1
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Shi G, Hu Y. TNFR1 and TNFR2, Which Link NF-κB Activation, Drive Lung Cancer Progression, Cell Dedifferentiation, and Metastasis. Cancers (Basel) 2023; 15:4299. [PMID: 37686574 PMCID: PMC10487001 DOI: 10.3390/cancers15174299] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
TNFR1 and TNFR2, encoded by TNFRSF1A and TNFRSF1B, respectively, are the most well-characterized members among the TNFR superfamily. TNFR1 is expressed in most cell types, while TNFR2 has been reported to be preferentially expressed in leukocytes. Lung cancer remains the leading cause of cancer mortality worldwide but TNFRs' activities in lung cancer development have not been fully evaluated. Recently, overexpressed TNFR1 was reported in a large proportion of human lung squamous cell carcinomas. Increased TNFR1 coupled with increased UBCH10 caused lung SCC cell dedifferentiation with epithelial-mesenchymal transition features and the metastasis in a combined spontaneous lung SCC and TNFR1 transgenic mouse model. UBCH10, an E2 ubiquitin-conjugating enzyme that is an oncogene, increased Sox2, c-Myc, Twist1, and Bcl2 levels. Increased TNFR1 upregulated UBCH10 expression by activating c-Rel and p65 NF-κB. Lung SCC patients overexpressing TNFRSF1A and one of these target genes died early compared to lung SCC patients expressing lower levels of these genes. Recently, we also revealed that TNFR2 was required for lung adenocarcinoma progression, delivering a signaling pathway of TNF/TNFR2/NF-κB-c-Rel, in which macrophage-produced ROS and TNF converted CD4 T cells to Foxp3 Treg cells, generating an immunosuppressive tumor microenvironment and promoting lung ADC progression. In human lung ADC cohorts, TNFRSF1B expression was highly correlated with TNF, FOXP3, and CD4 expression. Of note, TNF stimulated the activities of TNFR1 and TNFR2, two membrane-binding receptors, which accelerate tumorigenesis through diverse mechanisms. This review focuses on these new findings regarding the roles of TNFR1 and TNFR2 in lung SCC and ADC development in humans and mice, and highlights the potential therapeutic targets of human lung cancers.
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Affiliation(s)
| | - Yinling Hu
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA;
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2
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Vunnam N, Been M, Huber E, Paulson C, Szymonski S, Hackel BJ, Sachs JN. Discovery of a Non-competitive TNFR1 Antagonist Affibody with Picomolar Monovalent Potency That Does Not Affect TNFR2 Function. Mol Pharm 2023; 20:1884-1897. [PMID: 36897792 PMCID: PMC10849843 DOI: 10.1021/acs.molpharmaceut.2c00385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Tumor necrosis factor (TNF) is a key regulator of immune responses and plays a significant role in the initiation and maintenance of inflammation. Upregulation of TNF expression leads to several inflammatory diseases, such as Crohn's, ulcerative colitis, and rheumatoid arthritis. Despite the clinical success of anti-TNF treatments, the use of these therapies is limited because they can induce adverse side effects through inhibition of TNF biological activity, including blockade of TNF-induced immunosuppressive function of TNFR2. Using yeast display, we identified a synthetic affibody ligand (ABYTNFR1-1) with high binding affinity and specificity for TNFR1. Functional assays showed that the lead affibody potently inhibits TNF-induced NF-κB activation (IC50 of 0.23 nM) and, crucially, does not block the TNFR2 function. Additionally, ABYTNFR1-1 acts non-competitively─it does not block TNF binding or inhibit receptor-receptor interactions in pre-ligand-assembled dimers─thereby enhancing inhibitory robustness. The mechanism, monovalent potency, and affibody scaffold give this lead molecule uniquely strong potential as a therapeutic candidate for inflammatory diseases.
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Affiliation(s)
- Nagamani Vunnam
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - MaryJane Been
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Evan Huber
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Carolyn Paulson
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sophia Szymonski
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jonathan N. Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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3
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Papadopoulou D, Drakopoulos A, Lagarias P, Melagraki G, Kollias G, Afantitis A. In Silico Identification and Evaluation of Natural Products as Potential Tumor Necrosis Factor Function Inhibitors Using Advanced Enalos Asclepios KNIME Nodes. Int J Mol Sci 2021; 22:10220. [PMID: 34638561 PMCID: PMC8508374 DOI: 10.3390/ijms221910220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/10/2021] [Accepted: 09/17/2021] [Indexed: 12/26/2022] Open
Abstract
Tumor necrosis factor (TNF) is a regulator of several chronic inflammatory diseases, such as rheumatoid arthritis. Although anti-TNF biologics have been used in clinic, they render several drawbacks, such as patients' progressive immunodeficiency and loss of response, high cost, and intravenous administration. In order to find new potential anti-TNF small molecule inhibitors, we employed an in silico approach, aiming to find natural products, analogs of Ampelopsin H, a compound that blocks the formation of TNF active trimer. Two out of nine commercially available compounds tested, Nepalensinol B and Miyabenol A, efficiently reduced TNF-induced cytotoxicity in L929 cells and production of chemokines in mice joints' synovial fibroblasts, while Nepalensinol B also abolished TNF-TNFR1 binding in non-toxic concentrations. The binding mode of the compounds was further investigated by molecular dynamics and free energy calculation studies, using and advancing the Enalos Asclepios pipeline. Conclusively, we propose that Nepalensinol B, characterized by the lowest free energy of binding and by a higher number of hydrogen bonds with TNF, qualifies as a potential lead compound for TNF inhibitors' drug development. Finally, the upgraded Enalos Asclepios pipeline can be used for improved identification of new therapeutics against TNF-mediated chronic inflammatory diseases, providing state-of-the-art insight on their binding mode.
