1
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FitzGerald EA, Vagrys D, Opassi G, Klein HF, Hamilton DJ, Talibov VO, Abramsson M, Moberg A, Lindgren MT, Holmgren C, Davis B, O'Brien P, Wijtmans M, Hubbard RE, de Esch IJP, Danielson UH. Multiplexed experimental strategies for fragment library screening against challenging drug targets using SPR biosensors. SLAS Discov 2024; 29:40-51. [PMID: 37714432 DOI: 10.1016/j.slasd.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
Surface plasmon resonance (SPR) biosensor methods are ideally suited for fragment-based lead discovery. However, generally applicable experimental procedures and detailed protocols are lacking, especially for structurally or physico-chemically challenging targets or when tool compounds are not available. Success depends on accounting for the features of both the target and the chemical library, purposely designing screening experiments for identification and validation of hits with desired specificity and mode-of-action, and availability of orthogonal methods capable of confirming fragment hits. The range of targets and libraries amenable to an SPR biosensor-based approach for identifying hits is considerably expanded by adopting multiplexed strategies, using multiple complementary surfaces or experimental conditions. Here we illustrate principles and multiplexed approaches for using flow-based SPR biosensor systems for screening fragment libraries of different sizes (90 and 1056 compounds) against a selection of challenging targets. It shows strategies for the identification of fragments interacting with 1) large and structurally dynamic targets, represented by acetyl choline binding protein (AChBP), a Cys-loop receptor ligand gated ion channel homologue, 2) targets in multi protein complexes, represented by lysine demethylase 1 and a corepressor (LSD1/CoREST), 3) structurally variable or unstable targets, represented by farnesyl pyrophosphate synthase (FPPS), 4) targets containing intrinsically disordered regions, represented by protein tyrosine phosphatase 1B (PTP1B), and 5) aggregation-prone proteins, represented by an engineered form of human tau (tau K18M). Practical considerations and procedures accounting for the characteristics of the proteins and libraries, and that increase robustness, sensitivity, throughput and versatility are highlighted. The study shows that the challenges for addressing these types of targets is not identification of potentially useful fragments per se, but establishing methods for their validation and evolution into leads.
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Affiliation(s)
- Edward A FitzGerald
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Beactica Therapeutics AB, Virdings allé 2, Uppsala, Sweden
| | - Darius Vagrys
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Giulia Opassi
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Hanna F Klein
- Department of Chemistry, University of York, York, United Kingdom
| | - David J Hamilton
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | | | - Mia Abramsson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | - Ben Davis
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom
| | - Peter O'Brien
- Department of Chemistry, University of York, York, United Kingdom
| | - Maikel Wijtmans
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Roderick E Hubbard
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Iwan J P de Esch
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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2
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Cederfelt D, Badgujar D, Au Musse A, Lohkamp B, Danielson UH, Dobritzsch D. The Allosteric Regulation of Β-Ureidopropionase Depends on Fine-Tuned Stability of Active-Site Loops and Subunit Interfaces. Biomolecules 2023; 13:1763. [PMID: 38136634 PMCID: PMC10741476 DOI: 10.3390/biom13121763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The activity of β-ureidopropionase, which catalyses the last step in the degradation of uracil, thymine, and analogous antimetabolites, is cooperatively regulated by the substrate and product of the reaction. This involves shifts in the equilibrium of the oligomeric states of the enzyme, but how these are achieved and result in changes in enzyme catalytic competence has yet to be determined. Here, the regulation of human β-ureidopropionase was further explored via site-directed mutagenesis, inhibition studies, and cryo-electron microscopy. The active-site residue E207, as well as H173 and H307 located at the dimer-dimer interface, are shown to play crucial roles in enzyme activation. Dimer association to larger assemblies requires closure of active-site loops, which positions the catalytically crucial E207 stably in the active site. H173 and H307 likely respond to ligand-induced changes in their environment with changes in their protonation states, which fine-tunes the active-site loop stability and the strength of dimer-dimer interfaces and explains the previously observed pH influence on the oligomer equilibrium. The correlation between substrate analogue structure and effect on enzyme assembly suggests that the ability to favourably interact with F205 may distinguish activators from inhibitors. The cryo-EM structure of human β-ureidopropionase assembly obtained at low pH provides first insights into the architecture of its activated state. and validates our current model of the allosteric regulation mechanism. Closed entrance loop conformations and dimer-dimer interfaces are highly conserved between human and fruit fly enzymes.
