1
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Frye C, Cunningham CL, Mihailescu MR. Characterization of the SARS-CoV-2 Genome 3'-Untranslated Region Interactions with Host MicroRNAs. ACS OMEGA 2024; 9:36148-36164. [PMID: 39220490 PMCID: PMC11360049 DOI: 10.1021/acsomega.4c01050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 07/23/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
The 2019 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has marked the spread of a novel human coronavirus. SARS-CoV-2 has exhibited increased disease severity and immune evasion across its variants, and the molecular mechanisms behind these phenomena remain largely unknown. Conserved elements of the viral genome, such as secondary structures within the 3'-untranslated region (UTR), could prove crucial in furthering our understanding of the host-virus interface. Analysis of the SARS-CoV-2 viral genome 3'-UTR revealed the potential for host microRNA (miR) binding sites, allowing for sequence-specific interactions. In this study, we demonstrate that the SARS-CoV-2 genome 3'-UTR binds the host cellular miRs miR-34a-5p, miR-34b-5p, and miR-760-3p in vitro. Native gel electrophoresis and steady-state fluorescence spectroscopy were utilized to biophysically characterize the binding of these miRs to their predicted sites within the SARS-CoV-2 genome 3'-UTR. Additionally, we investigated 2'-fluoro-d-arabinonucleic acid (FANA) analogs as competitive binding inhibitors for these interactions. These miRs modulate the translation of granulin (GRN), interleukin-6 (IL-6), and the IL-6 receptor (IL-6R), all of which are key modulators and activators of JAK/STAT3 signaling and are implicated in regulation of the immune response. Thus, we propose that hijacking of these miRs by SARS-CoV-2 could identify a mechanism of host immune modulation by the virus. The mechanisms detailed in this study have the potential to drive the development of antiviral treatments for SARS-CoV-2, through direct targeting of the virus-host interface.
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Affiliation(s)
- Caleb
J. Frye
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Caylee L. Cunningham
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Mihaela Rita Mihailescu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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2
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Chen H, Lye MF, Gorgulla C, Ficarro SB, Cuny GD, Scott DA, Wu F, Rothlauf PW, Wang X, Fernandez R, Pesola JM, Draga S, Marto JA, Hogle JM, Arthanari H, Coen DM. A small molecule exerts selective antiviral activity by targeting the human cytomegalovirus nuclear egress complex. PLoS Pathog 2023; 19:e1011781. [PMID: 37976321 PMCID: PMC10691697 DOI: 10.1371/journal.ppat.1011781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 12/01/2023] [Accepted: 10/28/2023] [Indexed: 11/19/2023] Open
Abstract
Human cytomegalovirus (HCMV) is an important pathogen for which new antiviral drugs are needed. HCMV, like other herpesviruses, encodes a nuclear egress complex (NEC) composed of two subunits, UL50 and UL53, whose interaction is crucial for viral replication. To explore whether small molecules can exert selective antiviral activity by inhibiting NEC subunit interactions, we established a homogeneous time-resolved fluorescence (HTRF) assay of these interactions and used it to screen >200,000 compound-containing wells. Two compounds, designated GK1 and GK2, which selectively inhibited this interaction in the HTRF assay with GK1 also active in a co-immunoprecipitation assay, exhibited more potent anti-HCMV activity than cytotoxicity or activity against another herpesvirus. At doses that substantially reduced HCMV plaque formation, GK1 and GK2 had little or no effect on the expression of viral proteins and reduced the co-localization of UL53 with UL50 at the nuclear rim in a subset of cells. GK1 and GK2 contain an acrylamide moiety predicted to covalently interact with cysteines, and an analog without this potential lacked activity. Mass spectrometric analysis showed binding of GK2 to multiple cysteines on UL50 and UL53. Nevertheless, substitution of cysteine 214 of UL53 with serine (C214S) ablated detectable inhibitory activity of GK1 and GK2 in vitro, and the C214S substitution engineered into HCMV conferred resistance to GK1, the more potent of the two inhibitors. Thus, GK1 exerts selective antiviral activity by targeting the NEC. Docking studies suggest that the acrylamide tethers one end of GK1 or GK2 to C214 within a pocket of UL53, permitting the other end of the molecule to sterically hinder UL50 to prevent NEC formation. Our results prove the concept that targeting the NEC with small molecules can selectively block HCMV replication. Such compounds could serve as a foundation for development of anti-HCMV drugs and as chemical tools for studying HCMV.
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Affiliation(s)
- Han Chen
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ming F. Lye
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Structural Biology, St. Jude’s Children’s Research Hospital, Memphis Tennessee United States of America
| | - Scott B. Ficarro
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gregory D. Cuny
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston College of Pharmacy, Houston, Texas, United States of America
| | - David A. Scott
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Medicinal Chemistry Core, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Fan Wu
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paul W. Rothlauf
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xiaoou Wang
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rosio Fernandez
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jean M. Pesola
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sorin Draga
- Virtual Discovery, Inc. Chestnut Hill, Massachusetts United States of America
- Non-Governmental Research Organization Biologic, Bucharest Romania
| | - Jarrod A. Marto
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - James M. Hogle
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Donald M. Coen
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
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3
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Almodóvar-Rivera CM, Zhang Z, Li J, Xie H, Zhao Y, Guo L, Mannhardt MG, Tang W. A Modular Chemistry Platform for the Development of a Cereblon E3 Ligase-Based Partial PROTAC Library. Chembiochem 2023; 24:e202300482. [PMID: 37418320 PMCID: PMC10591699 DOI: 10.1002/cbic.202300482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) are a promising therapeutic strategy to selectively promote the degradation of protein targets by exploiting the ubiquitin-proteasome system. Among the limited number of E3 ligase ligands discovered for the PROTAC technology, ligands of cereblon (CRBN) E3 ligase, such as pomalidomide, thalidomide, or lenalidomide, are the most frequently used for the development of PROTACs. Our group previously reported that a phenyl group could be tolerated on the C4-position of lenalidomide as the ligand of CRBN to develop PROTACs. Herein, we report a modular chemistry platform for the efficient attachment of various ortho-, meta-, and para-substituted phenyls to the C4-position of the lenalidomide via Suzuki cross-coupling reaction, which allows the systematic investigation of the linker effect for the development of PROTACs against any target. We examined the substrate scope by preparing twelve lenalidomide-derived CRBN E3 ligase ligands with different linkers.
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Affiliation(s)
- Chelsi M Almodóvar-Rivera
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Zhen Zhang
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Jingyao Li
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Haibo Xie
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Yu Zhao
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Le Guo
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Marissa G Mannhardt
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Weiping Tang
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
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4
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Hunt AC, Vögeli B, Hassan AO, Guerrero L, Kightlinger W, Yoesep DJ, Krüger A, DeWinter M, Diamond MS, Karim AS, Jewett MC. A rapid cell-free expression and screening platform for antibody discovery. Nat Commun 2023; 14:3897. [PMID: 37400446 DOI: 10.1038/s41467-023-38965-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/23/2023] [Indexed: 07/05/2023] Open
Abstract
Antibody discovery is bottlenecked by the individual expression and evaluation of antigen-specific hits. Here, we address this bottleneck by developing a workflow combining cell-free DNA template generation, cell-free protein synthesis, and binding measurements of antibody fragments in a process that takes hours rather than weeks. We apply this workflow to evaluate 135 previously published antibodies targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including all 8 antibodies previously granted emergency use authorization for coronavirus disease 2019 (COVID-19), and demonstrate identification of the most potent antibodies. We also evaluate 119 anti-SARS-CoV-2 antibodies from a mouse immunized with the SARS-CoV-2 spike protein and identify neutralizing antibody candidates, including the antibody SC2-3, which binds the SARS-CoV-2 spike protein of all tested variants of concern. We expect that our cell-free workflow will accelerate the discovery and characterization of antibodies for future pandemics and for research, diagnostic, and therapeutic applications more broadly.
