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Stincone P, Naimi A, Saviola AJ, Reher R, Petras D. Decoding the molecular interplay in the central dogma: An overview of mass spectrometry-based methods to investigate protein-metabolite interactions. Proteomics 2024; 24:e2200533. [PMID: 37929699 DOI: 10.1002/pmic.202200533] [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] [Received: 07/07/2023] [Revised: 10/15/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
With the emergence of next-generation nucleotide sequencing and mass spectrometry-based proteomics and metabolomics tools, we have comprehensive and scalable methods to analyze the genes, transcripts, proteins, and metabolites of a multitude of biological systems. Despite the fascinating new molecular insights at the genome, transcriptome, proteome and metabolome scale, we are still far from fully understanding cellular organization, cell cycles and biology at the molecular level. Significant advances in sensitivity and depth for both sequencing as well as mass spectrometry-based methods allow the analysis at the single cell and single molecule level. At the same time, new tools are emerging that enable the investigation of molecular interactions throughout the central dogma of molecular biology. In this review, we provide an overview of established and recently developed mass spectrometry-based tools to probe metabolite-protein interactions-from individual interaction pairs to interactions at the proteome-metabolome scale.
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Affiliation(s)
- Paolo Stincone
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of Tuebingen, Center for Plant Molecular Biology, Tuebingen, Germany
| | - Amira Naimi
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | | | - Raphael Reher
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | - Daniel Petras
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of California Riverside, Department of Biochemistry, Riverside, USA
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2
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Scheller J, Ettich J, Wittich C, Pudewell S, Floss DM, Rafii P. Exploring the landscape of synthetic IL-6-type cytokines. FEBS J 2024; 291:2030-2050. [PMID: 37467060 DOI: 10.1111/febs.16909] [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] [Received: 05/05/2023] [Revised: 06/30/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023]
Abstract
Interleukin-6 (IL-6)-type cytokines not only have key immunomodulatory functions that affect the pathogenesis of diseases such as autoimmune diseases, chronic inflammatory conditions, and cancer, but also fulfill important homeostatic tasks. Even though the pro-inflammatory arm has hindered the development of therapeutics based on natural-like IL-6-type cytokines to date, current synthetic trends might pave the way to overcome these limitations and eventually lead to immune-inert designer cytokines to aid type 2 diabetes and brain injuries. Those synthetic biology approaches include mutations, fusion proteins, and inter-cytokine swapping, and resulted in IL-6-type cytokines with altered receptor affinities, extended target cell profiles, and targeting of non-natural cytokine receptor complexes. Here, we survey synthetic cytokine developments within the IL-6-type cytokine family and discuss potential clinical applications.
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Affiliation(s)
- Jürgen Scheller
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Julia Ettich
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Christoph Wittich
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Silke Pudewell
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Doreen M Floss
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Puyan Rafii
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
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3
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Nitthikan N, Preedalikit W, Supadej K, Chaichit S, Leelapornpisid P, Kiattisin K. Exploring the Wound Healing Potential of a Cuscuta chinensis Extract-Loaded Nanoemulsion-Based Gel. Pharmaceutics 2024; 16:573. [PMID: 38794235 PMCID: PMC11124339 DOI: 10.3390/pharmaceutics16050573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/17/2024] [Accepted: 04/20/2024] [Indexed: 05/26/2024] Open
Abstract
Cuscuta chinensis (C. chinensis) presents many pharmacological activities, including antidiabetic effects, and antioxidant, anti-inflammatory, and antitumor properties. However, the wound care properties of this plant have not yet been reported. Therefore, this research aimed to evaluate the antioxidant, anti-inflammatory, and antibacterial activities of ethanol and ethyl acetate C. chinensis extracts. The phytochemical markers in the extracts were analyzed using high-performance liquid chromatography (HPLC). Then, the selected C. chinensis extract was developed into a nanoemulsion-based gel for wound care testing in rats. The results showed that both of the C. chinensis extracts exhibited antioxidant activity when tested using 2,2-Diphenyl-1-picrylhydrazyl (DPPH), ferric reducing antioxidant power (FRAP), and lipid peroxidation inhibition assays. They reduced the expression of IL-1β, IL-6, and TNF-α in RAW264.7 cells induced with lipopolysaccharide (LPS). The ethyl acetate extract also had antibacterial properties. Kaempferol was found in both extracts, whereas hyperoside was found only in the ethanol extract. These compounds were found to be related to the biological activities of the extracts, confirmed via molecular docking. The C. chinensis extract-loaded nanoemulsions had a small particle size, a narrow polydispersity index (PDI), and good stability. Furthermore, the C. chinensis extract-loaded nanoemulsion-based gel had a positive effect on wound healing, presenting a better percentage wound contraction Fucidin cream. In conclusion, this formulation has the potential for use as an alternative wound treatment and warrants further study in clinical trials.
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Affiliation(s)
- Nichcha Nitthikan
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand; (N.N.); (S.C.); (P.L.)
| | - Weeraya Preedalikit
- Department of Cosmetic Sciences, School of Pharmaceutical Sciences, University of Phayao, Phayao 56000, Thailand;
| | - Kanittapon Supadej
- Department of Medical Technology, School of Allied Health Sciences, University of Phayao, Phayao 56000, Thailand;
| | - Siripat Chaichit
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand; (N.N.); (S.C.); (P.L.)
| | - Pimporn Leelapornpisid
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand; (N.N.); (S.C.); (P.L.)
| | - Kanokwan Kiattisin
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand; (N.N.); (S.C.); (P.L.)
- Innovation Center for Holistic Health, Nutraceuticals, and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
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4
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Meksiriporn B, Spangler JB. Directed-evolution approach to empower EGFR targeting for immunotherapy. CELL REPORTS METHODS 2024; 4:100762. [PMID: 38631347 PMCID: PMC11046029 DOI: 10.1016/j.crmeth.2024.100762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
Advances in directed-evolution technologies are enabling new strategies to isolate binding proteins that recognize disease-associated states of a target protein. In this issue of Cell Reports Methods, Dobersberger et al. devised a yeast display-based selection scheme to discover proteins that engage the cancer-associated activated state of a receptor to enable design of safe and effective immunotherapies.
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Affiliation(s)
- Bunyarit Meksiriporn
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Jamie B Spangler
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Molecular Microbiology & Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.
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5
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Castel J, Delaux S, Hernandez-Alba O, Cianférani S. Recent advances in structural mass spectrometry methods in the context of biosimilarity assessment: from sequence heterogeneities to higher order structures. J Pharm Biomed Anal 2023; 236:115696. [PMID: 37713983 DOI: 10.1016/j.jpba.2023.115696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023]
Abstract
Biotherapeutics and their biosimilar versions have been flourishing in the biopharmaceutical market for several years. Structural and functional characterization is needed to achieve analytical biosimilarity through the assessment of critical quality attributes as required by regulatory authorities. The role of analytical strategies, particularly mass spectrometry-based methods, is pivotal to gathering valuable information for the in-depth characterization of biotherapeutics and biosimilarity assessment. Structural mass spectrometry methods (native MS, HDX-MS, top-down MS, etc.) provide information ranging from primary sequence assessment to higher order structure evaluation. This review focuses on recent developments and applications in structural mass spectrometry for biotherapeutic and biosimilar characterization.
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Affiliation(s)
- Jérôme Castel
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Delaux
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France.