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Affiliation(s)
- Dimitra Papadopoulou
- Biomedical Sciences Research Center "Alexander Fleming", Institute for Bioinnovation, 16672 Vari, Greece
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | | | | | - Georgia Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, 16673 Vari, Greece
| | - George Kollias
- Biomedical Sciences Research Center "Alexander Fleming", Institute for Bioinnovation, 16672 Vari, Greece
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Center of New Biotechnologies & Precision Medicine, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece
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4
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New contributions to the drug profile of TNFα inhibitor SPD304: Affinity, selectivity and ADMET considerations. Eur J Pharmacol 2021; 907:174285. [PMID: 34181962 DOI: 10.1016/j.ejphar.2021.174285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/11/2021] [Accepted: 06/22/2021] [Indexed: 11/24/2022]
Abstract
Tumor necrosis factor alpha (TNFα) is a relevant clinical target for the treatment of chronic inflammatory diseases. Currently, only few small molecules are known as direct inhibitors of TNFα. To date, none of these molecules has shown both an efficient activity and a low toxicity to be considered for clinical trials. The SPD304 is considered as a reference of direct inhibitors of TNFα because of its well demonstrated mechanism (He et al., 2005). Herein, we provide new insights regarding the drug profile, selectivity and absorption, distribution, metabolism, excretion and toxicity (ADMET) considerations of SPD304 to evaluate its potential as a hit for the structure-based design of novel TNFα inhibitors. ELISA experiments confirmed the inhibition of TNFα/TNF receptor 1 binding (IC50 = 12 μM). Cellular-based assays highlighted the cytotoxicity of SPD304, as well as its ability to inhibit TNFα signaling pathways at non-cytotoxic concentrations. A surface acoustic wave (SAW) experiment highlighted only one binding site with a dissociation constant of 6.1 ± 4.7 nM. SPD304 inhibited the binding of the cytokines like interleukins (IL)-4 and IL-13 to their receptors and showed no direct inhibition on proteins involved in the TNFα pathway. Finally, the thermodynamic solubility and Caco-2 cells permeability of SPD304 were experimentally evaluated and ADMET in silico predictions are also discussed. The physicochemical, pharmacological and ADMET studies of SPD304 have shown that is not an ideal hit for a drug optimization program based on its chemical structure.
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5
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Kaur B, Mishra S, Kaur R, Kalotra S, Singh P. Rationally designed TNF-α inhibitors: Identification of promising cytotoxic agents. Bioorg Med Chem Lett 2021; 41:127982. [PMID: 33766762 DOI: 10.1016/j.bmcl.2021.127982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/17/2022]
Abstract
Design and synthesis of new indole derivatives as tumor growth inhibiting agents via inhibiting the TNF-α is described. The preliminary results showed the inhibition of LPS induced production of NO, TNF-α and IL-6 by these compounds out of which compounds 2d and 2g exhibited appreciable cytotoxicity against the 60 cell lines panel of human cancer. The rationale behind the design of the molecules and the results of their biological studies are presented. 2009 Elsevier Ltd. All rights reserved.
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Affiliation(s)
- Baljit Kaur
- Department of Chemistry, Centre for Advanced Studies, Guru Nanak Dev University, Amritsar 143005, India
| | - Sahil Mishra
- Department of Chemistry, Centre for Advanced Studies, Guru Nanak Dev University, Amritsar 143005, India
| | - Ramandeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, India
| | - Shikha Kalotra
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, India
| | - Palwinder Singh
- Department of Chemistry, Centre for Advanced Studies, Guru Nanak Dev University, Amritsar 143005, India.
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6
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Xiao HY, Li N, Duan JJW, Jiang B, Lu Z, Ngu K, Tino J, Kopcho LM, Lu H, Chen J, Tebben AJ, Sheriff S, Chang CY, Yanchunas J, Calambur D, Gao M, Shuster DJ, Susulic V, Xie JH, Guarino VR, Wu DR, Gregor KR, Goldstine CB, Hynes J, Macor JE, Salter-Cid L, Burke JR, Shaw PJ, Dhar TGM. Biologic-like In Vivo Efficacy with Small Molecule Inhibitors of TNFα Identified Using Scaffold Hopping and Structure-Based Drug Design Approaches. J Med Chem 2020; 63:15050-15071. [DOI: 10.1021/acs.jmedchem.0c01732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hai-Yun Xiao
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Ning Li
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - James J.-W. Duan
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Bin Jiang
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Zhonghui Lu
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Khehyong Ngu
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Joseph Tino
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Lisa M. Kopcho
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Hao Lu
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Jing Chen
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Andrew J. Tebben
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Steven Sheriff
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - ChiehYing Y. Chang
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Joseph Yanchunas
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Deepa Calambur
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Mian Gao
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - David J. Shuster
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Vojkan Susulic
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Jenny H. Xie
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Victor R. Guarino
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Dauh-Rurng Wu
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Kurt R. Gregor
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Christine B. Goldstine
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - John Hynes
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - John E. Macor
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Luisa Salter-Cid
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - James R. Burke
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - Patrick J. Shaw
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
| | - T. G. Murali Dhar
- Research and Early Development, Bristol Myers Squibb, 3551 Lawrenceville Road, Princeton, New Jersey 08540, United States
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7
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Vunnam N, Szymonski S, Hirsova P, Gores GJ, Sachs JN, Hackel BJ. Noncompetitive Allosteric Antagonism of Death Receptor 5 by a Synthetic Affibody Ligand. Biochemistry 2020; 59:3856-3868. [PMID: 32941010 PMCID: PMC7658720 DOI: 10.1021/acs.biochem.0c00529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Fatty acid-induced upregulation of death receptor 5 (DR5) and its cognate ligand, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), promotes hepatocyte lipoapoptosis, which is a key mechanism in the progression of fatty liver disease. Accordingly, inhibition of DR5 signaling represents an attractive strategy for treating fatty liver disease. Ligand competition strategies are prevalent in tumor necrosis factor receptor antagonism, but recent studies have suggested that noncompetitive inhibition through perturbation of the receptor conformation may be a compelling alternative. To this end, we used yeast display and a designed combinatorial library to identify a synthetic 58-amino acid affibody ligand that specifically binds DR5. Biophysical and biochemical studies show that the affibody neither blocks TRAIL binding nor prevents the receptor-receptor interaction. Live-cell fluorescence lifetime measurements indicate that the affibody induces a conformational change in transmembrane dimers of DR5 and favors an inactive state of the receptor. The affibody inhibits apoptosis in TRAIL-treated Huh-7 cells, an in vitro model of fatty liver disease. Thus, this lead affibody serves as a potential drug candidate, with a unique mechanism of action, for fatty liver disease.