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Affiliation(s)
- Daniela Cederfelt
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
| | - Dilip Badgujar
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
- Department of Cell and Molecular Biology, Uppsala University, 751 23 Uppsala, Sweden
| | - Ayan Au Musse
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
- School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - Bernhard Lohkamp
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden;
| | - U. Helena Danielson
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
| | - Doreen Dobritzsch
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
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3
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Fekry M, Dave KK, Badgujar D, Hamnevik E, Aurelius O, Dobritzsch D, Danielson UH. The Crystal Structure of Tyrosinase from Verrucomicrobium spinosum Reveals It to Be an Atypical Bacterial Tyrosinase. Biomolecules 2023; 13:1360. [PMID: 37759761 PMCID: PMC10526336 DOI: 10.3390/biom13091360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Tyrosinases belong to the type-III copper enzyme family, which is involved in melanin production in a wide range of organisms. Despite similar overall characteristics and functions, their structures, activities, substrate specificities and regulation vary. The tyrosinase from the bacterium Verrucomicrobium spinosum (vsTyr) is produced as a pre-pro-enzyme in which a C-terminal extension serves as an inactivation domain. It does not require a caddie protein for copper ion incorporation, which makes it similar to eukaryotic tyrosinases. To gain an understanding of the catalytic machinery and regulation of vsTyr activity, we determined the structure of the catalytically active "core domain" of vsTyr by X-ray crystallography. The analysis showed that vsTyr is an atypical bacterial tyrosinase not only because it is independent of a caddie protein but also because it shows the highest structural (and sequence) similarity to plant-derived members of the type-III copper enzyme family and is more closely related to fungal tyrosinases regarding active site features. By modelling the structure of the pre-pro-enzyme using AlphaFold, we observed that Phe453, located in the C-terminal extension, is appropriately positioned to function as a "gatekeeper" residue. Our findings raise questions concerning the evolutionary origin of vsTyr.
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Affiliation(s)
- Mostafa Fekry
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
- Biophysics Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Khyati K. Dave
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
| | - Dilip Badgujar
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
| | - Emil Hamnevik
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
| | | | - Doreen Dobritzsch
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
| | - U. Helena Danielson
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
- Science for Life Laboratory, Drug Discovery & Development Platform, Uppsala University, SE 751 23 Uppsala, Sweden
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4
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Al-Amin RA, Muthelo PM, Abdurakhmanov E, Vincke C, Amin SP, Muyldermans S, Danielson UH, Landegren U. Sensitive Protein Detection Using Site-Specifically Oligonucleotide-Conjugated Nanobodies. Anal Chem 2022; 94:10054-10061. [PMID: 35786874 PMCID: PMC9310004 DOI: 10.1021/acs.analchem.2c00584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
High-quality affinity
probes are critical for sensitive and specific
protein detection, in particular for detection of protein biomarkers
in the early phases of disease development. Proximity extension assays
(PEAs) have been used for high-throughput multiplexed protein detection
of up to a few thousand different proteins in one or a few microliters
of plasma. Clonal affinity reagents can offer advantages over the
commonly used polyclonal antibodies (pAbs) in terms of reproducibility
and standardization of such assays. Here, we explore nanobodies (Nbs)
as an alternative to pAbs as affinity reagents for PEA. We describe
an efficient site-specific approach for preparing high-quality oligo-conjugated
Nb probes via enzyme coupling using Sortase A (SrtA). The procedure
allows convenient removal of unconjugated affinity reagents after
conjugation. The purified high-grade Nb probes were used in PEA, and
the reactions provided an efficient means to select optimal pairs
of binding reagents from a group of affinity reagents. We demonstrate
that Nb-based PEA (nano-PEA) for interleukin-6 (IL6) detection can
augment assay performance, compared to the use of pAb probes. We identify
and validate Nb combinations capable of binding in pairs without competition
for IL6 antigen detection by PEA.