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Affiliation(s)
- Andrew C Hunt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Bastian Vögeli
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Ahmed O Hassan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Laura Guerrero
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Weston Kightlinger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Danielle J Yoesep
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Madison DeWinter
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA.
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
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5
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Malla A, Bose A, Sur R, Gupta S. Cellular, Biophysical and in Silico Binding Study of β-Estradiol-6-one 6- (O-carboxy methyl Oxime) with Tubulin in Search of Antimitotic Derivative of 2-Methoxy Estradiol. Cell Biochem Biophys 2023:10.1007/s12013-023-01142-3. [PMID: 37233844 DOI: 10.1007/s12013-023-01142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 05/07/2023] [Indexed: 05/27/2023]
Abstract
The tubulin-microtubule system is a major target for a variety of small molecules which can interfere in cell cycle progression. Therefore, it serves as a prospective to control the incessant division of cancer cells. To identify novel inhibitors of the tubulin-microtubule system, a group of estrogen derivatives has been tested with tubulin as a target since literature surveys portray coveted behaviour from the same. Out of them, β-Estradiol-6-one 6- (O-carboxy methyl Oxime) abbreviated as Oxime, disrupts the cytoskeleton network and induces apoptosis with nuclei fragmentation. It has been revealed from the work that Oxime targets the colchicine binding site and binds tubulin in an entropy-driven manner. This suggests that structural variation might play a key role in modulating the anti-mitotic role of estrogen derivatives. Our work reveals that Oxime might serve as a lead molecule to nurture anti-cancer research, having the potential for recovery of the vast cancer population.
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Affiliation(s)
- Avirup Malla
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
- Department of Biophysics Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, West Bengal, India
| | - Adrija Bose
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Runa Sur
- Department of Biophysics Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, West Bengal, India
| | - Suvroma Gupta
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India.
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6
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Frye CJ, Cunningham CL, Mihailescu MR. Host microRNA interactions with the SARS-CoV-2 viral genome 3'-untranslated region. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541401. [PMID: 37292986 PMCID: PMC10245713 DOI: 10.1101/2023.05.18.541401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The 2019 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has marked the spread of a novel human coronavirus. While the viral life cycle is well understood, most of the interactions at the virus-host interface remain elusive. Furthermore, the molecular mechanisms behind disease severity and immune evasion are still largely unknown. Conserved elements of the viral genome such as secondary structures within the 5'- and 3'-untranslated regions (UTRs) serve as attractive targets of interest and could prove crucial in furthering our understanding of virus-host interactions. It has been proposed that microRNA (miR) interactions with viral components could be used by both the virus and host for their own benefit. Analysis of the SARS-CoV-2 viral genome 3'-UTR has revealed the potential for host cellular miR binding sites, providing sites for specific interactions with the virus. In this study, we demonstrate that the SARS-CoV-2 genome 3'-UTR binds the host cellular miRNAs miR-760-3p, miR-34a-5p, and miR-34b-5p, which have been shown to influence translation of interleukin-6 (IL-6), the IL-6 receptor (IL-6R), as well as progranulin (PGRN), respectively, proteins that have roles in the host immune response and inflammatory pathways. Furthermore, recent work suggests the potential of miR-34a-5p and miR-34b-5p to target and inhibit translation of viral proteins. Native gel electrophoresis and steady-state fluorescence spectroscopy were utilized to characterize the binding of these miRs to their predicted sites within the SARS-CoV-2 genome 3'-UTR. Additionally, we investigated 2'-fluoro-D-arabinonucleic acid (FANA) analogs of these miRNAs as competitive binding inhibitors for these miR binding interactions. The mechanisms detailed in this study have the potential to drive the development of antiviral treatments for SARS-CoV-2 infection, and provide a potential molecular basis for cytokine release syndrome and immune evasion which could implicate the host-virus interface.
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Affiliation(s)
- Caleb J Frye
- Department of Chemistry & Biochemistry, Duquesne University, Pittsburgh, PA 15282, USA
| | - Caylee L Cunningham
- Department of Chemistry & Biochemistry, Duquesne University, Pittsburgh, PA 15282, USA
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7
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Wojciechowski MN, Schreiber S, Jose J. A Novel Flow Cytometry-Based Assay for the Identification of HCN4 CNBD Ligands. Pharmaceuticals (Basel) 2023; 16:ph16050710. [PMID: 37242492 DOI: 10.3390/ph16050710] [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: 03/29/2023] [Revised: 04/25/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Hyperpolarization-activated and cyclic nucleotide-gated (HCN) channels are promising therapeutic targets because of their association with the genesis of several diseases. The identification of selective compounds that alter cAMP-induced ion channel modulation by binding to the cyclic nucleotide-binding domain (CNBD) will facilitate HCN channel-specific drug development. In this study, a fast and protein purification-free ligand-binding approach with a surface-displayed HCN4 C-Linker-CNBD on E. coli is presented. 8-Fluo-cAMP ligand binding was monitored by single-cell analysis via flow cytometry, and a Kd-value of 173 ± 46 nM was determined. The Kd value was confirmed by ligand depletion analysis and equilibrium state measurements. Applying increasing concentrations of cAMP led to a concentration-dependent decrease in fluorescence intensity, indicating a displacement of 8-Fluo-cAMP. A Ki-value of 8.5 ± 2 µM was determined. The linear relationship of IC50 values obtained for cAMP as a function of ligand concentration confirmed the competitive binding mode: IC50: 13 ± 2 µM/16 ± 3 µM/23 ± 1 µM/27 ± 1 µM for 50 nM/150 nM/250 nM/500 nM 8-Fluo-cAMP. A similar competitive mode of binding was confirmed for 7-CH-cAMP, and an IC50 value of 230 ± 41 nM and a Ki of 159 ± 29 nM were determined. Two established drugs were tested in the assay. Ivabradine, an approved HCN channel pore blocker and gabapentin, is known to bind to HCN4 channels in preference to other isoforms with an unknown mode of action. As expected, ivabradine had no impact on ligand binding. In addition, gabapentin had no influence on 8-Fluo-cAMP's binding to HCN4-CNBD. This is the first indication that gabapentin is not interacting with this part of the HCN4 channel. The ligand-binding assay as described can be used to determine binding constants for ligands such as cAMP and derivatives. It could also be applied for the identification of new ligands binding to the HCN4-CNBD.
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Affiliation(s)
- Magdalena N Wojciechowski
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, Pharmacampus, 48149 Münster, Germany
| | - Sebastian Schreiber
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, Pharmacampus, 48149 Münster, Germany
| | - Joachim Jose
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, Pharmacampus, 48149 Münster, Germany
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8
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N-sulfonyl peptide-hybrids as a new class of dengue virus protease inhibitors. Eur J Med Chem 2023; 251:115227. [PMID: 36893626 DOI: 10.1016/j.ejmech.2023.115227] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/07/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
Dengue virus (DENV) from the Flaviviridae family causes an epidemic disease that seriously threatens human life. The viral serine protease NS2B-NS3 is a promising target for drug development against DENV and other flaviviruses. We here report the design, synthesis, and in-vitro characterization of potent peptidic inhibitors of DENV protease with a sulfonyl moiety as N-terminal cap, thereby creating sulfonamide-peptide hybrids. The in-vitro target affinities of some synthesized compounds were in the nanomolar range, with the most promising derivative reaching a Ki value of 78 nM against DENV-2 protease. The synthesized compounds did not have relevant off-target activity nor cytotoxicity. The metabolic stability of compounds against rat liver microsomes and pancreatic enzymes was remarkable. In general, the integration of sulfonamide moieties at the N-terminus of peptidic inhibitors proved to be a promising and attractive strategy for further drug development against DENV infections.