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6
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Gesiorowski A, Ettich J, Werner J, Wittich C, Pieper S, Padrini G, Behnke K, Floss DM, Lang PA, Moll JM, Scheller J. Bispecific soluble cytokine receptor-nanobody fusions inhibit Interleukin (IL-)6 trans-signaling and IL-12/23 or tumor necrosis factor (TNF) signaling. J Biol Chem 2023; 299:105343. [PMID: 37838173 PMCID: PMC10652096 DOI: 10.1016/j.jbc.2023.105343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/18/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023] Open
Abstract
At least 0.5% of people in the Western world develop inflammatory bowel disease (IBD). While antibodies that block tumor necrosis factor (TNF) α and Interleukin (IL-)23 have been approved for the treatment of IBD, IL-6 antibodies failed in the phase II clinical trial due to non-tolerable side effects. However, two clinical phase II studies suggest that inhibiting IL-6/soluble IL-6R (sIL-6R)-induced trans-signaling via the cytokine receptor gp130 benefit IBD patients with fewer adverse events. Here we develop inhibitors targeting a combination of IL-6/sIL-6R and TNF or IL-12/IL-23 signaling, named cs130-TNFVHHFc and cs130-IL-12/23VHHFc. Surface plasmon resonance experiments showed that recombinant cs130-TNFVHHFc and cs130-IL-12/23VHHFc bind with high affinity to IL-6/sIL-6R complexes and human TNFα (hTNFα) or IL-12/IL-23, respectively. Immunoprecipitation experiments have verified the higher ordered complex formation of the inhibitors with IL-6/sIL-6R and IL-12. We demonstrated that cs130-TNFVHHFc and cs130-IL-12/23VHHFc block IL-6/sIL-6R trans-signaling-induced proliferation and STAT3 phosphorylation of Ba/F3-gp130 cells, as well as hTNFα- or IL-23-induced signaling, respectively. In conclusion, cs130-TNFVHHFc and cs130-IL-12/23VHHFc represent a class of dimeric and bispecific chimeric cytokine inhibitors that consist of a soluble cytokine receptor fused to anti-cytokine nanobodies.
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Affiliation(s)
- Annika Gesiorowski
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Julia Ettich
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Julia Werner
- Institute of Molecular Medicine II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Christoph Wittich
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Stephan Pieper
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Giacomo Padrini
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Kristina Behnke
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Doreen M Floss
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Philipp A Lang
- Institute of Molecular Medicine II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Jens M Moll
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany; PROvendis GmbH, Muelheim an der Ruhr, Germany
| | - Jürgen Scheller
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.
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7
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Wang J, Zheng Q, Shi M, Wang H, Fan C, Wang G, Zhao Y, Si J. Isolation, Identification, Anti-Inflammatory, and In Silico Analysis of New Lignans from the Resin of Ferula sinkiangensis. Pharmaceuticals (Basel) 2023; 16:1351. [PMID: 37895822 PMCID: PMC10610263 DOI: 10.3390/ph16101351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Ferula sinkiangensis K. M. Shen (Apiaceae) is distributed in arid desert areas of Xinjiang, and its resin is a traditional Chinese medicine to treat gastrointestinal digestive diseases. To explore bioactive components from F. sinkiangensis, three new lignans and thirteen known components were isolated. The structural elucidation of the components was established utilizing spectroscopic analyses together with ECD calculations. Griess reaction results indicated new compounds 1 and 2 significantly decreased NO production in LPS-stimulated RAW 264.7 macrophages, and ELISA results indicated that they effectively attenuated LPS-induced inflammation by inhibiting TNF-α, IL-1β, and IL-6 expressions. The in silico approach confirmed that compound 1 docked into the receptors with strong binding energies of -5.84~-10.79 kcal/mol. In addition, compound 6 inhibited the proliferation of AGS gastric cancer cells with IC50 values of 15.2 μM by suppressing the cell migration and invasion. This study disclosed that F. sinkiangensis might be a promising potential resource for bioactive components.
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Affiliation(s)
- Junchi Wang
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (J.W.); (Q.Z.); (H.W.)
| | - Qi Zheng
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (J.W.); (Q.Z.); (H.W.)
| | - Minghui Shi
- Xinjiang Institute of Chinese Materia Medica and Ethnodrug, Urumqi 830002, China; (M.S.); (C.F.); (G.W.); (Y.Z.)
| | - Huaxiang Wang
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (J.W.); (Q.Z.); (H.W.)
| | - Congzhao Fan
- Xinjiang Institute of Chinese Materia Medica and Ethnodrug, Urumqi 830002, China; (M.S.); (C.F.); (G.W.); (Y.Z.)
| | - Guoping Wang
- Xinjiang Institute of Chinese Materia Medica and Ethnodrug, Urumqi 830002, China; (M.S.); (C.F.); (G.W.); (Y.Z.)
| | - Yaqin Zhao
- Xinjiang Institute of Chinese Materia Medica and Ethnodrug, Urumqi 830002, China; (M.S.); (C.F.); (G.W.); (Y.Z.)
| | - Jianyong Si
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (J.W.); (Q.Z.); (H.W.)
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8
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Li J, Kang G, Wang J, Yuan H, Wu Y, Meng S, Wang P, Zhang M, Wang Y, Feng Y, Huang H, de Marco A. Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization. Int J Biol Macromol 2023; 247:125733. [PMID: 37423452 DOI: 10.1016/j.ijbiomac.2023.125733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Routinely screened antibody fragments usually require further in vitro maturation to achieve the desired biophysical properties. Blind in vitro strategies can produce improved ligands by introducing random mutations into the original sequences and selecting the resulting clones under more and more stringent conditions. Rational approaches exploit an alternative perspective that aims first at identifying the specific residues potentially involved in the control of biophysical mechanisms, such as affinity or stability, and then to evaluate what mutations could improve those characteristics. The understanding of the antigen-antibody interactions is instrumental to develop this process the reliability of which, consequently, strongly depends on the quality and completeness of the structural information. Recently, methods based on deep learning approaches critically improved the speed and accuracy of model building and are promising tools for accelerating the docking step. Here, we review the features of the available bioinformatic instruments and analyze the reports illustrating the result obtained with their application to optimize antibody fragments, and nanobodies in particular. Finally, the emerging trends and open questions are summarized.
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Affiliation(s)
- Jiaqi Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Guangbo Kang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Jiewen Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Haibin Yuan
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yili Wu
- Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health and the Affiliated Kangning Hospital, Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Wenzhou Medical University, Oujiang Laboratory, Wenzhou, Zhejiang 325035, China
| | - Shuxian Meng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Ping Wang
- New Technology R&D Department, Tianjin Modern Innovative TCM Technology Company Limited, Tianjin 300392, China
| | - Miao Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; China Resources Biopharmaceutical Company Limited, Beijing 100029, China
| | - Yuli Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Tianjin Pharmaceutical Da Ren Tang Group Corporation Limited, Traditional Chinese Pharmacy Research Institute, Tianjin Key Laboratory of Quality Control in Chinese Medicine, Tianjin 300457, China; State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China
| | - Yuanhang Feng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - He Huang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia.
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Mufti A, Feriani A, Ouchari W, Mandour YM, Tlili N, Ibrahim MA, Mahmoud MF, Sobeh M. Leonotis ocymifolia (Burm.f.) Iwarsson aerial parts aqueous extract mitigates cisplatin-induced nephrotoxicity via attenuation of inflammation, and DNA damage. Front Pharmacol 2023; 14:1221486. [PMID: 37593171 PMCID: PMC10428015 DOI: 10.3389/fphar.2023.1221486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/17/2023] [Indexed: 08/19/2023] Open
Abstract
Herein, we explored the protective effect of Leonotis ocymifolia (Burm.f.) Iwarsson aerial parts extract (LO) against cisplatin (CP)-induced nephrotoxicity in rats and profiled their phytocontents. A total of 31 compounds belonging to organic and phenolic acids and their glycosides as well as flavonoids and their O- and C-glycosides were identified through LC-MS/MS. The DPPH and FRAP assays revealed that the extract had powerful antioxidant properties. The in vivo results demonstrated that administering LO extract for 30 days (40 and 80 mg/kg b. w.) significantly improved the altered renal injury markers via reducing creatinine (high dose only) and uric acid levels compared to the Cp-group. The deleterious action of cisplatin on renal oxidative stress markers (GSH, MDA, SOD, and CAT) were also mitigated by LO-pretreatment. The reduction of the inflammatory marker (IL-6), and inhibition of DNA fragmentation, highlighted the prophylactic action of LO in kidney tissue. Molecular docking followed by a 100 ns molecular dynamic simulation analyses revealed that, amongst the 31 identified compounds in LO, chlorogenic and caffeoylmalic acids had the most stable binding to IL-6. The nephroprotective effects were further confirmed by histopathological observations, which showed improvement in ultrastructural changes induced by cisplatin. The observed findings reinforce the conclusion that L. ocymifolia extract exerts nephroprotective properties, which could be related to its antioxidant and anti-inflammatory activities. Further studies are required to determine the therapeutic doses and the proper administration time.