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Affiliation(s)
- Nagamani Vunnam
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN
| | - Sophia Szymonski
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN
| | - Petra Hirsova
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Gregory J. Gores
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Jonathan N. Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN
| | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN
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8
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Qaiser H, Saeed M, Nerukh D, Ul-Haq Z. Structural insight into TNF-α inhibitors through combining pharmacophore-based virtual screening and molecular dynamic simulation. J Biomol Struct Dyn 2020; 39:5920-5939. [PMID: 32705954 DOI: 10.1080/07391102.2020.1796794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Tumor Necrosis Factor-alpha (TNF-α), a multifunctional cytokine responsible for providing resistance against infections, inflammation, and cancers. TNF-α has emerged as a promising drug target against several autoimmune and inflammatory disorders. Several synthetic antibodies (Infliximab, Etanercept, and Adalimumab) are available, but their potential to cause severe side effects has prompted them to develop alternative small molecules-based therapies for inhibition of TNF-α. In the present study, combined in silico approaches based on pharmacophore modeling, virtual screening, molecular docking, and molecular dynamics studies were employed to understand significant direct interactions between TNF-α protein and small molecule inhibitors. Initially, four different small molecule libraries (∼17.5 million molecules) were virtually screened against the selected pharmacophore model. The identified hits were further subjected to molecular docking studies. The three potent lead compounds (ZINC05848961, ZINC09402309, ZINC04502991) were further subjected to 100 ns molecular dynamic studies to examine their stability. Our docking and molecular dynamic analysis revealed that the selected lead compounds target the TNF receptor (TNFR) and efficiently block the production of TNF. Moreover, in silico ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) analysis revealed that all the predicted compounds have good pharmacokinetic properties with high gastrointestinal absorption and a decent bioavailability score. Furthermore, toxicity profiles further evidenced that these compounds have no risk of being mutagenic, tumorigenic, reproductive and irritant except ZINC11915498. In conclusion, the present study could serve as the starting point to develop new therapeutic regimens to treat various TNF- related diseases. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hina Qaiser
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan.,Department of Mathematics, Aston University, Birmingham, United Kingdom
| | - Maria Saeed
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan
| | - Dmitry Nerukh
- Department of Mathematics, Aston University, Birmingham, United Kingdom
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan
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10
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O'Connell J, Porter J, Kroeplien B, Norman T, Rapecki S, Davis R, McMillan D, Arakaki T, Burgin A, Fox Iii D, Ceska T, Lecomte F, Maloney A, Vugler A, Carrington B, Cossins BP, Bourne T, Lawson A. Small molecules that inhibit TNF signalling by stabilising an asymmetric form of the trimer. Nat Commun 2019; 10:5795. [PMID: 31857588 PMCID: PMC6923382 DOI: 10.1038/s41467-019-13616-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 11/14/2019] [Indexed: 02/08/2023] Open
Abstract
Tumour necrosis factor (TNF) is a cytokine belonging to a family of trimeric proteins; it has been shown to be a key mediator in autoimmune diseases such as rheumatoid arthritis and Crohn’s disease. While TNF is the target of several successful biologic drugs, attempts to design small molecule therapies directed to this cytokine have not led to approved products. Here we report the discovery of potent small molecule inhibitors of TNF that stabilise an asymmetrical form of the soluble TNF trimer, compromising signalling and inhibiting the functions of TNF in vitro and in vivo. This discovery paves the way for a class of small molecule drugs capable of modulating TNF function by stabilising a naturally sampled, receptor-incompetent conformation of TNF. Furthermore, this approach may prove to be a more general mechanism for inhibiting protein–protein interactions. While biologics have been successfully applied in TNF antagonist treatments, there are no clinically approved small molecules that target TNF. Here, the authors discover potent small molecule inhibitors of TNF, elucidate their molecular mechanism, and demonstrate TNF inhibition in vitro and in vivo.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Alex Burgin
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,The Institute for Protein Innovation, 4 Blackfan Circle, Boston, MA, 02115, USA
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11