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Affiliation(s)
- Rasel A Al-Amin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08 Uppsala, Sweden
| | - Phathutshedzo M Muthelo
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08 Uppsala, Sweden
| | - Eldar Abdurakhmanov
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Cécile Vincke
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, 1050 Brussels, Belgium
| | - Shahnaz P Amin
- Capio Vårdcentral Väsby, Dragonvägen 92, 194 33 Upplands Väsby, Sweden
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - U Helena Danielson
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08 Uppsala, Sweden
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5
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Luttens A, Gullberg H, Abdurakhmanov E, Vo DD, Akaberi D, Talibov VO, Nekhotiaeva N, Vangeel L, De Jonghe S, Jochmans D, Krambrich J, Tas A, Lundgren B, Gravenfors Y, Craig AJ, Atilaw Y, Sandström A, Moodie LWK, Lundkvist Å, van Hemert MJ, Neyts J, Lennerstrand J, Kihlberg J, Sandberg K, Danielson UH, Carlsson J. Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses. J Am Chem Soc 2022; 144:2905-2920. [PMID: 35142215 PMCID: PMC8848513 DOI: 10.1021/jacs.1c08402] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Drugs targeting SARS-CoV-2 could have saved millions of lives during the COVID-19 pandemic, and it is now crucial to develop inhibitors of coronavirus replication in preparation for future outbreaks. We explored two virtual screening strategies to find inhibitors of the SARS-CoV-2 main protease in ultralarge chemical libraries. First, structure-based docking was used to screen a diverse library of 235 million virtual compounds against the active site. One hundred top-ranked compounds were tested in binding and enzymatic assays. Second, a fragment discovered by crystallographic screening was optimized guided by docking of millions of elaborated molecules and experimental testing of 93 compounds. Three inhibitors were identified in the first library screen, and five of the selected fragment elaborations showed inhibitory effects. Crystal structures of target-inhibitor complexes confirmed docking predictions and guided hit-to-lead optimization, resulting in a noncovalent main protease inhibitor with nanomolar affinity, a promising in vitro pharmacokinetic profile, and broad-spectrum antiviral effect in infected cells.
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Affiliation(s)
- Andreas Luttens
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden
| | - Hjalmar Gullberg
- Science for Life Laboratory, Biochemical and Cellular Assay Facility, Drug Discovery and Development Platform, Department of Biochemistry and Biophysics, Stockholm University, Solna, SE-17121 Stockholm, Sweden
| | - Eldar Abdurakhmanov
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Duy Duc Vo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden
| | - Dario Akaberi
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, SE-75123 Uppsala, Sweden
| | | | - Natalia Nekhotiaeva
- Science for Life Laboratory, Biochemical and Cellular Assay Facility, Drug Discovery and Development Platform, Department of Biochemistry and Biophysics, Stockholm University, Solna, SE-17121 Stockholm, Sweden
| | - Laura Vangeel
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium.,Global Virus Network, Baltimore, Maryland 21201, United States
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium.,Global Virus Network, Baltimore, Maryland 21201, United States
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium.,Global Virus Network, Baltimore, Maryland 21201, United States
| | - Janina Krambrich