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Affiliation(s)
- Afoua Mufti
- Laboratory of Biotechnology and Biomonitoring of the Environment and Oasis Ecosystems, Faculty of Sciences of Gafsa, University of Gafsa, Gafsa, Tunisia
| | - Anouar Feriani
- Laboratory of Biotechnology and Biomonitoring of the Environment and Oasis Ecosystems, Faculty of Sciences of Gafsa, University of Gafsa, Gafsa, Tunisia
| | - Wafae Ouchari
- AgroBioSciences Program, College for Sustainable Agriculture and Environmental Science, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Yasmine M. Mandour
- School of Life and Medical Sciences, University of Hertfordshire Hosted By Global Academic Foundation, Cairo, Egypt
| | - Nizar Tlili
- Institut Supérieur des Sciences et Technologies de L’Environnement, Université de Carthage, Carthage, Tunisia
| | | | - Mona F. Mahmoud
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mansour Sobeh
- AgroBioSciences Program, College for Sustainable Agriculture and Environmental Science, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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10
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Sabikunnahar B, Caldwell S, Varnum S, Hogan T, Cooper A, Lahue KG, Bivona JJ, Cousens PM, Symeonides M, Ballif BA, Poynter ME, Krementsov DN. Long Noncoding RNA U90926 Is Induced in Activated Macrophages, Is Protective in Endotoxic Shock, and Encodes a Novel Secreted Protein. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:807-819. [PMID: 36705532 PMCID: PMC9998366 DOI: 10.4049/jimmunol.2200215] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 01/03/2023] [Indexed: 01/28/2023]
Abstract
Thousands of long noncoding RNAs are encoded in mammalian genomes, yet most remain uncharacterized. In this study, we functionally characterized a mouse long noncoding RNA named U90926. Analysis of U90926 RNA levels revealed minimal expression across multiple tissues at steady state. However, the expression of this gene was highly induced in macrophages and dendritic cells by TLR activation, in a p38 MAPK- and MyD88-dependent manner. To study the function of U90926, we generated U90926-deficient (U9-KO) mice. Surprisingly, we found minimal effects of U90926 deficiency in cultured macrophages. Given the lack of macrophage-intrinsic effect, we investigated the subcellular localization of U90926 transcript and its protein-coding potential. We found that U90926 RNA localizes to the cytosol, associates with ribosomes, and contains an open reading frame that encodes a novel glycosylated protein (termed U9-ORF), which is secreted from the cell. An in vivo model of endotoxic shock revealed that, in comparison with wild type mice, U9-KO mice exhibited increased sickness responses and mortality. Mechanistically, serum levels of IL-6 were elevated in U9-KO mice, and IL-6 neutralization improved endotoxemia outcomes in U9-KO mice. Taken together, these results suggest that U90926 expression is protective during endotoxic shock, potentially mediated by the paracrine and/or endocrine actions of the novel U9-ORF protein secreted by activated myeloid cells.
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Affiliation(s)
- Bristy Sabikunnahar
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
- Cellular, Molecular, and Biomedical Sciences Doctoral Program, University of Vermont, Burlington, VT
| | - Sydney Caldwell
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
| | - Stella Varnum
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
| | - Tyler Hogan
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
| | - Alexei Cooper
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
| | - Karolyn G Lahue
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
| | - Joseph J Bivona
- Cellular, Molecular, and Biomedical Sciences Doctoral Program, University of Vermont, Burlington, VT
- Department of Medicine, University of Vermont, Burlington, VT
| | | | - Menelaos Symeonides
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT
| | - Bryan A Ballif
- Department of Biology, University of Vermont, Burlington, VT
| | | | - Dimitry N Krementsov
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
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11
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Ben Boubaker R, Tiss A, Henrion D, Chabbert M. Homology Modeling in the Twilight Zone: Improved Accuracy by Sequence Space Analysis. Methods Mol Biol 2023; 2627:1-23. [PMID: 36959439 DOI: 10.1007/978-1-0716-2974-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The analysis of the relationship between sequence and structure similarities during the evolution of a protein family has revealed a limit of sequence divergence for which structural conservation can be confidently assumed and homology modeling is reliable. Below this limit, the twilight zone corresponds to sequence divergence for which homology modeling becomes increasingly difficult and requires specific methods. Either with conventional threading methods or with recent deep learning methods, such as AlphaFold, the challenge relies on the identification of a template that shares not only a common ancestor (homology) but also a conserved structure with the query. As both homology and structural conservation are transitive properties, mining of sequence databases followed by multidimensional scaling (MDS) of the query sequence space can reveal intermediary sequences to infer homology and structural conservation between the query and the template. Here, as a case study, we studied the plethodontid receptivity factor isoform 1 (PRF1) from Plethodon jordani, a member of a pheromone protein family present only in lungless salamanders and weakly related to cytokines of the IL6 family. A variety of conventional threading methods led to the cytokine CNTF as a template. Sequence mining, followed by phylogenetic and MDS analysis, provided missing links between PRF1 and CNTF and allowed reliable homology modeling. In addition, we compared automated models obtained from web servers to a customized model to show how modeling can be improved by expert information.
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Affiliation(s)
- Rym Ben Boubaker
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Asma Tiss
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Daniel Henrion
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Marie Chabbert
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France.
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12
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Shin G, Lim SI. Unveiling the biological interface of protein complexes by mass spectrometry-coupled methods. Proteins 2022; 91:593-607. [PMID: 36573681 DOI: 10.1002/prot.26459] [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: 07/16/2022] [Revised: 11/28/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Most biomolecules become functional and bioactive by forming protein complexes through interaction with ligands that are diverse in size, shape, and physicochemical properties. In the complex biological milieu, the interaction is ligand-specific, driven by molecular sensing, and involves the recognition of a binding interface localized within a protein structure. Mapping interfaces of protein complexes is a highly sought area of research as it delivers fundamental insights into proteomes and pathology and hence strategies for therapeutics. While X-ray crystallography and electron microscopy remain the gold standard for structural elucidation of protein complexes, their artificial and static analytic nature often produces a non-native interface that otherwise might be negligible or non-existent in a biological environment. Recently, the mass spectrometry-coupled approaches, chemical crosslinking (CLMS) and hydrogen-deuterium exchange (HDMS) have become valuable analytic complements to the traditional techniques. These methods explicitly identify hot residues and motifs embedded in binding interfaces, especially when the interaction is predominantly dynamic, transient, and/or caused by an intrinsically disordered domain. Here, we review the principal role of CLMS and HDMS in protein structural biology with a particular emphasis on the contribution of recent examples to exploring biological interfaces. Additionally, we describe recent studies that utilized these methods to expand our understanding of protein complex formation and the related biological processes, to increase the probability of structure-based drug design.
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Affiliation(s)
- Goeun Shin
- Department of Chemical Engineering, Pukyong National University, Busan, South Korea
| | - Sung In Lim
- Department of Chemical Engineering, Pukyong National University, Busan, South Korea
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13
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Tran QH, Nguyen QT, Vo NQH, Mai TT, Tran TTN, Tran TD, Le MT, Trinh DTT, Thai KM. Structure-based 3D-Pharmacophore modeling to discover novel interleukin 6 inhibitors: An in silico screening, molecular dynamics simulations and binding free energy calculations. PLoS One 2022; 17:e0266632. [PMID: 35385549 PMCID: PMC8986010 DOI: 10.1371/journal.pone.0266632] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/23/2022] [Indexed: 11/24/2022] Open
Abstract
Interleukin 6 (IL-6) is a cytokine with various biological functions in immune regulation, hematopoiesis, and inflammation. Elevated IL-6 levels have been identified in several severe disorders such as sepsis, acute respiratory distress syndrome (ARDS), and most recently, COVID-19. The biological activity of IL-6 relies on interactions with its specific receptor, IL-6Rα, including the membrane-bound IL-6 receptor (mIL-6R) and the soluble IL-6 receptor (sIL-6R). Thus, inhibition of the interaction between these two proteins would be a potential treatment for IL-6 related diseases. To date, no orally available small-molecule drug has been approved. This study focuses on finding potential small molecules that can inhibit protein-protein interactions between IL-6 and its receptor IL-6Rα using its crystal structure (PDB ID: 5FUC). First, two pharmacophore models were constructed based on the interactions between key residues of IL-6 (Phe74, Phe78, Leu178, Arg179, Arg182) and IL-6Rα (Phe229, Tyr230, Glu277, Glu278, Phe279). A database of approximately 22 million compounds was screened using 3D-pharmacophore models, molecular docking models, and ADMET properties. By analyzing the interactive capability of successfully docked compounds with important amino acids, 12 potential ligands were selected for further analysis via molecular dynamics simulations. Based on the stability of the complexes, the high interactions rate of each ligand with the key residues of IL-6/IL-6Rα, and the low binding free energy calculation, two compounds ZINC83804241 and ZINC02997430, were identified as the most potential IL-6 inhibitor candidates. These results will pave the way for the design and optimization of more specific compounds to combat cytokine storm in severe coronavirus patients.