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Zaka M, Abbasi BH, Durdagi S. Novel tumor necrosis factor-α (TNF-α) inhibitors from small molecule library screening for their therapeutic activity profiles against rheumatoid arthritis using target-driven approaches and binary QSAR models. J Biomol Struct Dyn 2018; 37:2464-2476. [PMID: 30047845 DOI: 10.1080/07391102.2018.1491423] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Tumor necrosis factor alpha (TNF-α) is a multifunctional cytokine that acts as a central biological mediator for critical immune functions, including inflammation, infection, and antitumor responses. It plays pivotal role in autoimmune diseases like rheumatoid arthritis (RA). The synthetic antibodies etanercept, infliximab, and adalimumab are approved drugs for the treatment of inflammatory diseases bind to TNF-α directly, preventing its association with the tumor necrosis factor receptor (TNFR). These biologics causes serious side effects such as triggering an autoimmune anti-antibody response or the weakening of the body's immune defenses. Therefore, alternative small-molecule based therapies for TNF-α inhibition is a hot topic both in academia and industry. Most of small-molecule inhibitors reported in the literature target TNF-α, indirectly. In this study, combined in silico approaches have been applied to better understand the important direct interactions between TNF-α and small inhibitors. Our effort executed with the extensive literature review to select the compounds that inhibit TNF-α. High-throughput structure-based and ligand-based virtual screening methods are applied to identify TNF-α inhibitors from 3 different small molecule databases (∼256.000 molecules from Otava drug-like green chemical collection, ∼ 500.000 molecules from Otava Tangible database, ∼2.500.000 Enamine small molecule database) and ∼240.000 molecules from ZINC natural products libraries. Moreover, therapeutic activity prediction, as well as pharmacokinetic and toxicity profiles are also investigated using MetaCore/MetaDrug platform which is based on a manually curated database of molecular interactions, molecular pathways, gene-disease associations, chemical metabolism and toxicity information, uses binary QSAR models. Particular therapeutic activity and toxic effect predictions are based on the ChemTree ability to correlate structural descriptors to that property using recursive partitioning algorithm. Molecular Dynamics (MD) simulations were also performed for selected hits to investigate their detailed structural and dynamical analysis beyond docking studies. As a result, at least one hit from each database were identified as novel TNF-α inhibitors after comprehensive virtual screening, multiple docking, e-Pharmacophore modeling (structure-based pharmacophore modeling), MD simulations, and MetaCore/MetaDrug analysis. Identified hits show predicted promising anti-arthritic activity and no toxicity. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mehreen Zaka
- a Department of Biophysics, School of Medicine, Computational Biology and Molecular Simulations Laboratory , Bahcesehir University (BAU) , Istanbul , Turkey.,b Department of Biotechnology , Quaid-i-Azam University , Islamabad , Pakistan
| | - Bilal Haider Abbasi
- b Department of Biotechnology , Quaid-i-Azam University , Islamabad , Pakistan
| | - Serdar Durdagi
- a Department of Biophysics, School of Medicine, Computational Biology and Molecular Simulations Laboratory , Bahcesehir University (BAU) , Istanbul , Turkey.,c Neuroscience Program, Institute of Health Sciences , Bahcesehir University , Istanbul , Turkey
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12
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Melagraki G, Ntougkos E, Papadopoulou D, Rinotas V, Leonis G, Douni E, Afantitis A, Kollias G. In Silico Discovery of Plant-Origin Natural Product Inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL). Front Pharmacol 2018; 9:800. [PMID: 30090063 PMCID: PMC6068282 DOI: 10.3389/fphar.2018.00800] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/03/2018] [Indexed: 01/08/2023] Open
Abstract
An in silico drug discovery pipeline for the virtual screening of plant-origin natural products (NPs) was developed to explore new direct inhibitors of TNF and its close relative receptor activator of nuclear factor kappa-B ligand (RANKL), both representing attractive therapeutic targets for many chronic inflammatory conditions. Direct TNF inhibition through identification of potent small molecules is a highly desired goal; however, it is often hampered by severe limitations. Our approach yielded a priority list of 15 NPs as potential direct TNF inhibitors that were subsequently tested in vitro against TNF and RANKL. We thus identified two potent direct inhibitors of TNF function with low micromolar IC50 values and minimal toxicity even at high concentrations. Most importantly, one of them (A11) was proved to be a dual inhibitor of both TNF and RANKL. Extended molecular dynamics simulations with the fully automated EnalosMD suite rationalized the mode of action of the compounds at the molecular level. To our knowledge, these compounds constitute the first NP TNF inhibitors, one of which being the first NP small-molecule dual inhibitor of TNF and RANKL, and could serve as lead compounds for the development of novel treatments for inflammatory and autoimmune diseases.