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9
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Kanasuwan A, Deuther-Conrad W, Chongruchiroj S, Sarasamkan J, Chotipanich C, Vajragupta O, Arunrungvichian K. Selective α 3β 4 Nicotinic Acetylcholine Receptor Ligand as a Potential Tracer for Drug Addiction. Int J Mol Sci 2023; 24:ijms24043614. [PMID: 36835028 PMCID: PMC9959096 DOI: 10.3390/ijms24043614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
α3β4 Nicotinic acetylcholine receptor (nAChR) has been recognized as an emerging biomarker for the early detection of drug addiction. Herein, α3β4 nAChR ligands were designed and synthesized to improve the binding affinity and selectivity of two lead compounds, (S)-QND8 and (S)-T2, for the development of an α3β4 nAChR tracer. The structural modification was achieved by retaining the key features and expanding the molecular structure with a benzyloxy group to increase the lipophilicity for blood-brain barrier penetration and to extend the ligand-receptor interaction. The preserved key features are a fluorine atom for radiotracer development and a p-hydroxyl motif for ligand-receptor binding affinity. Four (R)- and (S)-quinuclidine-triazole (AK1-AK4) were synthesized and the binding affinity, together with selectivity to α3β4 nAChR subtype, were determined by competitive radioligand binding assay using [3H]epibatidine as a radioligand. Among all modified compounds, AK3 showed the highest binding affinity and selectivity to α3β4 nAChR with a Ki value of 3.18 nM, comparable to (S)-QND8 and (S)-T2 and 3069-fold higher affinity to α3β4 nAChR in comparison to α7 nAChR. The α3β4 nAChR selectivity of AK3 was considerably higher than those of (S)-QND8 (11.8-fold) and (S)-T2 (294-fold). AK3 was shown to be a promising α3β4 nAChR tracer for further development as a radiotracer for drug addiction.
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Affiliation(s)
- Apinan Kanasuwan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayutthaya Rd., Bangkok 10400, Thailand
- National Cyclotron and PET Centre, Chulabhorn Hospital, Chulabhorn Royal Academy, 906 Kamphaengphet 6 Rd., Bangkok 10210, Thailand
| | - Winnie Deuther-Conrad
- Department of Neuroradiopharmaceuticals, Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf, Permoserstraße 15, 04318 Leipzig, Germany
| | - Sumet Chongruchiroj
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayutthaya Rd., Bangkok 10400, Thailand
| | - Jiradanai Sarasamkan
- Department of Radiology, Faculty of Medicine, Khon Kaen University, 123 Mittraphap Rd., Khon Kaen 40002, Thailand
| | - Chanisa Chotipanich
- National Cyclotron and PET Centre, Chulabhorn Hospital, Chulabhorn Royal Academy, 906 Kamphaengphet 6 Rd., Bangkok 10210, Thailand
| | - Opa Vajragupta
- Molecular Probes for Imaging Research Network, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Phayathai Rd., Bangkok 10330, Thailand
| | - Kuntarat Arunrungvichian
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayutthaya Rd., Bangkok 10400, Thailand
- Correspondence:
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10
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Nieman AN, Dunn Hoffman KK, Dominguez ER, Wilkinson J, Vasta JD, Robers MB, Lam N. NanoBRET™ Live-Cell Kinase Selectivity Profiling Adapted for High-Throughput Screening. Methods Mol Biol 2023; 2706:97-124. [PMID: 37558944 DOI: 10.1007/978-1-0716-3397-7_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Kinases represent one of the most therapeutically tractable targets for drug discovery in the twenty-first century. However, confirming engagement and achieving intracellular kinase selectivity for small-molecule kinase inhibitors can represent noteworthy challenges. The NanoBRETTM platform enables broad-spectrum live-cell kinase selectivity profiling in most laboratory settings, without advanced instrumentation or expertise. However, the prototype workflow for this selectivity profiling is currently limited to manual liquid handling and 96-well plates. Herein, we describe a scalable workflow with automation and acoustic dispensing, thus dramatically improving the throughput. Such adaptations enable profiling of larger compound sets against 192 full-length protein kinases in live cells, with statistical robustness supporting quantitative analysis.
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Affiliation(s)
| | | | | | | | | | | | - Ngan Lam
- Promega Corporation, Madison, WI, USA.
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11
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Exploiting ELIOT for Scaffold-Repurposing Opportunities: TRIM33 a Possible Novel E3 Ligase to Expand the Toolbox for PROTAC Design. Int J Mol Sci 2022; 23:ijms232214218. [PMID: 36430693 PMCID: PMC9698485 DOI: 10.3390/ijms232214218] [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: 10/26/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
The field of targeted protein degradation, through the control of the ubiquitin-proteasome system (UPS), is progressing considerably; to exploit this new therapeutic modality, the proteolysis targeting chimera (PROTAC) technology was born. The opportunity to use PROTACs engaging of new E3 ligases that can hijack and control the UPS system could greatly extend the applicability of degrading molecules. To this end, here we show a potential application of the ELIOT (E3 LIgase pocketOme navigaTor) platform, previously published by this group, for a scaffold-repurposing strategy to identify new ligands for a novel E3 ligase, such as TRIM33. Starting from ELIOT, a case study of the cross-relationship using GRID Molecular Interaction Field (MIF) similarities between TRIM24 and TRIM33 binding sites was selected. Based on the assumption that similar pockets could bind similar ligands and considering that TRIM24 has 12 known co-crystalised ligands, we applied a scaffold-repurposing strategy for the identification of TRIM33 ligands exploiting the scaffold of TRIM24 ligands. We performed a deeper computational analysis to identify pocket similarities and differences, followed by docking and water analysis; selected ligands were synthesised and subsequently tested against TRIM33 via HTRF binding assay, and we obtained the first-ever X-ray crystallographic complexes of TRIM33α with three of the selected compounds.
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12
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Gündel D, Deuther-Conrad W, Ueberham L, Kaur S, Otikova E, Teodoro R, Toussaint M, Lai TH, Clauß O, Scheunemann M, Bormans G, Bachmann M, Kopka K, Brust P, Moldovan RP. Structure-Based Design, Optimization, and Development of [ 18F]LU13: A Novel Radioligand for Cannabinoid Receptor Type 2 Imaging in the Brain with PET. J Med Chem 2022; 65:9034-9049. [PMID: 35771668 DOI: 10.1021/acs.jmedchem.2c00256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The cannabinoid receptor type 2 (CB2R) is an attractive target for the diagnosis and therapy of neurodegenerative diseases and cancer. In this study, we aimed at the development of a novel 18F-labeled radioligand starting from the structure of the known naphthyrid-2-one CB2R ligands. Compound 28 (LU13) was identified with the highest binding affinity and selectivity versus CB1R (CB2RKi = 0.6 nM; CB1RKi/CB2RKi > 1000) and was selected for radiolabeling with fluorine-18 and biological characterization. The new radioligand [18F]LU13 showed high CB2R affinity in vitro as well as high metabolic stability in vivo. PET imaging with [18F]LU13 in a rat model of vector-based/-related hCB2R overexpression in the striatum revealed a high signal-to-background ratio. Thus, [18F]LU13 is a novel and highly promising PET radioligand for the imaging of upregulated CB2R expression under pathological conditions in the brain.