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Affiliation(s)
- Que-Huong Tran
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- Department of Pharmaceutical Chemistry Da Nang University of Medical Technology and Pharmacy, Da Nang, Vietnam
| | - Quoc-Thai Nguyen
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- * E-mail: (QTN); (DTTT); , (KMT)
| | - Nguyen-Quynh-Huong Vo
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Tan Thanh Mai
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thi-Thuy-Nga Tran
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- Department of Pharmaceutical Chemistry Da Nang University of Medical Technology and Pharmacy, Da Nang, Vietnam
| | - Thanh-Dao Tran
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Minh-Tri Le
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- School of Medicine, Vietnam National University Ho Chi Minh City, Linh Trung Ward., Thu Duc Dist., Ho Chi Minh City, Vietnam
| | - Dieu-Thuong Thi Trinh
- Faculty of Traditional Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- * E-mail: (QTN); (DTTT); , (KMT)
| | - Khac-Minh Thai
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
- * E-mail: (QTN); (DTTT); , (KMT)
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14
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Chou CC, Hua KT, Chen MW, Wu CJ, Hsu CH, Wang JT, Hsiao M, Wei LH. Discovery and characterization of a monoclonal antibody targeting a conformational epitope of IL-6/IL-6Rα to inhibit IL-6/ IL-6Rα/gp130 hexameric signaling complex formation. MAbs 2022; 14:2029675. [PMID: 35133941 PMCID: PMC8837245 DOI: 10.1080/19420862.2022.2029675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The functional interleukin 6 (IL-6) signaling complex is a hexameric structure composed of IL-6, IL-6Rα, and the signaling receptor gp130. There are three different modes of IL-6 signaling, classic signaling, trans-signaling, and trans-presentation, which are not functionally redundant and mediate pleiotropic effects on both physiological and pathophysiological states. Monoclonal antibodies against IL-6 or IL-6Rα have been successfully developed for clinical application. However, designing therapeutic interventions that block specific modes of IL-6 signaling in a pathologically relevant manner remains a great challenge. Here, we constructed a fusion protein Hyper-IL-6 (HyIL-6) composed of human IL-6 and IL-6Rα to develop specific blocking antibodies against the IL-6/IL-6Rα complex. We successfully screened the monoclonal antibody C14mab, which can bind to HyIL-6 with the binding constant 2.86 × 10-10 and significantly inhibit IL-6/IL-6Rα/gp130 complex formation. In vitro, C14mab effectively inhibited HyIL-6-stimulated signal transducer and activator of transcription 3 (STAT3) activation and related vascular endothelial growth factor (VEGF) induction. Moreover, C14mab efficaciously suppressed HyIL-6-induced acute phase response in vivo. Our data from hydrogen-deuterium exchange mass spectrometry demonstrate that C14mab mainly binds to site IIIa of IL-6 and blocks the final step in the interaction between gp130 and IL-6/IL-6Rα complex. Additionally, data from enzyme-linked immunosorbent assays and kinetics assays indicate that C14mab interacts simultaneously with IL-6 and IL-6Rα, while it does not interact with IL-6Rα alone. The unique features of C14mab may offer a novel alternative for IL-6 blockade and illuminate a better therapeutic intervention targeting IL-6.
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Affiliation(s)
- Chun-Chi Chou
- Department of Obstetrics & Gynecology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Kuo-Tai Hua
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Min-Wei Chen
- Department of Obstetrics & Gynecology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chin-Jui Wu
- Department of Obstetrics & Gynecology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Hua Hsu
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Jann-Tay Wang
- Division of Infectious Diseases, Department of Internal Medicine, National Taiwan University, Hospital, Taipei, Taiwan
| | - Michael Hsiao
- The Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Lin-Hung Wei
- Department of Obstetrics & Gynecology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
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15
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Schardt JS, Jhajj HS, O’Meara RL, Lwo TS, Smith MD, Tessier PM. Agonist antibody discovery: Experimental, computational, and rational engineering approaches. Drug Discov Today 2022; 27:31-48. [PMID: 34571277 PMCID: PMC8714685 DOI: 10.1016/j.drudis.2021.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/19/2021] [Accepted: 09/20/2021] [Indexed: 01/03/2023]
Abstract
Agonist antibodies that activate cellular signaling have emerged as promising therapeutics for treating myriad pathologies. Unfortunately, the discovery of rare antibodies with the desired agonist functions is a major bottleneck during drug development. Nevertheless, there has been important recent progress in discovering and optimizing agonist antibodies against a variety of therapeutic targets that are activated by diverse signaling mechanisms. Herein, we review emerging high-throughput experimental and computational methods for agonist antibody discovery as well as rational molecular engineering methods for optimizing their agonist activity.
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Affiliation(s)
- John S. Schardt
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Harkamal S. Jhajj
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryen L. O’Meara
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Timon S. Lwo
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew D. Smith
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M. Tessier
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
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16
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A hybrid soluble gp130/spike-nanobody fusion protein simultaneously blocks IL-6 trans-signaling and cellular infection with SARS-CoV2. J Virol 2021; 96:e0162221. [PMID: 34935434 PMCID: PMC8865451 DOI: 10.1128/jvi.01622-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can induce mild to life-threatening symptoms. Especially individuals over 60 years of age or with underlying comorbidities, including heart or lung disease and diabetes, or immunocompromised patients are at a higher risk. Fatal multiorgan damage in coronavirus disease 2019 (COVID-19) patients can be attributed to an interleukin-6 (IL-6)-dominated cytokine storm. Consequently, IL-6 receptor (IL-6R) monoclonal antibody treatment for severe COVID-19 cases has been approved for therapy. High concentrations of soluble IL-6R (sIL-6R) were found in COVID-19 intensive care unit patients, suggesting the involvement of IL-6 trans-signaling in disease pathology. Here, in analogy to bispecific antibodies (bsAbs), we developed the first bispecific IL-6 trans-signaling inhibitor, c19s130Fc, which blocks viral infection and IL-6 trans-signaling. c19s130Fc is a designer protein of the IL-6 trans-signaling inhibitor cs130 fused to a single-domain nanobody directed against the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. c19s130Fc binds with high affinity to IL-6:sIL-6R complexes as well as the spike protein of SARS-CoV-2, as shown by surface plasmon resonance. Using cell-based assays, we demonstrate that c19s130Fc blocks IL-6 trans-signaling-induced proliferation and STAT3 phosphorylation in Ba/F3-gp130 cells as well as SARS-CoV-2 infection and STAT3 phosphorylation in Vero cells. Taken together, c19s130Fc represents a new class of bispecific inhibitors consisting of a soluble cytokine receptor fused to antiviral nanobodies and principally demonstrates the multifunctionalization of trans-signaling inhibitors. IMPORTANCE The availability of effective SARS-CoV-2 vaccines is a large step forward in managing the pandemic situation. In addition, therapeutic options, e.g., monoclonal antibodies to prevent viral cell entry and anti-inflammatory therapies, including glucocorticoid treatment, are currently developed or in clinical use to treat already infected patients. Here, we report a novel dual-specificity inhibitor to simultaneously target SARS-CoV-2 infection and virus-induced hyperinflammation. This was achieved by fusing an inhibitor of viral cell entry with a molecule blocking IL-6, a key mediator of SARS-CoV-2-induced hyperinflammation. Through this dual action, this molecule may have the potential to efficiently ameliorate symptoms of COVID-19 in infected individuals.