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Affiliation(s)
| | - Evangelos Ntougkos
- Division of Immunology Biomedical Sciences Research Center "Alexander Fleming,", Vari, Greece
| | - Dimitra Papadopoulou
- Division of Immunology Biomedical Sciences Research Center "Alexander Fleming,", Vari, Greece.,Department of Experimental Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Vagelis Rinotas
- Division of Immunology Biomedical Sciences Research Center "Alexander Fleming,", Vari, Greece.,Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | | | - Eleni Douni
- Division of Immunology Biomedical Sciences Research Center "Alexander Fleming,", Vari, Greece.,Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Antreas Afantitis
- Division of Immunology Biomedical Sciences Research Center "Alexander Fleming,", Vari, Greece.,NovaMechanics Ltd., Nicosia, Cyprus
| | - George Kollias
- Division of Immunology Biomedical Sciences Research Center "Alexander Fleming,", Vari, Greece.,Department of Experimental Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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13
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Deng X, Zhang X, Tang B, Liu H, Shen Q, Liu Y, Lai L. Design, Synthesis, and Evaluation of Dihydrobenzo[ cd]indole-6-sulfonamide as TNF-α Inhibitors. Front Chem 2018; 6:98. [PMID: 29670876 PMCID: PMC5893771 DOI: 10.3389/fchem.2018.00098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/20/2018] [Indexed: 11/26/2022] Open
Abstract
Tumor necrosis factor-α (TNF-α) plays a pivotal role in inflammatory response. Dysregulation of TNF can lead to a variety of disastrous pathological effects, including auto-inflammatory diseases. Antibodies that directly targeting TNF-α have been proven effective in suppressing symptoms of these disorders. Compared to protein drugs, small molecule drugs are normally orally available and less expensive. Till now, peptide and small molecule TNF-α inhibitors are still in the early stage of development, and much more efforts should be made. In a previously study, we reported a TNF-α inhibitor, EJMC-1 with modest activity. Here, we optimized this compound by shape screen and rational design. In the first round, we screened commercial compound library for EJMC-1 analogs based on shape similarity. Out of the 68 compounds tested, 20 compounds showed better binding affinity than EJMC-1 in the SPR competitive binding assay. These 20 compounds were tested in cell assay and the most potent compound was 2-oxo-N-phenyl-1,2-dihydrobenzo[cd]indole-6-sulfonamide (S10) with an IC50 of 14 μM, which was 2.2-fold stronger than EJMC-1. Based on the docking analysis of S10 and EJMC-1 binding with TNF-α, in the second round, we designed S10 analogs, purchased seven of them, and synthesized seven new compounds. The best compound, 4e showed an IC50-value of 3 μM in cell assay, which was 14-fold stronger than EJMC-1. 4e was among the most potent TNF-α organic compound inhibitors reported so far. Our study demonstrated that 2-oxo-N-phenyl-1,2-dihydrobenzo[cd]indole-6-sulfonamide analogs could be developed as potent TNF-α inhibitors. 4e can be further optimized for its activity and properties. Our study provides insights into designing small molecule inhibitors directly targeting TNF-α and for protein–protein interaction inhibitor design.
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Affiliation(s)
- Xiaobing Deng
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaoling Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bo Tang
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hongbo Liu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Qi Shen
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Ying Liu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Luhua Lai
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
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14
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Hofmann D, Salmon L, Wider G. Activity of Tumor Necrosis Factor α Is Modulated by Dynamic Conformational Rearrangements. J Am Chem Soc 2017; 140:167-175. [PMID: 29192773 DOI: 10.1021/jacs.7b05050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The homotrimeric ligand tumor necrosis factor α (TNFα) is a key cytokine and immune regulator; however, when deregulated, it leads to several major chronic inflammatory diseases. Perturbation of the protein-protein interface has proven to be an efficient strategy to inactivate TNFα, but the atomic-resolution mechanism of its inactivation remains poorly understood. Here, we probe the solution structure and dynamics of active and inactive TNFα using NMR spectroscopy. The data reveal that TNFα undergoes motions on different time scales. Furthermore, by site-directed mutagenesis of residues at the trimerization interface and by targeting the interface with a low molecular weight inhibitor, we show that TNFα retains its overall structure and trimeric state. However, upon perturbation, TNFα exhibits increased conformational dynamics spanning from the trimerization interface to the regions mediating receptor binding. These findings provide novel insights into the inactivation mechanism of TNFα and the basis for strategies to target TNFα activity.
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Affiliation(s)
- Daniela Hofmann
- Institute of Molecular Biology and Biophysics, ETH Zürich , 8093 Zürich, Switzerland
| | - Loïc Salmon
- Institute of Molecular Biology and Biophysics, ETH Zürich , 8093 Zürich, Switzerland
| | - Gerhard Wider
- Institute of Molecular Biology and Biophysics, ETH Zürich , 8093 Zürich, Switzerland
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15
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Sellner S, Kocabey S, Zhang T, Nekolla K, Hutten S, Krombach F, Liedl T, Rehberg M. Dexamethasone-conjugated DNA nanotubes as anti-inflammatory agents in vivo. Biomaterials 2017; 134:78-90. [DOI: 10.1016/j.biomaterials.2017.04.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/12/2017] [Accepted: 04/15/2017] [Indexed: 12/24/2022]
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16
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Chen S, Feng Z, Wang Y, Ma S, Hu Z, Yang P, Chai Y, Xie X. Discovery of Novel Ligands for TNF-α and TNF Receptor-1 through Structure-Based Virtual Screening and Biological Assay. J Chem Inf Model 2017; 57:1101-1111. [PMID: 28422491 PMCID: PMC6732210 DOI: 10.1021/acs.jcim.6b00672] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Tumor necrosis factor α (TNF-α) is overexpressed in various diseases, and it has been a validated therapeutic target for autoimmune diseases. All therapeutics currently used to target TNF-α are biomacromolecules, and limited numbers of TNF-α chemical inhibitors have been reported, which makes the identification of small-molecule alternatives an urgent need. Recent studies have mainly focused on identifying small molecules that directly bind to TNF-α or TNF receptor-1 (TNFR1), inhibit the interaction between TNF-α and TNFR1, and/or regulate related signaling pathways. In this study, we combined in silico methods with biophysical and cell-based assays to identify novel antagonists that bind to TNF-α or TNFR1. Pharmacophore model filtering and molecular docking were applied to identify potential TNF-α antagonists. In regard to TNFR1, we constructed a three-dimensional model of the TNF-α-TNFR1 complex and carried out molecular dynamics simulations to sample the conformations. The residues in TNF-α that have been reported to play important roles in the TNF-α-TNFR1 complex were removed to form a pocket for further virtual screening of TNFR1-binding ligands. We obtained 20 virtual hits and tested them using surface plasmon resonance-based assays, which resulted in one ligand that binds to TNFR1 and four ligands with different scaffolds that bind to TNF-α. T1 and R1, the two most active compounds with Kd values of 11 and 16 μM for TNF-α and TNFR1, respectively, showed activities similar to those of known antagonists. Further cell-based assays also demonstrated that T1 and R1 have similar activities compared to the known TNF-α antagonist C87. Our work has not only produced several TNF-α and TNFR1 antagonists with novel scaffolds for further structural optimization but also showcases the power of our in silico methods for TNF-α- and TNFR1-based drug discovery.
