V.); (G.L.); (A.C.)
| | - Claudia Finamore
- Department of Pharmacy, University of Naples, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.F.); (S.D.M.)
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Isernia, Italy; (M.G.C.); (G.S.); (V.D.F.); (F.F.)
| | - Gabriella Saviano
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Isernia, Italy; (M.G.C.); (G.S.); (V.D.F.); (F.F.)
| | - Vincenzo De Felice
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Isernia, Italy; (M.G.C.); (G.S.); (V.D.F.); (F.F.)
| | - Simona De Marino
- Department of Pharmacy, University of Naples, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.F.); (S.D.M.)
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Salerno, Italy; (S.D.V.); (G.L.); (A.C.)
| | - Agostino Casapullo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Salerno, Italy; (S.D.V.); (G.L.); (A.C.)
| | - Francesca Fantasma
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Isernia, Italy; (M.G.C.); (G.S.); (V.D.F.); (F.F.)
| | - Federico Trombetta
- Societa Cooperativa Agricola MarcheSana, Localita San Biagio 40, 61032 Fano, Italy;
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Salerno, Italy; (S.D.V.); (G.L.); (A.C.)
- Correspondence: (G.B.); (M.I.); Tel.: +39-089969741 (G.B.); +39-087-4404100 (M.I.)
| | - Maria Iorizzi
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Isernia, Italy; (M.G.C.); (G.S.); (V.D.F.); (F.F.)
- Correspondence: (G.B.); (M.I.); Tel.: +39-089969741 (G.B.); +39-087-4404100 (M.I.)
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5
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Song S, Zhou J, Li Y, Liu J, Li J, Shu P. Network pharmacology and experimental verification based research into the effect and mechanism of Aucklandiae Radix-Amomi Fructus against gastric cancer. Sci Rep 2022; 12:9401. [PMID: 35672352 PMCID: PMC9174187 DOI: 10.1038/s41598-022-13223-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/23/2022] [Indexed: 12/19/2022] Open
Abstract
To investigate the mechanism of the Aucklandiae Radix–Amomi Fructus (AR–AF) herb pair in treating gastric cancer (GC) by using network pharmacology and experimental verification. Using the traditional Chinese medicine system pharmacology database and analysis platform (TCMSP), the major active components and their corresponding targets were estimated and screened out. Using Cytoscape 3.7.2 software, a visual network was established using the active components of AR–AF and the targets of GC. Based on STRING online database, the protein interaction network of vital targets was built and analyzed. With the Database for Annotation, Visualization, and Integrated Discovery (DAVID) server, the gene ontology (GO) biological processes and the Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways of the target enrichment were performed. AutoDock Vina was used to perform molecular docking and calculate the binding affinity. The mRNA and protein expression levels of the hub targets were analyzed by the Oncomine, GEPIA, HPA databases and TIMER online tool, and the predicted targets were verified by qRT–PCR in vitro. Eremanthin, cynaropicrin, and aceteugenol were identified as vital active compounds, and AKT1, MAPK3, IL6, MAPK1, as well as EGFR were considered as the major targets. These targets exerted therapeutic effects on GC by regulating the cAMP signaling pathway, and PI3K-Akt signaling pathway. Molecular docking revealed that these active compounds and targets showed good binding interactions. The validation in different databases showed that most of the results were consistent with this paper. The experimental results confirmed that eremanthin could inhibit the proliferation of AGS by reducing the mRNA expression of hub targets. As predicted by network pharmacology and validated by the experimental results, AR–AF exerts antitumor effects through multiple components, targets, and pathways, thereby providing novel ideas and clues for the development of preparations and the treatment of GC.
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Affiliation(s)
- Siyuan Song
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China.,Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China.,Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Jiayu Zhou
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China.,Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China.,Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Ye Li
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China.,Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China.,Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Jiatong Liu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China.,Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Jingzhan Li
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China.,Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China.,Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Peng Shu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China. .,Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China. .,Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210029, Jiangsu, China.
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6
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Combarnous Y, Nguyen TMD. Membrane Hormone Receptors and Their Signaling Pathways as Targets for Endocrine Disruptors. J Xenobiot 2022; 12:64-73. [PMID: 35466213 PMCID: PMC9036253 DOI: 10.3390/jox12020007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/14/2022] [Accepted: 03/21/2022] [Indexed: 12/19/2022] Open
Abstract
The endocrine disruptors are mostly small organic molecules developed for numerous and very diverse industrial applications. They essentially act through nuclear receptors with small and hydrophobic endogenous ligands. Nevertheless, potential adverse effects through membrane hormone receptors cannot be ruled out, and have indeed been observed. The present paper reviews how orthosteric and allosteric binding sites of the different families of membrane receptors can be targets for man-made hydrophobic molecules (components of plastics, paints, flame retardants, herbicides, pesticides, etc.). We also review potential target proteins for such small hydrophobic molecules downstream of membrane receptors at the level of their intracellular signaling pathways. From the currently available information, although endocrine disruptors primarily affect nuclear receptors’ signaling, membrane receptors for hormones, cytokines, neuro-mediators, and growth factors can be affected as well and deserve attention.