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Affiliation(s)
- Daniel Gündel
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany
| | - Winnie Deuther-Conrad
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany
| | - Lea Ueberham
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany
| | - Sarandeep Kaur
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany
| | - Elina Otikova
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany
| | - Rodrigo Teodoro
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany
| | - Magali Toussaint
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany
| | - Thu Hang Lai
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany.,Department of Research and Development, ROTOP Pharmaka GmbH, 01069 Dresden, Germany
| | - Oliver Clauß
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany
| | - Matthias Scheunemann
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany
| | - Guy Bormans
- Radiopharmaceutical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, BE-3000 Leuven, Belgium
| | - Michael Bachmann
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany
| | - Klaus Kopka
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany.,Faculty of Chemistry and Food Chemistry, School of Science, TU Dresden, 01069 Dresden, Germany
| | - Peter Brust
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany.,The Lübeck Institute of Experimental Dermatology, University Medical Center Schleswig-Holstein, 23562 Lübeck, Germany
| | - Rareş-Petru Moldovan
- Institute of Radiopharmaceutical Cancer Research, Department of Neuroradiopharmaceuticals, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Research Site Leipzig, 04318 Leipzig, Germany
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13
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Monteiro NRC, Simões CJV, Ávila HV, Abbasi M, Oliveira JL, Arrais JP. Explainable deep drug-target representations for binding affinity prediction. BMC Bioinformatics 2022; 23:237. [PMID: 35715734 PMCID: PMC9204982 DOI: 10.1186/s12859-022-04767-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background Several computational advances have been achieved in the drug discovery field, promoting the identification of novel drug–target interactions and new leads. However, most of these methodologies have been overlooking the importance of providing explanations to the decision-making process of deep learning architectures. In this research study, we explore the reliability of convolutional neural networks (CNNs) at identifying relevant regions for binding, specifically binding sites and motifs, and the significance of the deep representations extracted by providing explanations to the model’s decisions based on the identification of the input regions that contributed the most to the prediction. We make use of an end-to-end deep learning architecture to predict binding affinity, where CNNs are exploited in their capacity to automatically identify and extract discriminating deep representations from 1D sequential and structural data. Results The results demonstrate the effectiveness of the deep representations extracted from CNNs in the prediction of drug–target interactions. CNNs were found to identify and extract features from regions relevant for the interaction, where the weight associated with these spots was in the range of those with the highest positive influence given by the CNNs in the prediction. The end-to-end deep learning model achieved the highest performance both in the prediction of the binding affinity and on the ability to correctly distinguish the interaction strength rank order when compared to baseline approaches. Conclusions This research study validates the potential applicability of an end-to-end deep learning architecture in the context of drug discovery beyond the confined space of proteins and ligands with determined 3D structure. Furthermore, it shows the reliability of the deep representations extracted from the CNNs by providing explainability to the decision-making process. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04767-y.
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Affiliation(s)
- Nelson R C Monteiro
- Univ Coimbra, Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering, Coimbra, Portugal.
| | | | - Henrique V Ávila
- Univ Coimbra, Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering, Coimbra, Portugal
| | - Maryam Abbasi
- Univ Coimbra, Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering, Coimbra, Portugal
| | - José L Oliveira
- IEETA, Department of Electronics, Telecommunications and Informatics, University of Aveiro, Aveiro, Portugal
| | - Joel P Arrais
- Univ Coimbra, Centre for Informatics and Systems of the University of Coimbra, Department of Informatics Engineering, Coimbra, Portugal
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Conjugation of Aminoadamantane and γ-Carboline Pharmacophores Gives Rise to Unexpected Properties of Multifunctional Ligands. Molecules 2021; 26:molecules26185527. [PMID: 34576998 PMCID: PMC8471380 DOI: 10.3390/molecules26185527] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/01/2021] [Accepted: 09/09/2021] [Indexed: 11/21/2022] Open
Abstract
A new series of conjugates of aminoadamantane and γ-carboline, which are basic scaffolds of the known neuroactive agents, memantine and dimebon (Latrepirdine) was synthesized and characterized. Conjugates act simultaneously on several biological structures and processes involved in the pathogenesis of Alzheimer’s disease and some other neurodegenerative disorders. In particular, these compounds inhibit enzymes of the cholinesterase family, exhibiting higher inhibitory activity against butyrylcholinesterase (BChE), but having almost no effect on the activity of carboxylesterase (anti-target). The compounds serve as NMDA-subtype glutamate receptor ligands, show mitoprotective properties by preventing opening of the mitochondrial permeability transition (MPT) pore, and act as microtubule stabilizers, stimulating the polymerization of tubulin and microtubule-associated proteins. Structure–activity relationships were studied, with particular attention to the effect of the spacer on biological activity. The synthesized conjugates showed new properties compared to their prototypes (memantine and dimebon), including the ability to bind to the ifenprodil-binding site of the NMDA receptor and to occupy the peripheral anionic site of acetylcholinesterase (AChE), which indicates that these compounds can act as blockers of AChE-induced β-amyloid aggregation. These new attributes of the conjugates represent improvements to the pharmacological profiles of the separate components by conferring the potential to act as neuroprotectants and cognition enhancers with a multifunctional mode of action.
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15
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Tian F, Tong B, Sun L, Shi S, Zheng B, Wang Z, Dong X, Zheng P. N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. eLife 2021; 10:e69091. [PMID: 34414884 PMCID: PMC8455130 DOI: 10.7554/elife.69091] [Citation(s) in RCA: 209] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 08/19/2021] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 has been spreading around the world for the past year. Recently, several variants such as B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma), which share a key mutation N501Y on the receptor-binding domain (RBD), appear to be more infectious to humans. To understand the underlying mechanism, we used a cell surface-binding assay, a kinetics study, a single-molecule technique, and a computational method to investigate the interaction between these RBD (mutations) and ACE2. Remarkably, RBD with the N501Y mutation exhibited a considerably stronger interaction, with a faster association rate and a slower dissociation rate. Atomic force microscopy (AFM)-based single-molecule force microscopy (SMFS) consistently quantified the interaction strength of RBD with the mutation as having increased binding probability and requiring increased unbinding force. Molecular dynamics simulations of RBD-ACE2 complexes indicated that the N501Y mutation introduced additional π-π and π-cation interactions that could explain the changes observed by force microscopy. Taken together, these results suggest that the reinforced RBD-ACE2 interaction that results from the N501Y mutation in the RBD should play an essential role in the higher rate of transmission of SARS-CoV-2 variants, and that future mutations in the RBD of the virus should be under surveillance.
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Affiliation(s)
- Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing UniversityNanjingChina
| | - Bei Tong
- Institute of Botany, Jiangsu Province and Chinese Academy of SciencesNanjingChina
| | - Liang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing UniversityNanjingChina
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing UniversityNanjingChina
| | - Zibin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
| | - Xianchi Dong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjingChina
- Engineering Research Center of Protein and Peptide Medicine, Ministry of EducationNanjingChina
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing UniversityNanjingChina
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16
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Nath N, Godat B, Flemming R, Urh M. Deciphering the Interaction between Neonatal Fc Receptor and Antibodies Using a Homogeneous Bioluminescent Immunoassay. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:1211-1221. [PMID: 34312257 PMCID: PMC8358922 DOI: 10.4049/jimmunol.2100181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/22/2021] [Indexed: 11/19/2022]
Abstract
Long half-life of therapeutic Abs and Fc fusion proteins is crucial to their efficacy and is, in part, regulated by their interaction with neonatal Fc receptor (FcRn). However, the current methods (e.g., surface plasmon resonance and biolayer interferometry) for measurement of interaction between IgG and FcRn (IgG/FcRn) require either FcRn or IgG to be immobilized on the surface, which is known to introduce experimental artifacts and have led to conflicting data. To study IgG/FcRn interactions in solution, without a need for surface immobilization, we developed a novel (to our knowledge), solution-based homogeneous binding immunoassay based on NanoBiT luminescent protein complementation technology. We optimized the assay (NanoBiT FcRn assay) for human FcRn, mouse FcRn, rat FcRn, and cynomolgus FcRn and used them to determine the binding affinities of a panel of eight Abs. Assays could successfully capture the modulation in IgG/FcRn binding based on changes in Fc fragment of the Abs. We also looked at the individual contribution of Fc and F(ab)2 on the IgG/FcRn interaction and found that Fc is the main driver for the interaction at pH 6. Our work highlights the importance of using orthogonal methods to validate affinity data generated using biosensor platforms. Moreover, the simple add-and-read format of the NanoBiT FcRn assay is amenable for high-throughput screening during early Ab discovery phase.