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17
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Martínez-Pérez C, Kay C, Meehan J, Gray M, Dixon JM, Turnbull AK. The IL6-like Cytokine Family: Role and Biomarker Potential in Breast Cancer. J Pers Med 2021; 11:1073. [PMID: 34834425 PMCID: PMC8624266 DOI: 10.3390/jpm11111073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 02/07/2023] Open
Abstract
IL6-like cytokines are a family of regulators with a complex, pleiotropic role in both the healthy organism, where they regulate immunity and homeostasis, and in different diseases, including cancer. Here we summarise how these cytokines exert their effect through the shared signal transducer IL6ST (gp130) and we review the extensive evidence on the role that different members of this family play in breast cancer. Additionally, we discuss how the different cytokines, their related receptors and downstream effectors, as well as specific polymorphisms in these molecules, can serve as predictive or prognostic biomarkers with the potential for clinical application in breast cancer. Lastly, we also discuss how our increasing understanding of this complex signalling axis presents promising opportunities for the development or repurposing of therapeutic strategies against cancer and, specifically, breast neoplasms.
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Affiliation(s)
- Carlos Martínez-Pérez
- Breast Cancer Now Edinburgh Research Team, MRC Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK; (C.K.); (J.M.D.); (A.K.T.)
- Translational Oncology Research Group, MRC Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH8 9YL, UK; (J.M.); (M.G.)
| | - Charlene Kay
- Breast Cancer Now Edinburgh Research Team, MRC Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK; (C.K.); (J.M.D.); (A.K.T.)
- Translational Oncology Research Group, MRC Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH8 9YL, UK; (J.M.); (M.G.)
| | - James Meehan
- Translational Oncology Research Group, MRC Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH8 9YL, UK; (J.M.); (M.G.)
| | - Mark Gray
- Translational Oncology Research Group, MRC Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH8 9YL, UK; (J.M.); (M.G.)
| | - J. Michael Dixon
- Breast Cancer Now Edinburgh Research Team, MRC Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK; (C.K.); (J.M.D.); (A.K.T.)
| | - Arran K. Turnbull
- Breast Cancer Now Edinburgh Research Team, MRC Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK; (C.K.); (J.M.D.); (A.K.T.)
- Translational Oncology Research Group, MRC Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh, Edinburgh EH8 9YL, UK; (J.M.); (M.G.)
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18
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Dong Y, Tao B, Xue X, Feng C, Ren Y, Ma H, Zhang J, Si Y, Zhang S, Liu S, Li H, Zhou J, Li G, Wang Z, Xie J, Zhu Z. Molecular mechanism of Epicedium treatment for depression based on network pharmacology and molecular docking technology. BMC Complement Med Ther 2021; 21:222. [PMID: 34479552 PMCID: PMC8417989 DOI: 10.1186/s12906-021-03389-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 08/10/2021] [Indexed: 01/15/2023] Open
Abstract
Background Increasing attention has been paid to the effect of Epimedium on the nervous system, particularly anti-depression function. In the present study, we applied network pharmacology to introduce a testable hypothesis on the multi-target mechanisms of Epicedium against depression. Methods By reconstructing the network of protein–protein interaction and drug–component–target, we predicted the key protein targets of Epicedium for the treatment of depression. Then, through molecular docking, the interaction of the main active components of Epicedium and predicted candidate targets were verified. Results Nineteen active compounds were selected from Epicedium. There were 200 targets associated with Epicedium and 537 targets related to depression. The key targets of Epicedium for treating depression were IL6, VEGFA, AKT1, and EGF. According to gene ontology functional enrichment analysis, 22 items of biological process (BP), 13 items of cell composition (CC) and 9 items of molecular function (MF) were obtained. A total of 56 signaling pathways (P < 0.05) were identified by Kyoto Encyclopedia of Genes and Genomes analysis, mainly involving depression-related pathways such as dopaminergic synapse, TNF signaling pathway, and prolactin signaling pathway. The results of molecular docking showed that the most important activity components, including luteoklin, quercetin and kaempferol, were well combined with the key targets. Conclusions Luteoklin, quercetin, kaempferol and other active compounds in Epicedium can regulate multiple signaling pathways and targets such as IL6, AKT1, and EGF, therefore playing therapeutic roles in depression. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-021-03389-w.
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Affiliation(s)
- Yankai Dong
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Institute of Maternal and Infant health, Northwest University, Xi'an, 710069, Shanxi Province, China
| | - Bo Tao
- Department of Orthopaedic, Tianjin Medical University General Hospital, Anshan Road No.154, Tianjin, 300052, Heping District, China
| | - Xing Xue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Institute of Maternal and Infant health, Northwest University, Xi'an, 710069, Shanxi Province, China
| | - Caixia Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Institute of Maternal and Infant health, Northwest University, Xi'an, 710069, Shanxi Province, China
| | - Yating Ren
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Institute of Maternal and Infant health, Northwest University, Xi'an, 710069, Shanxi Province, China
| | - Hengyu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Institute of Maternal and Infant health, Northwest University, Xi'an, 710069, Shanxi Province, China
| | - Junli Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Institute of Maternal and Infant health, Northwest University, Xi'an, 710069, Shanxi Province, China
| | - Yufang Si
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Institute of Maternal and Infant health, Northwest University, Xi'an, 710069, Shanxi Province, China
| | - Sisi Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Institute of Maternal and Infant health, Northwest University, Xi'an, 710069, Shanxi Province, China
| | - Si Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Institute of Maternal and Infant health, Northwest University, Xi'an, 710069, Shanxi Province, China
| | - Hui Li
- Department of Neonatology, The First Affiliated Hospital of Medical College,Xi'an Jiaotong University, Xi'an, 710069, Shanxi Province, China
| | - Jiahao Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Institute of Maternal and Infant health, Northwest University, Xi'an, 710069, Shanxi Province, China
| | - Ge Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Institute of Maternal and Infant health, Northwest University, Xi'an, 710069, Shanxi Province, China
| | - Zhifei Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Institute of Maternal and Infant health, Northwest University, Xi'an, 710069, Shanxi Province, China
| | - Juanping Xie
- Qinba Chinese Medicine Resources R&D Center, School of Medicine, Ankang University, Ankang, 710069, Shanxi Province, China.
| | - Zhongliang Zhu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Institute of Maternal and Infant health, Northwest University, Xi'an, 710069, Shanxi Province, China.
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19
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Felicetti L, Femminella M, Reali G. A Molecular Communications System for the Detection of Inflammatory Levels Related to COVID-19 Disease. IEEE TRANSACTIONS ON MOLECULAR, BIOLOGICAL AND MULTI-SCALE COMMUNICATIONS 2021; 7:165-174. [PMID: 35782715 PMCID: PMC8544947 DOI: 10.1109/tmbmc.2021.3071788] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/27/2021] [Accepted: 03/15/2021] [Indexed: 12/29/2022]
Abstract
A recent and extensive research activity highlighted the process behind the attack and spread of COVID-19 in the human body. What emerged is that the SARS-CoV-2 virus makes use of both the ACE2 receptor, expressed by pneumocytes in the ephitelial alveolar lining, and by the endothelium to spread the disease and to replicate itself. Since the endothelium is an extended tissue lying in the circulatory system, this may lead to a large state of diffuse endothelial inflammation with serious clinical consequences. This situation may be further compromised by the immune system, that may generate pro-inflammatory cytokines (IL-6) as a consequence of the infection. In this paper we propose and analyze a molecular communication system, designed for the detection of excessive IL-6 level, that allows monitoring its evolution in the blood vessels. The proposed analysis was performed by using the BiNS2 simulator, which is suitable for the numerical analysis of flow-based molecular communications in blood vessels, as well as Markov models of the endothelium.