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, SE-75123 Uppsala, Sweden
| | - Ali Tas
- Department of Medical Microbiology, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Bo Lundgren
- Science for Life Laboratory, Biochemical and Cellular Assay Facility, Drug Discovery and Development Platform, Department of Biochemistry and Biophysics, Stockholm University, Solna, SE-17121 Stockholm, Sweden
| | - Ylva Gravenfors
- Science for Life Laboratory, Drug Discovery & Development Platform, Department of Organic Chemistry, Stockholm University, Solna, SE-17121 Stockholm, Sweden
| | - Alexander J Craig
- Department of Medicinal Chemistry, Uppsala University, SE-75123 Uppsala, Sweden
| | - Yoseph Atilaw
- Department of Chemistry-BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Anja Sandström
- Department of Medicinal Chemistry, Uppsala University, SE-75123 Uppsala, Sweden
| | - Lindon W K Moodie
- Department of Medicinal Chemistry, Uppsala University, SE-75123 Uppsala, Sweden.,Uppsala Antibiotic Centre, Uppsala University, SE-75123 Uppsala, Sweden
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, SE-75123 Uppsala, Sweden
| | - Martijn J van Hemert
- Department of Medical Microbiology, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium.,Global Virus Network, Baltimore, Maryland 21201, United States
| | - Johan Lennerstrand
- Department of Medical Sciences, Section of Clinical Microbiology, Uppsala University, SE-75185 Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry-BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Kristian Sandberg
- Department of Medicinal Chemistry, Uppsala University, SE-75123 Uppsala, Sweden.,Department of Physiology and Pharmacology, Karolinska Institutet, SE-17177 Stockholm, Sweden.,Science for Life Laboratory, Drug Discovery & Development Platform, Uppsala Biomedical Center, Uppsala University, SE-75123 Uppsala, Sweden
| | - U Helena Danielson
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden
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6
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Talibov VO, Fabini E, FitzGerald EA, Tedesco D, Cederfeldt D, Talu MJ, Rachman MM, Mihalic F, Manoni E, Naldi M, Sanese P, Forte G, Lepore Signorile M, Barril X, Simone C, Bartolini M, Dobritzsch D, Del Rio A, Danielson UH. Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase. Chembiochem 2021; 22:1597-1608. [PMID: 33400854 PMCID: PMC8248052 DOI: 10.1002/cbic.202000736] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/30/2020] [Indexed: 12/15/2022]
Abstract
SMYD3 is a multifunctional epigenetic enzyme with lysine methyltransferase activity and various interaction partners. It is implicated in the pathophysiology of cancers but with an unclear mechanism. To discover tool compounds for clarifying its biochemistry and potential as a therapeutic target, a set of drug-like compounds was screened in a biosensor-based competition assay. Diperodon was identified as an allosteric ligand; its R and S enantiomers were isolated, and their affinities to SMYD3 were determined (KD =42 and 84 μM, respectively). Co-crystallization revealed that both enantiomers bind to a previously unidentified allosteric site in the C-terminal protein binding domain, consistent with its weak inhibitory effect. No competition between diperodon and HSP90 (a known SMYD3 interaction partner) was observed although SMYD3-HSP90 binding was confirmed (KD =13 μM). Diperodon clearly represents a novel starting point for the design of tool compounds interacting with a druggable allosteric site, suitable for the exploration of noncatalytic SMYD3 functions and therapeutics with new mechanisms of action.