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Affiliation(s)
- Si Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yun Wang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Shifan Ma
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ziheng Hu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Peng Yang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yifeng Chai
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Xiangqun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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17
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Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL). PLoS Comput Biol 2017; 13:e1005372. [PMID: 28426652 PMCID: PMC5398486 DOI: 10.1371/journal.pcbi.1005372] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/17/2017] [Indexed: 12/20/2022] Open
Abstract
We present an in silico drug discovery pipeline developed and applied for the identification and virtual screening of small-molecule Protein-Protein Interaction (PPI) compounds that act as dual inhibitors of TNF and RANKL through the trimerization interface. The cheminformatics part of the pipeline was developed by combining structure-based with ligand-based modeling using the largest available set of known TNF inhibitors in the literature (2481 small molecules). To facilitate virtual screening, the consensus predictive model was made freely available at: http://enalos.insilicotox.com/TNFPubChem/. We thus generated a priority list of nine small molecules as candidates for direct TNF function inhibition. In vitro evaluation of these compounds led to the selection of two small molecules that act as potent direct inhibitors of TNF function, with IC50 values comparable to those of a previously-described direct inhibitor (SPD304), but with significantly reduced toxicity. These molecules were also identified as RANKL inhibitors and validated in vitro with respect to this second functionality. Direct binding of the two compounds was confirmed both for TNF and RANKL, as well as their ability to inhibit the biologically-active trimer forms. Molecular dynamics calculations were also carried out for the two small molecules in each protein to offer additional insight into the interactions that govern TNF and RANKL complex formation. To our knowledge, these compounds, namely T8 and T23, constitute the second and third published examples of dual small-molecule direct function inhibitors of TNF and RANKL, and could serve as lead compounds for the development of novel treatments for inflammatory and autoimmune diseases.
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18
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Alizadeh AA, Hamzeh-Mivehroud M, Farajzadeh M, Dastmalchi S. Identification of novel peptides against TNF-α using phage display technique and in silico modeling of their modes of binding. Eur J Pharm Sci 2017; 96:490-498. [DOI: 10.1016/j.ejps.2016.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/03/2016] [Accepted: 10/04/2016] [Indexed: 01/15/2023]
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19
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Hydrostatin-TL1, an Anti-Inflammatory Active Peptide from the Venom Gland of Hydrophis cyanocinctus in the South China Sea. Int J Mol Sci 2016; 17:ijms17111940. [PMID: 27879679 PMCID: PMC5133935 DOI: 10.3390/ijms17111940] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 10/31/2016] [Accepted: 11/14/2016] [Indexed: 12/12/2022] Open
Abstract
Tumor necrosis factor (TNF)-α is a pleiotropic cytokine with intense pro-inflammatory and immunomodulatory properties, and anti-TNF-α biologics are effective therapies for various inflammatory diseases such as inflammatory bowel disease (IBD) and sepsis. Snake venom, as a traditional Chinese medicine, has been used in the treatment of inflammatory diseases in China for centuries. In this research, we constructed a venom gland T7 phage display library of the sea snake Hydrophis cyanocinctus to screen bioactive compounds that antagonize TNF-α and identified a novel nine-amino-acid peptide, termed hydrostatin-TL1 (H-TL1). In enzyme-linked immunosorbent assay (ELISA) and surface plasmon resonance (SPR) analyses, H-TL1 inhibited the interaction between TNF-α and TNF receptor 1 (TNFR1). Further, H-TL1 attenuated the cytotoxicity of TNF-α in L929 cells as determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay. H-TL1 also decreased the mRNA expression of TNF-α/TNFR1 downstream targets and suppressed the phosphorylation of well-characterized proteins of downstream signal transduction pathways in HEK-293 cells. In vivo data demonstrated that H-TL1 protects animals against dextran sodium sulfate (DSS)-induced acute colitis and lipopolysaccharide (LPS)-induced acute shock. Given its significant anti-inflammatory activity in vitro and in vivo, H-TL1 is a potential peptide for the development of new agents to treat TNF-α-associated inflammatory diseases.
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20
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Shen Q, Zhang C, Liu H, Liu Y, Cao J, Zhang X, Liang Y, Zhao M, Lai L. De novo design of helical peptides to inhibit tumor necrosis factor-α by disrupting its trimer formation. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00549c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Helical peptide TNFα inhibitors were designed by targeting their dimer structure.