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Affiliation(s)
- Luca Felicetti
- Department of EngineeringUniversity of Perugia 06123 Perugia Italy
- Consorzio Nazionale Interuniversitario per le TelecomunicazioniUniversity of Perugia 06123 Perugia Italy
| | - Mauro Femminella
- Department of EngineeringUniversity of Perugia 06123 Perugia Italy
- Consorzio Nazionale Interuniversitario per le TelecomunicazioniUniversity of Perugia 06123 Perugia Italy
| | - Gianluca Reali
- Department of EngineeringUniversity of Perugia 06123 Perugia Italy
- Consorzio Nazionale Interuniversitario per le TelecomunicazioniUniversity of Perugia 06123 Perugia Italy
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20
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Cui S, Zhou Z, Chen X, Wei F, Richards RG, Alini M, Grad S, Li Z. Transcriptional profiling of intervertebral disc in a post-traumatic early degeneration organ culture model. JOR Spine 2021; 4:e1146. [PMID: 34611583 PMCID: PMC8479529 DOI: 10.1002/jsp2.1146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/19/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION The goal of this study is to characterize transcriptome changes and gene regulation networks in an organ culture system that mimics early post-traumatic intervertebral disc (IVD) degeneration. METHODS To mimic a traumatic insult, bovine caudal IVDs underwent one strike loading. The control group was cultured under physiological loading. At 24 hours after one strike or physiological loading, RNA was extracted from nucleus pulposus (NP) and annulus fibrosus (AF) tissue. High throughput next generation RNA sequencing was performed to identify differentially expressed genes (DEGs) between the one strike loading group and the control group. Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes analyses were performed to analyze DEGs and pathways. Protein-protein interaction (PPI) network was analyzed with cytoscape software. DEGs were verified using qRT-PCR. Degenerated human IVD tissue was collected for immunofluorescence staining to verify the expression of DEGs in human disc tissue. RESULTS One strike loading resulted in significant gene expression changes compared with physiological loading. In total 253 DEGs were found in NP tissue and 208 DEGs in AF tissue. Many of the highly dysregulated genes have known functions in disc degeneration and extracellular matrix (ECM) homeostasis. ACTB, ACTG, PFN1, MYL12B in NP tissue and FGF1, SPP1 in AF tissue were verified by qRT-PCR and immunofluorescence imaging. The identified DEGs were involved in focal adhesion, ECM-receptor interaction, PI3K-AKT, and cytokine-cytokine receptor interaction pathways. Three clusters of PPI networks were identified. GO enrichment revealed that these DEGs were mainly involved in inflammatory response, the ECM and growth factor signaling and protein folding biological process. CONCLUSION Our study revealed different DEGs, pathways, biological process and PPI networks involved in post-traumatic IVD degeneration. These findings will advance the understanding of the pathogenesis of IVD degeneration, and help to identify novel biomarkers for the disease diagnosis.
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Affiliation(s)
- Shangbin Cui
- AO Research Institute DavosDavosSwitzerland
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | - Zhiyu Zhou
- The Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenChina
| | - Xu Chen
- The Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenChina
| | - Fuxin Wei
- The Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenChina
| | - R. Geoff Richards
- AO Research Institute DavosDavosSwitzerland
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
| | | | | | - Zhen Li
- AO Research Institute DavosDavosSwitzerland
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21
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Heise D, Derrac Soria A, Hansen S, Dambietz C, Akbarzadeh M, Berg AF, Waetzig GH, Jones SA, Dvorsky R, Ahmadian MR, Scheller J, Moll JM. Selective inhibition of IL-6 trans-signaling by a miniaturized, optimized chimeric soluble gp130 inhibits T H17 cell expansion. Sci Signal 2021; 14:eabc3480. [PMID: 34404751 DOI: 10.1126/scisignal.abc3480] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The cytokine interleukin-6 (IL-6) signals through three mechanisms called classic signaling, trans-signaling, and trans-presentation. IL-6 trans-signaling is distinctly mediated through a soluble form of its transmembrane receptor IL-6R (sIL-6R) and the coreceptor gp130 and is implicated in multiple autoimmune diseases. Although a soluble form of gp130 (sgp130) inhibits only IL-6 trans-signaling, it also blocks an analogous trans-signaling mechanism of IL-11 and its soluble receptor sIL-11R. Here, we report miniaturized chimeric soluble gp130 variants that efficiently trap IL-6:sIL-6R but not IL-11:sIL-11R complexes. We designed a novel IL-6 trans-signaling trap by fusing a miniaturized sgp130 variant to an IL-6:sIL-6R complex-binding nanobody and the Fc portion of immunoglobulin G (IgG). This trap, called cs-130Fc, exhibited improved inhibition of as well as increased selectivity for IL-6 trans-signaling compared to the conventional fusion protein sgp130Fc. We introduced affinity-enhancing mutations in cs-130Fc and sgp130Fc that further improved selectivity toward IL-6 trans-signaling. Moreover, cs-130Fc efficiently inhibited the expansion of T helper 17 (TH17) cells in cultures of mouse CD4+ T cells treated with IL-6:sIL-6R. Thus, these variants may provide or lead to the development of more precisely targeted therapeutics for inflammatory disorders associated with IL-6 trans-signaling.
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Affiliation(s)
- Denise Heise
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Alicia Derrac Soria
- Division of Infection and Immunity, School of Medicine, Systems Immunity University Research Institute, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF14 4XN, UK
| | - Selina Hansen
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Christine Dambietz
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Mohammad Akbarzadeh
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Anna F Berg
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Georg H Waetzig
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
- CONARIS Research Institute AG, Kiel 24118, Germany
| | - Simon A Jones
- Division of Infection and Immunity, School of Medicine, Systems Immunity University Research Institute, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF14 4XN, UK
| | - Radovan Dvorsky
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Mohammad R Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Jürgen Scheller
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany.
| | - Jens M Moll
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany.
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22
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Skeene K, Khatri K, Soloviev Z, Lapthorn C. Current status and future prospects for ion-mobility mass spectrometry in the biopharmaceutical industry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140697. [PMID: 34246790 DOI: 10.1016/j.bbapap.2021.140697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/11/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022]
Abstract
Detailed characterization of protein reagents and biopharmaceuticals is key in defining successful drug discovery campaigns, aimed at bringing molecules through different discovery stages up to development and commercialization. There are many challenges in this process, with complex and detailed analyses playing paramount roles in modern industry. Mass spectrometry (MS) has become an essential tool for characterization of proteins ever since the onset of soft ionization techniques and has taken the lead in quality assessment of biopharmaceutical molecules, and protein reagents, used in the drug discovery pipeline. MS use spans from identification of correct sequences, to intact molecule analyses, protein complexes and more recently epitope and paratope identification. MS toolkits could be incredibly diverse and with ever evolving instrumentation, increasingly novel MS-based techniques are becoming indispensable tools in the biopharmaceutical industry. Here we discuss application of Ion Mobility MS (IMMS) in an industrial setting, and what the current applications and outlook are for making IMMS more mainstream.
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Affiliation(s)
- Kirsty Skeene
- Biopharm Process Research, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
| | - Kshitij Khatri
- Structure and Function Characterization, CMC-Analytical, GlaxoSmithKline, Collegeville, PA 19406, USA.
| | - Zoja Soloviev
- Protein, Cellular and Structural Sciences, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
| | - Cris Lapthorn
- Structure and Function Characterization, CMC-Analytical, GlaxoSmithKline, Stevenage SG1 2NY, UK.
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23
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Zegeye MM, Andersson JSO, Wennberg P, Repsilber D, Sirsjö A, Ljungberg LU. IL-6 as a Mediator of the Association Between Traditional Risk Factors and Future Myocardial Infarction: A Nested Case-Control Study. Arterioscler Thromb Vasc Biol 2021; 41:1570-1579. [PMID: 33657883 DOI: 10.1161/atvbaha.120.315793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Mulugeta M Zegeye
- Cardiovascular Research Centre, School of Medical Sciences, Örebro University, Sweden (M.M.Z., D.R., A.S., L.U.L.)
| | - Jonas S O Andersson
- Skellefteå Research Unit, Department of Public Health and Clinical Medicine (J.S.O.A.), Umeå University, Sweden
| | - Patrik Wennberg
- Department of Public Health and Clinical Medicine, Family Medicine (P.W.), Umeå University, Sweden
| | - Dirk Repsilber
- Cardiovascular Research Centre, School of Medical Sciences, Örebro University, Sweden (M.M.Z., D.R., A.S., L.U.L.)
| | - Allan Sirsjö
- Cardiovascular Research Centre, School of Medical Sciences, Örebro University, Sweden (M.M.Z., D.R., A.S., L.U.L.)
| | - Liza U Ljungberg
- Cardiovascular Research Centre, School of Medical Sciences, Örebro University, Sweden (M.M.Z., D.R., A.S., L.U.L.)