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Affiliation(s)
- Yves Combarnous
- INRAe, CNRS, Tours University Joint Unit, Physiologie de la Reproduction et des Comportements, 37380 Nouzilly, France;
- Correspondence: ; Tel.: +33-(0)24-7427-650
| | - Thi Mong Diep Nguyen
- INRAe, CNRS, Tours University Joint Unit, Physiologie de la Reproduction et des Comportements, 37380 Nouzilly, France;
- Faculty of Natural Sciences, Quy Nhon University, Quy Nhon 820000, Vietnam
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7
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Healey RD, Saied EM, Cong X, Karsai G, Gabellier L, Saint-Paul J, Del Nero E, Jeannot S, Drapeau M, Fontanel S, Maurel D, Basu S, Leyrat C, Golebiowski J, Bossis G, Bechara C, Hornemann T, Arenz C, Granier S. Discovery and Mechanism of Action of Small Molecule Inhibitors of Ceramidases. Angew Chem Int Ed Engl 2022; 61:e202109967. [PMID: 34668624 DOI: 10.1002/anie.202109967] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/21/2021] [Indexed: 01/09/2023]
Abstract
Sphingolipid metabolism is tightly controlled by enzymes to regulate essential processes in human physiology. The central metabolite is ceramide, a pro-apoptotic lipid catabolized by ceramidase enzymes to produce pro-proliferative sphingosine-1-phosphate. Alkaline ceramidases are transmembrane enzymes that recently attracted attention for drug development in fatty liver diseases. However, due to their hydrophobic nature, no specific small molecule inhibitors have been reported. We present the discovery and mechanism of action of the first drug-like inhibitors of alkaline ceramidase 3 (ACER3). In particular, we chemically engineered novel fluorescent ceramide substrates enabling screening of large compound libraries and characterized enzyme:inhibitor interactions using mass spectrometry and MD simulations. In addition to revealing a new paradigm for inhibition of lipid metabolising enzymes with non-lipidic small molecules, our data lay the ground for targeting ACER3 in drug discovery efforts.
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Affiliation(s)
- Robert D Healey
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Essa M Saied
- Institute for chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
- Chemistry Department, Faculty of Science, Suez Canal University, 41522, Ismailia, Egypt
| | - Xiaojing Cong
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Gergely Karsai
- Institute of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, 8091, Switzerland
| | | | - Julie Saint-Paul
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Elise Del Nero
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Sylvain Jeannot
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Marion Drapeau
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Simon Fontanel
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Damien Maurel
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Shibom Basu
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, France
| | - Cedric Leyrat
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
| | - Jérôme Golebiowski
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice, 06108, France
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu, 711-873, South Korea
| | | | - Cherine Bechara
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
- Institut Universitaire de France (IUF), Paris, France
| | - Thorsten Hornemann
- Institute of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, 8091, Switzerland
| | - Christoph Arenz
- Institute for chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Sebastien Granier
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France
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8
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Conformation-locking antibodies for the discovery and characterization of KRAS inhibitors. Nat Biotechnol 2022; 40:769-778. [PMID: 34992247 DOI: 10.1038/s41587-021-01126-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/07/2021] [Indexed: 11/08/2022]
Abstract
Small molecules that stabilize inactive protein conformations are an underutilized strategy for drugging dynamic or otherwise intractable proteins. To facilitate the discovery and characterization of such inhibitors, we created a screening platform to identify conformation-locking antibodies for molecular probes (CLAMPs) that distinguish and induce rare protein conformational states. Applying the approach to KRAS, we discovered CLAMPs that recognize the open conformation of KRASG12C stabilized by covalent inhibitors. One CLAMP enables the visualization of KRASG12C covalent modification in vivo and can be used to investigate response heterogeneity to KRASG12C inhibitors in patient tumors. A second CLAMP enhances the affinity of weak ligands binding to the KRASG12C switch II region (SWII) by stabilizing a specific conformation of KRASG12C, thereby enabling the discovery of such ligands that could serve as leads for the development of drugs in a high-throughput screen. We show that combining the complementary properties of antibodies and small molecules facilitates the study and drugging of dynamic proteins.