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Affiliation(s)
- Nidhi Nath
- Research and Development Department, Promega Corp., Madison, WI
| | - Becky Godat
- Research and Development Department, Promega Corp., Madison, WI
| | - Rod Flemming
- Research and Development Department, Promega Corp., Madison, WI
| | - Marjeta Urh
- Research and Development Department, Promega Corp., Madison, WI
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17
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Kopra K, Sharina I, Martin E, Härmä H. Homogeneous single-label cGMP detection platform for the functional study of nitric oxide-sensitive (soluble) guanylyl cyclases and cGMP-specific phosphodiesterases. Sci Rep 2020; 10:17469. [PMID: 33060787 PMCID: PMC7562898 DOI: 10.1038/s41598-020-74611-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 09/07/2020] [Indexed: 11/09/2022] Open
Abstract
Cardiovascular diseases are the number one death worldwide. Nitric oxide (NO)-NO-sensitive (soluble) guanylyl cyclase (sGC)-cyclic guanosine monophosphate (cGMP) pathway regulates diverse set of important physiological functions, including maintenance of cardiovascular homeostasis. Resting and activated sGC enzyme converts guanosine triphosphate to an important second messenger cGMP. In addition to traditional NO generators, a number of sGC activators and stimulators are currently in clinical trials aiming to support or increase sGC activity in various pathological conditions. cGMP-specific phosphodiesterases (PDEs), which degrade cGMP to guanosine monophosphate, play key role in controlling the cGMP level and the strength or length of the cGMP-dependent cellular signaling. Thus, PDE inhibitors also have clear clinical applications. Here, we introduce a homogeneous quenching resonance energy transfer (QRET) for cGMP to monitor both sGC and PDE activities using high throughput screening adoptable method. We demonstrate that using cGMP-specific antibody, sGC or PDE activity and the effect of small molecules modulating their function can be studied with sub-picomole cGMP sensitivity. The results further indicate that the method is suitable for monitoring enzyme reactions also in complex biological cellular homogenates and mixture.
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Affiliation(s)
- Kari Kopra
- Department of Chemistry, Chemistry of Drug Development, University of Turku, Vatselankatu 2, 20500, Turku, Finland.
| | - Iraida Sharina
- Division of Cardiology, Department of Internal Medicine, University of Texas Medical School At Houston, 1941 East Road, Houston, TX, 77054, USA
| | - Emil Martin
- Division of Cardiology, Department of Internal Medicine, University of Texas Medical School At Houston, 1941 East Road, Houston, TX, 77054, USA
| | - Harri Härmä
- Department of Chemistry, Chemistry of Drug Development, University of Turku, Vatselankatu 2, 20500, Turku, Finland
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18
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Thevendran R, Navien TN, Meng X, Wen K, Lin Q, Sarah S, Tang TH, Citartan M. Mathematical approaches in estimating aptamer-target binding affinity. Anal Biochem 2020; 600:113742. [PMID: 32315616 DOI: 10.1016/j.ab.2020.113742] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/25/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
Abstract
The performance of aptamers as versatile tools in numerous analytical applications is critically dependent on their high target binding specificity and selectivity. However, only the technical or methodological aspects of measuring aptamer-target binding affinities are focused, ignoring the equally important mathematical components that play pivotal roles in affinity measurements. In this study, we aim to provide a comprehensive review regarding the utilization of different mathematical models and equations, along with a detailed description of the computational steps involved in mathematically deriving the binding affinity of aptamers against their specific target molecules. Mathematical models ranging from one-site binding to multiple aptameric binding site-based models are explained in detail. Models applied in several different approaches of affinity measurements such as thermodynamics and kinetic analysis, including cooperativity and competitive-assay based mathematical models have been elaborately discussed. Mathematical models incorporating factors that could potentially affect affinity measurements are also further scrutinized.
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Affiliation(s)
- Ramesh Thevendran
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Tholasi Nadhan Navien
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Xin Meng
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, United States
| | - Kechun Wen
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, United States
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027, United States
| | - Shigdar Sarah
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria, 3216, Australia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia; Department of Mechanical Engineering, Columbia University, New York, NY, 10027, United States.
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19
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Manoharan GB, Kopra K, Eskonen V, Härmä H, Abankwa D. High-throughput amenable fluorescence-assays to screen for calmodulin-inhibitors. Anal Biochem 2019; 572:25-32. [PMID: 30825429 DOI: 10.1016/j.ab.2019.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/21/2019] [Accepted: 02/17/2019] [Indexed: 12/12/2022]
Abstract
The KRAS gene is highly mutated in human cancers and the focus of current Ras drug development efforts. Recently the interface between the C-terminus of K-Ras and calmodulin (CaM) was proposed as a target site to block K-Ras driven cancer cell stemness. We therefore aimed at developing a high-throughput amenable screening assay to identify novel CaM-inhibitors as potential K-Ras stemness-signaling disruptors. A modulated time-resolved Förster resonance energy transfer (mTR-FRET)-assay was developed and benchmarked against an identically designed fluorescence anisotropy (FA)-assay. In both assays, two CaM-binding peptides were labeled with Eu(III)-chelate or fluorescein and used as single-label reporter probes that were displaced from CaM upon competitor binding. Thus, peptidic and small molecule competitors with nanomolar to micromolar affinities to CaM could be detected, including a peptide that was derived from the C-terminus of K-Ras. In order to detect CaM-residue specific covalent inhibitors, a cell lysate-based Förster resonance energy transfer (FRET)-assay was furthermore established. This assay enabled us to measure the slow, residue-specific, covalent inhibition by ophiobolin A in the presence of other endogenous proteins. In conclusion, we have developed a panel of fluorescence-assays that allows identification of conventional and covalent CaM-inhibitors as potential disruptors of K-Ras driven cancer cell stemness.
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Affiliation(s)
- Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery Group, Life Sciences Research Unit, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg; Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Kari Kopra
- Materials Chemistry and Chemical Analysis, University of Turku, 20500, Turku, Finland
| | - Ville Eskonen
- Materials Chemistry and Chemical Analysis, University of Turku, 20500, Turku, Finland
| | - Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, 20500, Turku, Finland
| | - Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Life Sciences Research Unit, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg; Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520, Turku, Finland.
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20
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Quantitative, Real-Time Measurements of Intracellular Target Engagement Using Energy Transfer. Methods Mol Biol 2019; 1888:45-71. [PMID: 30519940 DOI: 10.1007/978-1-4939-8891-4_3] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intracellular target affinity and residence time are fundamental aspects of pharmacological mechanism (Lu and Tonge, Curr Opin Chem Biol 14:467-474, 2010). Although various robust biochemical approaches exist to measure these binding characteristics, analysis of compound binding with isolated targets may not accurately reflect engagement in the milieu of living cells. To realize the influence of cellular context, methods are needed that are capable of quantifying affinity and residence time in the presence of the intracellular factors that may impact target engagement. Bioluminescence resonance energy transfer (BRET) offers a solution for intracellular target engagement when quantitative metrics or kinetic analyses are required.