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24
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Sun H, Ma L, Wang L, Xiao P, Li H, Zhou M, Song D. Research advances in hydrogen-deuterium exchange mass spectrometry for protein epitope mapping. Anal Bioanal Chem 2021; 413:2345-2359. [PMID: 33404742 DOI: 10.1007/s00216-020-03091-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 12/01/2022]
Abstract
With the development of biomedical technology, epitope mapping of proteins has become critical for developing and evaluating new protein drugs. The application of hydrogen-deuterium exchange for protein epitope mapping holds great potential. Although several reviews addressed the hydrogen-deuterium exchange, to date, only a few systematic reviews have focused on epitope mapping using this technology. Here, we introduce the basic principles, development history, and review research progress in hydrogen-deuterium exchange epitope mapping technology and discuss its advantages. We summarize the main hurdles in applying hydrogen-deuterium exchange epitope mapping technology, combined with relevant examples to provide specific solutions. We describe the epitope mapping of virus assemblies, disease-associated proteins, and polyclonal antibodies as examples of pattern introduction. Finally, we discuss the outlook of hydrogen-deuterium exchange epitope mapping technology. This review will help researchers studying protein epitopes to gain a more comprehensive understanding of this technology.
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Affiliation(s)
- Haofeng Sun
- National Institute of Metrology, Beijing, 100029, China
- College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lingyun Ma
- National Institute of Metrology, Beijing, 100029, China
| | - Leyu Wang
- College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Peng Xiao
- National Institute of Metrology, Beijing, 100029, China
| | - Hongmei Li
- National Institute of Metrology, Beijing, 100029, China
| | - Min Zhou
- School of Chemical and Engineering, Nanjing University of Science and Technology, Jiangsu, 210094, China.
| | - Dewei Song
- National Institute of Metrology, Beijing, 100029, China.
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25
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Metcalfe RD, Putoczki TL, Griffin MDW. Structural Understanding of Interleukin 6 Family Cytokine Signaling and Targeted Therapies: Focus on Interleukin 11. Front Immunol 2020; 11:1424. [PMID: 32765502 PMCID: PMC7378365 DOI: 10.3389/fimmu.2020.01424] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/02/2020] [Indexed: 12/12/2022] Open
Abstract
Cytokines are small signaling proteins that have central roles in inflammation and cell survival. In the half-century since the discovery of the first cytokines, the interferons, over fifty cytokines have been identified. Amongst these is interleukin (IL)-6, the first and prototypical member of the IL-6 family of cytokines, nearly all of which utilize the common signaling receptor, gp130. In the last decade, there have been numerous advances in our understanding of the structural mechanisms of IL-6 family signaling, particularly for IL-6 itself. However, our understanding of the detailed structural mechanisms underlying signaling by most IL-6 family members remains limited. With the emergence of new roles for IL-6 family cytokines in disease and, in particular, roles of IL-11 in cardiovascular disease, lung disease, and cancer, there is an emerging need to develop therapeutics that can progress to clinical use. Here we outline our current knowledge of the structural mechanism of signaling by the IL-6 family of cytokines. We discuss how this knowledge allows us to understand the mechanism of action of currently available inhibitors targeting IL-6 family cytokine signaling, and most importantly how it allows for improved opportunities to pharmacologically disrupt cytokine signaling. We focus specifically on the need to develop and understand inhibitors that disrupt IL-11 signaling.
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Affiliation(s)
- Riley D Metcalfe
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Technology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Tracy L Putoczki
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Technology Institute, The University of Melbourne, Parkville, VIC, Australia
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26
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Spangler JB, Moraga I, Jude KM, Savvides CS, Garcia KC. A strategy for the selection of monovalent antibodies that span protein dimer interfaces. J Biol Chem 2019; 294:13876-13886. [PMID: 31387945 PMCID: PMC6755802 DOI: 10.1074/jbc.ra119.009213] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/15/2019] [Indexed: 11/06/2022] Open
Abstract
Ligand-induced dimerization is the predominant mechanism through which secreted proteins activate cell surface receptors to transmit essential biological signals. Cytokines are a large class of soluble proteins that dimerize transmembrane receptors into precise signaling topologies, but there is a need for alternative, engineerable ligand scaffolds that specifically recognize and stabilize these protein interactions. Recombinant antibodies can potentially serve as robust and versatile platforms for cytokine complex stabilization, and their specificity allows for tunable modulation of dimerization equilibrium. Here, we devised an evolutionary strategy to isolate monovalent antibody fragments that bridge together two different receptor subunits in a cytokine-receptor complex, precisely as the receptors are disposed in their natural signaling orientations. To do this, we screened a naive antibody library against a stabilized ligand-receptor ternary complex that acted as a "molecular cast" of the natural receptor dimer conformation. Our selections elicited "stapler" single-chain variable fragments (scFvs) of antibodies that specifically engage the interleukin-4 receptor heterodimer. The 3.1 Å resolution crystal structure of one such stapler revealed that, as intended, this scFv recognizes a composite epitope between the two receptors as they are positioned in the complex. Extending our approach, we evolved a stapler scFv that specifically binds to and stabilizes the interface between the interleukin-2 cytokine and one of its receptor subunits, leading to a 15-fold enhancement in interaction affinity. This demonstration that scFvs can be selected to recognize epitopes that span protein interfaces presents new opportunities to engineer structurally defined antibodies for a broad range of research and therapeutic applications.
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Affiliation(s)
- Jamie B Spangler
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305 .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218
| | - Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Christina S Savvides
- Department of Biology, Stanford University School of Medicine, Stanford, California 94305
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305 .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
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27
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Masson GR, Burke JE, Ahn NG, Anand GS, Borchers C, Brier S, Bou-Assaf GM, Engen JR, Englander SW, Faber J, Garlish R, Griffin PR, Gross ML, Guttman M, Hamuro Y, Heck AJR, Houde D, Iacob RE, Jørgensen TJD, Kaltashov IA, Klinman JP, Konermann L, Man P, Mayne L, Pascal BD, Reichmann D, Skehel M, Snijder J, Strutzenberg TS, Underbakke ES, Wagner C, Wales TE, Walters BT, Weis DD, Wilson DJ, Wintrode PL, Zhang Z, Zheng J, Schriemer DC, Rand KD. Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods 2019; 16:595-602. [PMID: 31249422 PMCID: PMC6614034 DOI: 10.1038/s41592-019-0459-y] [Citation(s) in RCA: 382] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful biophysical technique being increasingly applied to a wide variety of problems. As the HDX-MS community continues to grow, adoption of best practices in data collection, analysis, presentation and interpretation will greatly enhance the accessibility of this technique to nonspecialists. Here we provide recommendations arising from community discussions emerging out of the first International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX; 2017). It is meant to represent both a consensus viewpoint and an opportunity to stimulate further additions and refinements as the field advances.
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Affiliation(s)
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - Natalie G Ahn
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Ganesh S Anand
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Christoph Borchers
- Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Sébastien Brier
- Institut Pasteur, Chemistry and Structural Biology Department, Paris, France
| | | | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - S Walter Englander
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Patrick R Griffin
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Yoshitomo Hamuro
- Johnson & Johnson Pharmaeutical Research and Development, Jersey City, NJ, USA
| | - Albert J R Heck
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | | | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej, Odense, Denmark
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, Canada
| | - Petr Man
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Leland Mayne
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Dana Reichmann
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Joost Snijder
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Timothy S Strutzenberg
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | | | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Benjamin T Walters
- Department of Early Stage Pharmaceutical Development, Genentech, Inc., South San Francisco, CA, USA
| | - David D Weis
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, ON, Canada
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | | | - Jie Zheng
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB, Canada.