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Affiliation(s)
- Qi Shen
- Center for Quantitative Biology
- Peking University
- Beijing 100871
- China
| | - Changsheng Zhang
- BNLMS
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Peking-Tsinghua Center for Life Sciences
- Peking University
- Beijing 100871
- China
| | - Hongbo Liu
- BNLMS
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Peking-Tsinghua Center for Life Sciences
- Peking University
- Beijing 100871
- China
| | - Yuting Liu
- BNLMS
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Junyue Cao
- School of Life Sciences
- Peking University
- Beijing 100871
- China
| | - Xiaolin Zhang
- Center for Quantitative Biology
- Peking University
- Beijing 100871
- China
| | - Yuan Liang
- BNLMS
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Meiping Zhao
- BNLMS
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Luhua Lai
- Center for Quantitative Biology
- Peking University
- Beijing 100871
- China
- BNLMS
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21
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Song Y, Buchwald P. TNF superfamily protein-protein interactions: feasibility of small- molecule modulation. Curr Drug Targets 2015; 16:393-408. [PMID: 25706111 PMCID: PMC4408546 DOI: 10.2174/1389450116666150223115628] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 01/09/2023]
Abstract
The tumor necrosis factor (TNF) superfamily (TNFSF) contains about thirty structurally related receptors (TNFSFRs) and about twenty protein ligands that bind to one or more of these receptors. Almost all of these cell surface protein-protein interactions (PPIs) represent high-value therapeutic targets for inflammatory or immune modulation in autoimmune diseases, transplant recipients, or cancers, and there are several biologics including antibodies and fusion proteins targeting them that are in various phases of clinical development. Small-molecule inhibitors or activators could represent possible alternatives if the difficulties related to the targeting of protein-protein interactions by small molecules can be addressed. Compounds proving the feasibility of such approaches have been identified through different drug discovery approaches for a number of these TNFSFR-TNFSF type PPIs including CD40-CD40L, BAFFR-BAFF, TRAIL-DR5, and OX40-OX40L. Corresponding structural, signaling, and medicinal chemistry aspects are briefly reviewed here. While none of these small-molecule modulators identified so far seems promising enough to be pursued for clinical development, they provide proof-of-principle evidence that these interactions are susceptible to small-molecule modulation and can serve as starting points toward the identification of more potent and selective candidates.
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Affiliation(s)
| | - Peter Buchwald
- Diabetes Research Institute, Miller School of Medicine, University of Miami, 1450 NW 10 Ave (R-134), Miami, FL 33136, USA.
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22
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Papaneophytou C, Alexiou P, Papakyriakou A, Ntougkos E, Tsiliouka K, Maranti A, Liepouri F, Strongilos A, Mettou A, Couladouros E, Eliopoulos E, Douni E, Kollias G, Kontopidis G. Synthesis and biological evaluation of potential small moleculeinhibitors of tumor necrosis factor. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00023h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A series of 39 novel SPD-304 analogs were designed synthesized and evaluated as inhibitors of TNF.
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Affiliation(s)
| | - Polyxeni Alexiou
- Laboratory of General Chemistry
- Department of Science
- Agricultural University of Athens
- Athens 11855
- Greece
| | - Athanasios Papakyriakou
- Laboratory of Genetics
- Department of Biotechnology
- Agricultural University of Athens
- Athens 11855
- Greece
| | | | | | | | | | | | - Anthi Mettou
- Department of Biochemistry
- Veterinary School
- University of Thessaly
- Karditsa 43100
- Greece
| | - Elias Couladouros
- Laboratory of General Chemistry
- Department of Science
- Agricultural University of Athens
- Athens 11855
- Greece
| | - Elias Eliopoulos
- Laboratory of Genetics
- Department of Biotechnology
- Agricultural University of Athens
- Athens 11855
- Greece
| | - Eleni Douni
- Laboratory of Genetics
- Department of Biotechnology
- Agricultural University of Athens
- Athens 11855
- Greece
| | - George Kollias
- Biomedical Sciences Research Center “Alexander Fleming”
- Vari
- Greece
| | - George Kontopidis
- Department of Biochemistry
- Veterinary School
- University of Thessaly
- Karditsa 43100
- Greece
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23
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Shen Q, Chen J, Wang Q, Deng X, Liu Y, Lai L. Discovery of highly potent TNFα inhibitors using virtual screen. Eur J Med Chem 2014; 85:119-26. [PMID: 25078315 DOI: 10.1016/j.ejmech.2014.07.091] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/24/2014] [Accepted: 07/24/2014] [Indexed: 12/14/2022]
Abstract
Tumor necrosis factor-α (TNFα) is a validated therapeutic target for various autoimmune disorders such as rheumatoid arthritis and asthma. All TNFα inhibitors currently on the market are biologics, making the development of small molecule alternatives in urgent need. However, only a few successful cases of direct TNFα antagonization in vitro have been reported. Here, we present the identification of several small molecule candidates able to effectively reduce TNFα activity in vitro and in cell assays. Virtual screen targeting TNFα dimer was performed on the SPECS database and 101 compounds were selected for experimental testing. Two compounds, 1 and 2, displayed considerable inhibitory activity. Follow-up structure-activity relationship analysis of compound 1 identified 3 molecules with low micromolar cell-level inhibitory activity. Compound 11 showed an IC50 value of 14 μM, making it among the most potent TNFα small molecule inhibitors reported. These compounds provide new scaffolds for future development of small molecule drugs against TNFα.