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21
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Vasta JD, Corona CR, Wilkinson J, Zimprich CA, Hartnett JR, Ingold MR, Zimmerman K, Machleidt T, Kirkland TA, Huwiler KG, Ohana RF, Slater M, Otto P, Cong M, Wells CI, Berger BT, Hanke T, Glas C, Ding K, Drewry DH, Huber KVM, Willson TM, Knapp S, Müller S, Meisenheimer PL, Fan F, Wood KV, Robers MB. Quantitative, Wide-Spectrum Kinase Profiling in Live Cells for Assessing the Effect of Cellular ATP on Target Engagement. Cell Chem Biol 2018; 25:206-214.e11. [PMID: 29174542 PMCID: PMC5814754 DOI: 10.1016/j.chembiol.2017.10.010] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/24/2017] [Accepted: 10/24/2017] [Indexed: 02/03/2023]
Abstract
For kinase inhibitors, intracellular target selectivity is fundamental to pharmacological mechanism. Although a number of acellular techniques have been developed to measure kinase binding or enzymatic inhibition, such approaches can fail to accurately predict engagement in cells. Here we report the application of an energy transfer technique that enabled the first broad-spectrum, equilibrium-based approach to quantitatively profile target occupancy and compound affinity in live cells. Using this method, we performed a selectivity profiling for clinically relevant kinase inhibitors against 178 full-length kinases, and a mechanistic interrogation of the potency offsets observed between cellular and biochemical analysis. For the multikinase inhibitor crizotinib, our approach accurately predicted cellular potency and revealed improved target selectivity compared with biochemical measurements. Due to cellular ATP, a number of putative crizotinib targets are unexpectedly disengaged in live cells at a clinically relevant drug dose.
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Affiliation(s)
- James D Vasta
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Cesear R Corona
- Promega Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, CA 93401, USA
| | | | - Chad A Zimprich
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - James R Hartnett
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Morgan R Ingold
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | | | - Thomas Machleidt
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Thomas A Kirkland
- Promega Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, CA 93401, USA
| | - Kristin G Huwiler
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | | | - Michael Slater
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Paul Otto
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Mei Cong
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Benedict-Tilman Berger
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Thomas Hanke
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Carina Glas
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ke Ding
- State Key Laboratory of Respiratory Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China; School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kilian V M Huber
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy M Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stefan Knapp
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | | | - Frank Fan
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Keith V Wood
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Matthew B Robers
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA.
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Yasgar A, Jadhav A, Simeonov A, Coussens NP. AlphaScreen-Based Assays: Ultra-High-Throughput Screening for Small-Molecule Inhibitors of Challenging Enzymes and Protein-Protein Interactions. Methods Mol Biol 2016; 1439:77-98. [PMID: 27316989 DOI: 10.1007/978-1-4939-3673-1_5] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
AlphaScreen technology has been routinely utilized in high-throughput screening assays to quantify analyte accumulation or depletion, bimolecular interactions, and post-translational modifications. The high signal-to-background, dynamic range, and sensitivity associated with AlphaScreens as well as the homogenous assay format and reagent stability make the technology particularly well suited for high-throughput screening applications. Here, we describe the development of AlphaScreen assays to identify small-molecule inhibitors of enzymes and protein-protein interactions using the highly miniaturized 1536-well format. The subsequent implementation of counter assays to identify false-positive compounds is also discussed.
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Affiliation(s)
- Adam Yasgar
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Building B, Rm. 1034E, Rockville, MD, 20850, USA
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Building B, Rm. 1034E, Rockville, MD, 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Building B, Rm. 1034E, Rockville, MD, 20850, USA
| | - Nathan P Coussens
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Building B, Rm. 1034E, Rockville, MD, 20850, USA.
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Lang I, Füllsack S, Wyzgol A, Fick A, Trebing J, Arana JAC, Schäfer V, Weisenberger D, Wajant H. Binding Studies of TNF Receptor Superfamily (TNFRSF) Receptors on Intact Cells. J Biol Chem 2015; 291:5022-37. [PMID: 26721880 DOI: 10.1074/jbc.m115.683946] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 01/17/2023] Open
Abstract
Ligands of the tumor necrosis factor superfamily (TNFSF) interact with members of the TNF receptor superfamily (TNFRSF). TNFSF ligand-TNFRSF receptor interactions have been intensively evaluated by many groups. The affinities of TNFSF ligand-TNFRSF receptor interactions are highly dependent on the oligomerization state of the receptor, and cellular factors (e.g. actin cytoskeleton and lipid rafts) influence the assembly of ligand-receptor complexes, too. Binding studies on TNFSF ligand-TNFRSF receptor interactions were typically performed using cell-free assays with recombinant fusion proteins that contain varying numbers of TNFRSF ectodomains. It is therefore not surprising that affinities determined for an individual TNFSF ligand-TNFRSF interaction differ sometimes by several orders of magnitude and often do not reflect the ligand activity observed in cellular assays. To overcome the intrinsic limitations of cell-free binding studies and usage of recombinant receptor domains, we performed comprehensive binding studies with Gaussia princeps luciferase TNFSF ligand fusion proteins for cell-bound TNFRSF members on intact cells at 37 °C. The affinities of the TNFSF ligand G. princeps luciferase-fusion proteins ranged between 0.01 and 19 nm and offer the currently most comprehensive and best suited panel of affinities for in silico studies of ligand-receptor systems of the TNF family.
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Affiliation(s)
- Isabell Lang
- From the Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Simone Füllsack
- From the Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Agnes Wyzgol
- From the Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Andrea Fick
- From the Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Johannes Trebing
- From the Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - José Antonio Carmona Arana
- From the Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Viktoria Schäfer
- From the Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Daniela Weisenberger
- From the Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Harald Wajant
- From the Division of Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Röntgenring 11, 97070 Würzburg, Germany
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24
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Behnam MAM, Graf D, Bartenschlager R, Zlotos DP, Klein CD. Discovery of Nanomolar Dengue and West Nile Virus Protease Inhibitors Containing a 4-Benzyloxyphenylglycine Residue. J Med Chem 2015; 58:9354-70. [PMID: 26562070 DOI: 10.1021/acs.jmedchem.5b01441] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The dengue virus (DENV) and West Nile Virus (WNV) NS2B-NS3 proteases are attractive targets for the development of dual-acting therapeutics against these arboviral pathogens. We present the synthesis and extensive biological evaluation of inhibitors that contain benzyl ethers of 4-hydroxyphenylglycine as non-natural peptidic building blocks synthesized via a copper-complex intermediate. A three-step optimization strategy, beginning with fragment growth of the C-terminal 4-hydroxyphenylglycine to the benzyloxy ether, followed by C- and N-terminal optimization, and finally fragment merging generated compounds with in vitro affinities in the low nanomolar range. The most promising derivative reached Ki values of 12 nM at the DENV-2 and 39 nM at the WNV proteases. Several of the newly discovered protease inhibitors yielded a significant reduction of dengue and West Nile virus titers in cell-based assays of virus replication, with an EC50 value of 3.4 μM at DENV-2 and 15.5 μM at WNV for the most active analogue.