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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28
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Lamertz L, Rummel F, Polz R, Baran P, Hansen S, Waetzig GH, Moll JM, Floss DM, Scheller J. Soluble gp130 prevents interleukin-6 and interleukin-11 cluster signaling but not intracellular autocrine responses. Sci Signal 2018; 11:11/550/eaar7388. [DOI: 10.1126/scisignal.aar7388] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Interleukin-6 (IL-6) is a proinflammatory cytokine of the IL-6 family, members of which signal through a complex of a cytokine-specific receptor and the signal-transducing subunit gp130. The interaction of IL-6 with the membrane-bound IL-6 receptor (IL-6R) and gp130 stimulates “classic signaling,” whereas the binding of IL-6 and a soluble version of the IL-6R to gp130 stimulates “trans-signaling.” Alternatively, “cluster signaling” occurs when membrane-bound IL-6:IL-6R complexes on transmitter cells activate gp130 receptors on neighboring receiver cells. The soluble form of gp130 (sgp130) is a selective trans-signaling inhibitor, but it does not affect classic signaling. We demonstrated that the interaction of soluble gp130 with natural and synthetic membrane-bound IL-6:IL-6R complexes inhibited IL-6 cluster signaling. Similarly, IL-11 cluster signaling through the IL-11R to gp130 was also inhibited by soluble gp130. However, autocrine classic and trans-signaling was not inhibited by extracellular inhibitors such as sgp130 or gp130 antibodies. Together, our results suggest that autocrine IL-6 signaling may occur intracellularly.
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29
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Zhang Q, Yang J, Bautista J, Badithe A, Olson W, Liu Y. Epitope Mapping by HDX-MS Elucidates the Surface Coverage of Antigens Associated with High Blocking Efficiency of Antibodies to Birch Pollen Allergen. Anal Chem 2018; 90:11315-11323. [DOI: 10.1021/acs.analchem.8b01864] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Qian Zhang
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, New York 10591, United States
| | - Janice Yang
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, New York 10591, United States
| | - Joannie Bautista
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, New York 10591, United States
| | - Ashok Badithe
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, New York 10591, United States
| | - William Olson
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, New York 10591, United States
| | - Yashu Liu
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, New York 10591, United States
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30
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Baran P, Hansen S, Waetzig GH, Akbarzadeh M, Lamertz L, Huber HJ, Ahmadian MR, Moll JM, Scheller J. The balance of interleukin (IL)-6, IL-6·soluble IL-6 receptor (sIL-6R), and IL-6·sIL-6R·sgp130 complexes allows simultaneous classic and trans-signaling. J Biol Chem 2018; 293:6762-6775. [PMID: 29559558 DOI: 10.1074/jbc.ra117.001163] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/12/2018] [Indexed: 01/24/2023] Open
Abstract
Interleukin (IL-)6 is the major pro-inflammatory cytokine within the IL-6 family. IL-6 signals via glycoprotein 130 (gp130) and the membrane-bound or soluble IL-6 receptor (IL-6R), referred to as classic or trans-signaling, respectively. Whereas inflammation triggers IL-6 expression, eventually rising to nanogram/ml serum levels, soluble IL-6R (sIL-6R) and soluble gp130 (sgp130) are constitutively present in the upper nanogram/ml range. Calculations based on intermolecular affinities have suggested that systemic IL-6 is immediately trapped in IL-6·sIL-6R and IL-6·sIL-6R·sgp130 complexes, indicating that sIL-6R and sgp130 constitute a buffer system that increases the serum half-life of IL-6 or restricts systemic IL-6 signaling. However, this scenario has not been experimentally validated. Here, we quantified IL-6·sIL-6R and IL-6·sIL-6R·sgp130 complexes over a wide concentration range. The amounts of IL-6 used in this study reflect concentrations found during active inflammatory events. Our results indicated that most IL-6 is free and not complexed with sIL-6R or sgp130, indicating that the level of endogenous sgp130 in the bloodstream is not sufficient to block IL-6 trans-signaling via sIL-6R. Importantly, addition of the single-domain antibody VHH6, which specifically stabilizes IL-6·sIL-6R complexes but did not bind to IL-6 or sIL-6R alone, drove free IL-6 into IL-6·sIL-6R complexes and boosted trans-signaling but not classic signaling, demonstrating that endogenous sIL-6R has at least the potential to form complexes with IL-6. Our findings indicate that even though high concentrations of sIL-6R and sgp130 are present in human serum, the relative ratio of free IL-6 to IL-6·sIL-6R allows for simultaneous classic and trans-signaling.
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Affiliation(s)
- Paul Baran
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Selina Hansen
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | | | - Mohammad Akbarzadeh
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Larissa Lamertz
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Heinrich J Huber
- the Institute for Automation Engineering, Otto-von-Guericke University, Magdeburg 39106, Germany
| | - M Reza Ahmadian
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Jens M Moll
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Jürgen Scheller
- From the Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany,
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Lago S, Nadai M, Rossetto M, Richter SN. Surface Plasmon Resonance kinetic analysis of the interaction between G-quadruplex nucleic acids and an anti-G-quadruplex monoclonal antibody. Biochim Biophys Acta Gen Subj 2018. [PMID: 29524541 PMCID: PMC5988565 DOI: 10.1016/j.bbagen.2018.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND G-quadruplexes (G4s) are nucleic acids secondary structures formed in guanine-rich sequences. Anti-G4 antibodies represent a tool for the direct investigation of G4s in cells. Surface Plasmon Resonance (SPR) is a highly sensitive technology, suitable for assessing the affinity between biomolecules. We here aimed at improving the orientation of an anti-G4 antibody on the SPR sensor chip to optimize detection of binding antigens. METHODS SPR was employed to characterize the anti-G4 antibody interaction with G4 and non-G4 oligonucleotides. Dextran-functionalized sensor chips were used both in covalent coupling and capturing procedures. RESULTS The use of two leading molecule for orienting the antibody of interest allowed to improve its activity from completely non-functional to 65% active. The specificity of the anti-G4 antobody for G4 structures could thus be assessed with high sensitivity and reliability. CONCLUSIONS Optimization of the immobilization protocol for SPR biosensing, allowed us to determine the anti-G4 antibody affinity and specificity for G4 antigens with higher sensitivity with respect to other in vitro assays such as ELISA. Anti-G4 antibody specificity is a fundamental assumption for the future utilization of this kind of antibodies for monitoring G4s directly in cells. GENERAL SIGNIFICANCE The heterogeneous orientation of amine-coupling immobilized ligands is a general problem that often leads to partial or complete inactivation of the molecules. Here we describe a new strategy for improving ligand orientation: driving it from two sides. This principle can be virtually applied to every molecule that loses its activity or is poorly immobilized after standard coupling to the SPR chip surface.
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Affiliation(s)
- Sara Lago
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Monica Rossetto
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via A. Gabelli 63, 35121 Padua, Italy.
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Masson GR, Jenkins ML, Burke JE. An overview of hydrogen deuterium exchange mass spectrometry (HDX-MS) in drug discovery. Expert Opin Drug Discov 2017; 12:981-994. [PMID: 28770632 DOI: 10.1080/17460441.2017.1363734] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful methodology to study protein dynamics, protein folding, protein-protein interactions, and protein small molecule interactions. The development of novel methodologies and technical advancements in mass spectrometers has greatly expanded the accessibility and acceptance of this technique within both academia and industry. Areas covered: This review examines the theoretical basis of how amide exchange occurs, how different mass spectrometer approaches can be used for HDX-MS experiments, as well as the use of HDX-MS in drug development, specifically focusing on how HDX-MS is used to characterize bio-therapeutics, and its use in examining protein-protein and protein small molecule interactions. Expert opinion: HDX-MS has been widely accepted within the pharmaceutical industry for the characterization of bio-therapeutics as well as in the mapping of antibody drug epitopes. However, there is room for this technique to be more widely used in the drug discovery process. This is particularly true in the use of HDX-MS as a complement to other high-resolution structural approaches, as well as in the development of small molecule therapeutics that can target both active-site and allosteric binding sites.
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Affiliation(s)
- Glenn R Masson
- a Protein and Nucleic Acid Chemistry Division , MRC Laboratory of Molecular Biology , Cambridge , UK
| | - Meredith L Jenkins
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , Canada
| | - John E Burke
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , Canada
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