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9
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Healey RD, Saied EM, Cong X, Karsai G, Gabellier L, Saint‐Paul J, Del Nero E, Jeannot S, Drapeau M, Fontanel S, Maurel D, Basu S, Leyrat C, Golebiowski J, Bossis G, Bechara C, Hornemann T, Arenz C, Granier S. Discovery and Mechanism of Action of Small Molecule Inhibitors of Ceramidases**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Robert D. Healey
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Essa M. Saied
- Institute for chemistry Humboldt-Universität zu Berlin Brook-Taylor-Str. 2 12489 Berlin Germany
- Chemistry Department Faculty of Science Suez Canal University 41522 Ismailia Egypt
| | - Xiaojing Cong
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Gergely Karsai
- Institute of Clinical Chemistry University Hospital Zurich University of Zurich Zurich 8091 Switzerland
| | | | - Julie Saint‐Paul
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Elise Del Nero
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Sylvain Jeannot
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Marion Drapeau
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Simon Fontanel
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Damien Maurel
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Shibom Basu
- EMBL Grenoble 71 Avenue des Martyrs, CS 90181 38042 Grenoble France
| | - Cedric Leyrat
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
| | - Jérôme Golebiowski
- Université Côte d'Azur CNRS Institut de Chimie de Nice UMR7272 Nice 06108 France
- Department of Brain and Cognitive Sciences Daegu Gyeongbuk Institute of Science and Technology Daegu 711-873 South Korea
| | | | - Cherine Bechara
- IGF University of Montpellier CNRS INSERM Montpellier 34094 France
- Institut Universitaire de France (IUF) Paris France
| | - Thorsten Hornemann
- Institute of Clinical Chemistry University Hospital Zurich University of Zurich Zurich 8091 Switzerland
| | - Christoph Arenz
- Institute for chemistry Humboldt-Universität zu Berlin Brook-Taylor-Str. 2 12489 Berlin Germany
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10
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Dömling A, Li X. TNF-α: The shape of small molecules to come? Drug Discov Today 2021; 27:3-7. [PMID: 34229081 DOI: 10.1016/j.drudis.2021.06.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/11/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022]
Abstract
In 2020, the anti-tumor necrosis factor (TNF) monoclonal antibody Humira® generated US$165.8 billion in cumulative sales and snatched the crown for the industry's most successful drug from Lipitor (atorvastatin). TNF-α is a major component in beneficial and disease-related inflammation and TNF-α-inhibitor biologics have gained widespread use in autoimmune diseases, such as rheumatoid arthritis (RA). Many more diseases could benefit from TNF-α inhibitors, such as Alzheimer's disease (AD) or major depression. However, the nature of TNF-α-inhibitor biologics prohibits central nervous system (CNS) applications. Moreover, high drug production costs and pricing, together with antidrug immune reactions and insufficient patient coverage, argue for the development of small-molecule drugs. Recently, drug-like orally available small molecules were described with high activity in animal disease models with activities comparable to those of antibodies.
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Affiliation(s)
| | - Xin Li
- Drug Design Department, University of Groningen, the Netherlands
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Lawson ADG, MacCoss M, Baeten DL, Macpherson A, Shi J, Henry AJ. Modulating Target Protein Biology Through the Re-mapping of Conformational Distributions Using Small Molecules. Front Chem 2021; 9:668186. [PMID: 34017820 PMCID: PMC8129178 DOI: 10.3389/fchem.2021.668186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
Abstract
Over the last 10 years considerable progress has been made in the application of small molecules to modulating protein-protein interactions (PPIs), and the navigation from "undruggable" to a host of candidate molecules in clinical trials has been well-charted in recent, comprehensive reviews. Structure-based design has played an important role in this scientific journey, with three dimensional structures guiding medicinal chemistry efforts. However, the importance of two additional dimensions: movement and time is only now being realised, as increasing computing power, closely aligned with wet lab validation, is applied to the challenge. Protein dynamics are fundamental to biology and disease, and application to PPI drug discovery has massively widened the scope for new chemical entities to influence function from allosteric, and previously unreported, sites. In this forward-looking perspective we highlight exciting, new opportunities for small molecules to modulate disease biology, by adjusting the frequency profile of natural conformational sampling, through the stabilisation of clinically desired conformers of target proteins.
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Affiliation(s)
| | | | | | | | - Jiye Shi
- UCB Pharma, Slough, United Kingdom
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