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Affiliation(s)
- Qi Shen
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Jing Chen
- Center for Quantitative Biology, Peking University, Beijing 100871, China; BNLMS, State Key Laboratory of Structural Chemistry for Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qian Wang
- BNLMS, State Key Laboratory of Structural Chemistry for Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaobing Deng
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Ying Liu
- Center for Quantitative Biology, Peking University, Beijing 100871, China; BNLMS, State Key Laboratory of Structural Chemistry for Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Luhua Lai
- Center for Quantitative Biology, Peking University, Beijing 100871, China; BNLMS, State Key Laboratory of Structural Chemistry for Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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24
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Dey D, Chaskar S, Athavale N, Chitre D. Inhibition of LPS-induced TNF-α and NO production in mouse macrophage and inflammatory response in rat animal models by a novel Ayurvedic formulation, BV-9238. Phytother Res 2014; 28:1479-85. [PMID: 24706581 DOI: 10.1002/ptr.5151] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 02/26/2014] [Accepted: 03/03/2014] [Indexed: 01/04/2023]
Abstract
Rheumatoid arthritis is a chronic crippling disease, where protein-based tumor necrosis factor-alpha (TNF-α) inhibitors show significant relief, but with potentially fatal side effects. A need for a safe, oral, cost-effective small molecule or phyto-pharmaceutical is warranted. BV-9238 is an Ayurvedic poly-herbal formulation containing specialized standardized extracts of Withania somnifera, Boswellia serrata, Zingiber officinale and Curcuma longa. The anti-inflammatory and anti-arthritic effects of BV-9238 were evaluated for inhibition of TNF-α and nitric oxide (NO) production, in lipopolysaccharide-stimulated, RAW 264.7, mouse macrophage cell line. BV-9238 reduced TNF-α and NO production, without any cytotoxic effects. Subsequently, the formulation was tested in adjuvant-induced arthritis (AIA) and carrageenan-induced paw edema (CPE) rat animal models. AIA was induced in rats by injecting Freund's complete adjuvant intra-dermally in the paw, and BV-9238 and controls were administered orally for 21 days. Arthritic scores in AIA study and inflamed paw volume in CPE study were significantly reduced upon treatment with BV-9238. These results suggest that the anti-inflammatory and anti-arthritic effects of BV-9238 are due to its inhibition of TNF-α, and NO, and this formulation shows promise as an alternate therapy for inflammatory disorders where TNF-α and NO play important roles.
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Affiliation(s)
- Debendranath Dey
- Bioved Pharmaceuticals Pvt. Ltd., BAIF Bhawan, Z Wing, Warje Malwadi, Pune, 411 052, India
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25
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Ma L, Gong H, Zhu H, Ji Q, Su P, Liu P, Cao S, Yao J, Jiang L, Han M, Ma X, Xiong D, Luo HR, Wang F, Zhou J, Xu Y. A novel small-molecule tumor necrosis factor α inhibitor attenuates inflammation in a hepatitis mouse model. J Biol Chem 2014; 289:12457-66. [PMID: 24634219 DOI: 10.1074/jbc.m113.521708] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Overexpression of tumor necrosis factor α (TNFα) is a hallmark of many inflammatory diseases, including rheumatoid arthritis, inflammatory bowel disease, and septic shock and hepatitis, making it a potential therapeutic target for clinical interventions. To explore chemical inhibitors against TNFα activity, we applied computer-aided drug design combined with in vitro and cell-based assays and identified a lead chemical compound, (E)-4-(2-(4-chloro-3-nitrophenyl) (named as C87 thereafter), which directly binds to TNFα, potently inhibits TNFα-induced cytotoxicity (IC50 = 8.73 μM) and effectively blocks TNFα-triggered signaling activities. Furthermore, by using a murine acute hepatitis model, we showed that C87 attenuates TNFα-induced inflammation, thereby markedly reducing injuries to the liver and improving animal survival. Thus, our results lead to a novel and highly specific small-molecule TNFα inhibitor, which can be potentially used to treat TNFα-mediated inflammatory diseases.
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Affiliation(s)
- Li Ma
- From the State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
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26
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Liposomal encapsulation of dexamethasone modulates cytotoxicity, inflammatory cytokine response, and migratory properties of primary human macrophages. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2014; 10:1209-20. [PMID: 24607939 DOI: 10.1016/j.nano.2014.02.011] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/12/2014] [Accepted: 02/24/2014] [Indexed: 02/02/2023]
Abstract
UNLABELLED The encapsulation of drugs into liposomes aims to enhance their efficacy and reduce their toxicity. Corticosteroid-loaded liposomes are currently being evaluated in patients suffering from rheumatoid arthritis, atherosclerosis, colitis, and cancer. Here, using several different fluorophore-labeled formulations, we comprehensively studied the impact of liposome encapsulation of the prototypic corticosteroid dexamethasone on various primary human cells in vitro. Liposomal dexamethasone targeted several primary cell types in a dose and time-dependent manner, but specifically reduced cytotoxicity against human fibroblasts and macrophages in comparison to the solute drug. Furthermore, macrophage maturation and polarization markers were altered. Interestingly, liposomal dexamethasone induced proinflammatory cytokine secretion (specifically TNF, IL1β, IL6) in unstimulated cells, but reduced this response under inflammatory conditions. Monocyte and macrophage migration was significantly inhibited by dexamethasone-loaded liposomes. The findings indicate that the encapsulation of dexamethasone into liposomes modulates their cellular mechanism of action, and provides important indications for follow-up in vivo investigations. FROM THE CLINICAL EDITOR This study investigates mechanism of action of liposomal dexamethason in the treatment of inflammatory conditions. It is concluded that liposomal dexamethasone actually induces proinflammatory cytokine secretion in unstimulated cells, but reduces the same response under inflammatory conditions. Monocyte and macrophage migration was also inhibited. The findings indicate that liposomal dexamethasone may have different mechanisms of action than its native counterpart.
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