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Affiliation(s)
- Mira A M Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Dominik Graf
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University , Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.,German Center for Infection Research, Heidelberg University , Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Darius P Zlotos
- Department of Pharmaceutical Chemistry, The German University in Cairo , New Cairo City, 11835 Cairo, Egypt
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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25
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Kopra K, Syrjänpää M, Hänninen P, Härmä H. Non-competitive aptamer-based quenching resonance energy transfer assay for homogeneous growth factor quantification. Analyst 2015; 139:2016-23. [PMID: 24611155 DOI: 10.1039/c3an01814h] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A non-competitive homogeneous, single-label quenching resonance energy transfer (QRET) assay for protein quantification is now presented using lanthanide-chelate labeled nucleic acid aptamers. A labeled ssDNA aptamer binding to a growth factor has been successfully used to provide luminescence signal protection of the lanthanide label. The QRET technology has previously been applied to competitive assay formats, but now for the first time a direct non-competitive assay is presented. The QRET system is based on the protection of the Eu(iii)-chelate from a soluble quencher molecule when the aptamer interacts with a specific target protein. The direct QRET assay is possible as the aptamer structure itself cannot protect the Eu(iii)-label from quenching. The dynamic range for the optimized vascular endothelial growth factor (VEGF) assay is 0.25-10 nM. A successful quantification of the basic fibroblast growth factor (bFGF) is also demonstrated using the same QRET assay format with a dynamic range of 0.75-50 nM. These assays evidently show the suitability of the direct QRET technique to simple and efficient detection of large biomolecules. The QRET assay can potentially be applied as a detection platform for any other protein targets with a known aptamer sequence.
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Affiliation(s)
- Kari Kopra
- Laboratory of Biophysics, Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Tykistökatu 6 A 5th floor, FI-20520 Turku, Finland.
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26
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Verbeken M, Wynendaele E, Mauchauffée E, Bracke N, Stalmans S, Bojnik E, Benyhe S, Peremans K, Polis I, Burvenich C, Gjedde A, Hernandez JF, De Spiegeleer B. Blood-brain transfer and antinociception of linear and cyclic N-methyl-guanidine and thiourea-enkephalins. Peptides 2015; 63:10-21. [PMID: 25451468 DOI: 10.1016/j.peptides.2014.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 10/20/2014] [Accepted: 10/20/2014] [Indexed: 01/09/2023]
Abstract
Enkephalins are active in regulation of nociception in the body and are key in development of new synthetic peptide analogs that target centrally located opioid receptors. In this study, we investigated the in vivo blood-brain barrier (BBB) penetration behavior and antinociceptive activity of two cyclic enkephalin analogs with a thiourea (CycS) or a N-methyl-guanidine bridge (CycNMe), and their linear counterparts (LinS and LinNMe) in mice, as well as their in vitro metabolic stability. (125)I-LinS had the highest blood-brain clearance (K1=3.46μL/gmin), followed by (125)I-LinNMe, (125)I-CycNMe, and (125)I-CycS (K1=1.64, 0.31, and 0.11μL/gmin, respectively). Also, these peptides had a high metabolic stability (t1/2>1h) in mouse serum and brain homogenate, and half-inhibition constant (Ki) values in the nanomolar range with predominantly μ-opioid receptor selectivity. The positively charged NMe-enkephalins showed a higher antinociceptive activity (LinNMe: 298% and CycNMe: 205%), expressed as molar-dose normalized area under the curve (AUC) relative to morphine, than the neutral S-enkephalins (CycS: 122% and LinS: 130%).
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Affiliation(s)
- Mathieu Verbeken
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Evelien Wynendaele
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Elodie Mauchauffée
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS, Universités Montpellier 1 and 2, Faculty of Pharmaceutical Sciences, 15 Avenue Charles Flahault, F-34093 Montpellier, France
| | - Nathalie Bracke
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Sofie Stalmans
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Engin Bojnik
- Biological Research Center, Institute of Biochemistry, POB 521, H-6702 Szeged, Hungary
| | - Sandor Benyhe
- Biological Research Center, Institute of Biochemistry, POB 521, H-6702 Szeged, Hungary
| | - Kathelijne Peremans
- Departments of Veterinary Medical Imaging and Small Animal Orthopaedics, Medicine and Clinical Biology of Small Animals and Comparative Physiology and Biometrics, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Ingeborgh Polis
- Departments of Veterinary Medical Imaging and Small Animal Orthopaedics, Medicine and Clinical Biology of Small Animals and Comparative Physiology and Biometrics, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Christian Burvenich
- Departments of Veterinary Medical Imaging and Small Animal Orthopaedics, Medicine and Clinical Biology of Small Animals and Comparative Physiology and Biometrics, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Albert Gjedde
- Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, Copenhagen University, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Jean-François Hernandez
- Institut des Biomolécules Max Mousseron, UMR5247 CNRS, Universités Montpellier 1 and 2, Faculty of Pharmaceutical Sciences, 15 Avenue Charles Flahault, F-34093 Montpellier, France
| | - Bart De Spiegeleer
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium.
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27
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Thornton P, Hatcher JP, Robinson I, Sargent B, Franzén B, Martino G, Kitching L, Glover CP, Anderson D, Forsmo-Bruce H, Low CP, Cusdin F, Dosanjh B, Williams W, Steffen AC, Thompson S, Eklund M, Lloyd C, Chessell I, Hughes J. Artemin-GFRα3 interactions partially contribute to acute inflammatory hypersensitivity. Neurosci Lett 2013; 545:23-8. [PMID: 23603259 DOI: 10.1016/j.neulet.2013.04.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 03/30/2013] [Accepted: 04/02/2013] [Indexed: 10/26/2022]
Abstract
The expression of artemin (ARTN), a glial cell line-derived neurotrophic factor (GDNF) family ligand, increases in pre-clinical models of nociception and recent evidence suggests this growth factor may play a causative role in inflammatory pain mechanisms. The aim of this study was to demonstrate functional inhibition of ARTN with monoclonal antibodies and to determine whether ARTN neutralisation could reverse inflammatory pain in mice. We show that monoclonal antibodies with high affinity to ARTN, completely inhibit ARTN-induced Ret and ERK activation in a human neuroblastoma cell line, and block capsaicin-induced CGRP secretion from primary rat DRG cultures. In addition, administration of anti-ARTN antibodies to mice provides a transient, partial reversal (41%) of FCA-induced mechanical hypersensitivity. Anti-ARTN antibodies had no effect on hypersensitivity in response to partial nerve ligation in mice. These data suggest that ARTN-GFRα3 interactions partially mediate early stage nociceptive signalling following an inflammatory insult.
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28
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Kopra K, Shweta, Martikkala E, Hänninen P, Petäjä-Repo U, Härmä H. A homogeneous single-label quenching resonance energy transfer assay for a δ-opioid receptor–ligand using intact cells. Analyst 2013; 138:4907-14. [DOI: 10.1039/c3an00736g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Newton P, O'Shea D, Wells E, Moakes K, Dunmore R, Butler RJ, Wilkinson T, Ward A, Casson N, Strain M, Vousden K, Lowe DC, Pattison DV, Carruthers AM, Sleeman MA, Vaughan TJ, Harrison P. Development of a homogeneous high-throughput screening assay for biological inhibitors of human rhinovirus infection. ACTA ACUST UNITED AC 2012. [PMID: 23207740 DOI: 10.1177/1087057112469047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Infection with human rhinovirus (HRV) is thought to result in acute respiratory exacerbations of chronic obstructive pulmonary disorder (COPD). Consequently, prevention of HRV infection may provide therapeutic benefit to these patients. As all major group HRV serotypes infect cells via an interaction between viral coat proteins and intercellular adhesion molecule-1 (ICAM-1), it is likely that inhibitors of this interaction would prevent or reduce infections. Our objective was to use phage display technology in conjunction with naive human antibody libraries to identify anti-ICAM-1 antibodies capable of functional blockade of HRV infection. Key to success was the development of a robust, functionally relevant high-throughput screen (HTS) compatible with the specific challenges of antibody screening. In this article, we describe the development of a novel homogeneous time-resolved fluorescence (HTRF) assay based on the inhibition of soluble ICAM-1 binding to live HRV16. We describe the implementation of the method in an antibody screening campaign and demonstrate the biological relevance of the assay by confirming the activity of resultant antibodies in a cell-based in vitro HRV infection assay.
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30
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Bao J, Krylov SN. Volatile kinetic capillary electrophoresis for studies of protein-small molecule interactions. Anal Chem 2012; 84:6944-7. [PMID: 22823518 DOI: 10.1021/ac301829t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Kinetic capillary electrophoresis (KCE) is a toolset of homogeneous affinity methods for studying kinetics of noncovalent binding. Sensitive KCE measurements are typically done with fluorescence detection and require a fluorescent label on a smaller-sized binding partner. KCE with fluorescence detection is difficult to use for study of protein-small molecule interactions since labeling small molecules is cumbersome and can affect binding. A combination of KCE with mass-spectrometry (KCE-MS) has been recently suggested for label-free studies of protein-small molecule interactions. The major obstacle for studies by KCE-MS is a buffer mismatch between KCE and MS; MS requires volatile buffers while KCE of protein-ligand interactions is always run in near-physiological buffers. Here we asked a simple question: can protein-ligand interactions be studied with KCE in a volatile buffer? We compared three volatile buffers (ammonium acetate, ammonium bicarbonate, and ammonium formate) with a near-physiological buffer (Tris-acetate) for three protein-ligand pairs. The volatile buffers were found not to significantly affect protein-ligand complex stability; moreover, when used as CE run buffers, they facilitated good-quality separation of free ligands from the protein-ligand complexes. The use of volatile buffers instead of Tris-acetate in detection of small molecules by MS improved the detection limit by approximately 2 orders of magnitude. These findings prove the principle of "volatile" KCE, which can be easily coupled with MS to facilitate label-free kinetic studies of protein-small molecule interactions.
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Affiliation(s)
- Jiayin Bao
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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31
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Yapici E, Reddy DR, Miller LW. An adaptable luminescence resonance energy transfer assay for measuring and screening protein-protein interactions and their inhibition. Chembiochem 2012; 13:553-8, 489. [PMID: 22271654 PMCID: PMC3729432 DOI: 10.1002/cbic.201100710] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Indexed: 11/06/2022]
Abstract
Protein-protein interactions (PPIs) are central to biological processes and represent an important class of therapeutic targets. Here we show that the interaction between FK506-binding protein 12 fused to green fluorescent protein (GFP-FKBP) and the rapamycin-binding domain of mTor fused to Escherichia coli dihydrofolate reductase (FRB-eDHFR) can be sensitively detected (signal-to-background ratio (S/B)>100) and accurately quantified within an impure cell lysate matrix using a luminescence resonance energy transfer (LRET) assay. Ascomycin-mediated inhibition of GFP-FKBP-rapamycin-FRB-eDHFR complex formation was also detected at high S/B ratio (>80) and Z'-factor (0.89). The method leverages the selective, stable binding of trimethoprim (TMP)-terbium complex conjugates to eDHFR, and time-resolved, background-free detection of the long-lifetime (∼ms) terbium-to-GFP LRET signal that indicates target binding. TMP-eDHFR labeling can be adapted to develop high-throughput screening assays and complementary, quantitative counter-screens for a wide variety of PPI targets with a broad range of affinities that may not be amenable to purification.
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Affiliation(s)
- Engin Yapici
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607, Fax: 312 996 0431,
| | - D. Rajasekhar Reddy
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607, Fax: 312 996 0431,
| | - Lawrence W. Miller
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607, Fax: 312 996 0431,
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32
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Mathis G, Bazin H. Stable Luminescent Chelates and Macrocyclic Compounds. LANTHANIDE LUMINESCENCE 2010. [DOI: 10.1007/4243_2010_5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Degorce F, Card A, Soh S, Trinquet E, Knapik GP, Xie B. HTRF: A technology tailored for drug discovery - a review of theoretical aspects and recent applications. CURRENT CHEMICAL GENOMICS 2009; 3:22-32. [PMID: 20161833 PMCID: PMC2802762 DOI: 10.2174/1875397300903010022] [Citation(s) in RCA: 327] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 03/29/2009] [Accepted: 03/30/2009] [Indexed: 12/26/2022]
Abstract
HTRF (Homogeneous Time Resolved Fluorescence) is the most frequently used generic assay technology to measure analytes in a homogenous format, which is the ideal platform used for drug target studies in high-throughput screening (HTS). This technology combines fluorescence resonance energy transfer technology (FRET) with time-resolved measurement (TR). In TR-FRET assays, a signal is generated through fluorescent resonance energy transfer between a donor and an acceptor molecule when in close proximity to each other. Buffer and media interference is dramatically reduced by dual-wavelength detection, and the final signal is proportional to the extent of product formation. The HTRF assay is usually sensitive and robust that can be miniaturized into the 384 and 1536-well plate formats. This assay technology has been applied to many antibody-based assays including GPCR signaling (cAMP and IP-One), kinases, cytokines and biomarkers, bioprocess (antibody and protein production), as well as the assays for protein-protein, proteinpeptide, and protein-DNA/RNA interactions.Since its introduction to the drug-screening world over ten years ago, researchers have used HTRF to expedite the study of GPCRs, kinases, new biomarkers, protein-protein interactions, and other targets of interest. HTRF has also been utilized as an alternative method for bioprocess monitoring. The first-generation HTRF technology, which uses Europium cryptate as a fluorescence donor to monitor reactions between biomolecules, was extended in 2008 through the introduction of a second-generation donor, Terbium cryptate (Tb), enhancing screening performance. Terbium cryptate possesses different photophysical properties compared to Europium, including increased quantum yield and a higher molar extinction coefficient. In addition to being compatible with the same acceptor fluorophors used with Europium, it can serve as a donor fluorophore to green-emitting fluors because it has multiple emission peaks including one at 490 nm. Moreover, all Terbium HTRF assays can be read on the same HTRF-compatible instruments as Europium HTRF assays.Overall, HTRF is a highly sensitive, robust technology for the detection of molecular interactions in vitro and is widely used for primary and secondary screening phases of drug development. This review addresses the general principles of HTRF and its current applications in drug discovery.
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Zhang S, Liu C, Huang P, Zhou S, Ren J, Kitamura Y, Tang P, Bi Z, Gao B. The affinity of human RANK binding to its ligand RANKL. Arch Biochem Biophys 2009; 487:49-53. [PMID: 19416721 DOI: 10.1016/j.abb.2009.04.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 04/23/2009] [Accepted: 04/29/2009] [Indexed: 11/17/2022]
Abstract
Receptor activator of nuclear factor-kappa B (RANK) and its ligand, RANKL play critical roles in bone re-modeling, immune function, vascular disease and mammary gland development. To study the interaction of RANK and RANKL, we have expressed both extracellular domain of RANK and ectodomain of RANKL using Escherichia coli expression system. RANK was expressed as an inclusion body first which properly refolded later, while RANKL was initially produced as a GST fusion protein, after which the GST was removed by enzyme digestion. Soluble RANK existed as a monomer while RANKL was seen as a trimer in solution, demonstrated by gel filtration chromatography and cross-linking experiment. The recombinant RANK and RANKL could bind to each other and the binding affinity of RANKL for RANK was measured with surface plasmon resonance technology and K(D) value is about 1.09 x 10(-10) M.
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Affiliation(s)
- Shiqian Zhang
- The Center for Molecular Immunology, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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