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Affiliation(s)
- Vladimir O. Talibov
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
| | - Edoardo Fabini
- Department of Pharmacy and BiotechnologyAlma Mater Studiorum University of BolognaVia Belmeloro 640126BolognaItaly
- Institute for Organic Synthesis and PhotoreactivityNational Research CouncilVia P. Gobetti 10140129BolognaItaly
| | - Edward A. FitzGerald
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
- Beactica Therapeutics ABVirdings allé 2754 50UppsalaSweden
| | - Daniele Tedesco
- Department of Pharmacy and BiotechnologyAlma Mater Studiorum University of BolognaVia Belmeloro 640126BolognaItaly
- Institute for Organic Synthesis and PhotoreactivityNational Research CouncilVia P. Gobetti 10140129BolognaItaly
| | - Daniela Cederfeldt
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
| | - Martin J. Talu
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
| | - Moira M. Rachman
- Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de FarmaciaUniversitat de BarcelonaAv. Joan XXIII 27–3108028BarcelonaSpain
| | - Filip Mihalic
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
| | - Elisabetta Manoni
- Institute for Organic Synthesis and PhotoreactivityNational Research CouncilVia P. Gobetti 10140129BolognaItaly
| | - Marina Naldi
- Department of Pharmacy and BiotechnologyAlma Mater Studiorum University of BolognaVia Belmeloro 640126BolognaItaly
- Centre for Applied Biomedical ResearchAlma Mater Studiorum University of BolognaVia Zamboni, 33Bologna40126Italy
| | - Paola Sanese
- Medical Genetics, National Institute for GastroenterologyIRCCS ‘S. de Bellis' Research Hospital70013BariItaly
| | - Giovanna Forte
- Medical Genetics, National Institute for GastroenterologyIRCCS ‘S. de Bellis' Research Hospital70013BariItaly
| | - Martina Lepore Signorile
- Medical Genetics, National Institute for GastroenterologyIRCCS ‘S. de Bellis' Research Hospital70013BariItaly
| | - Xavier Barril
- Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de FarmaciaUniversitat de BarcelonaAv. Joan XXIII 27–3108028BarcelonaSpain
- Catalan Institution for Research and Advanced Studies (ICREA)Passeig Lluis Companys 2308010BarcelonaSpain
| | - Cristiano Simone
- Medical Genetics, National Institute for GastroenterologyIRCCS ‘S. de Bellis' Research Hospital70013BariItaly
- Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO)University of Bari Aldo Moro70124BariItaly
| | - Manuela Bartolini
- Department of Pharmacy and BiotechnologyAlma Mater Studiorum University of BolognaVia Belmeloro 640126BolognaItaly
| | - Doreen Dobritzsch
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
| | - Alberto Del Rio
- Institute for Organic Synthesis and PhotoreactivityNational Research CouncilVia P. Gobetti 10140129BolognaItaly
- Innovamol Consulting SrlVia Giardini 470/H41124ModenaItaly
| | - U. Helena Danielson
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
- Science for Life LaboratoryUppsala UniversityUppsala752 37Sweden
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7
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FitzGerald EA, Butko MT, Boronat P, Cederfelt D, Abramsson M, Ludviksdottir H, van Muijlwijk-Koezen JE, de Esch IJP, Dobritzsch D, Young T, Danielson UH. Discovery of fragments inducing conformational effects in dynamic proteins using a second-harmonic generation biosensor. RSC Adv 2021; 11:7527-7537. [PMID: 35423271 PMCID: PMC8694943 DOI: 10.1039/d0ra09844b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/28/2021] [Indexed: 01/13/2023] Open
Abstract
Biophysical screening of compound libraries for the identification of ligands that interact with a protein is efficient, but does typically not reveal if (or how) ligands may interfere with its functional properties. For this a biochemical/functional assay is required. But for proteins whose function is dependent on a conformational change, such assays are typically complex or have low throughput. Here we have explored a high-throughput second-harmonic generation (SHG) biosensor to detect fragments that induce conformational changes upon binding to a protein in real time and identify dynamic regions. Multiwell plate format SHG assays were developed for wild-type and six engineered single-cysteine mutants of acetyl choline binding protein (AChBP), a homologue to ligand gated ion channels (LGICs). They were conjugated with second harmonic-active labels via amine or maleimide coupling. To validate the assay, it was confirmed that the conformational changes induced in AChBP by nicotinic acetyl choline receptor (nAChR) agonists and antagonists were qualitatively different. A 1056 fragment library was subsequently screened against all variants and conformational modulators of AChBP were successfully identified, with hit rates from 9-22%, depending on the AChBP variant. A subset of four hits was selected for orthogonal validation and structural analysis. A time-resolved grating-coupled interferometry-based biosensor assay confirmed the interaction to be a reversible 1-step 1 : 1 interaction, and provided estimates of affinities and interaction kinetic rate constants (K D = 0.28-63 μM, k a = 0.1-6 μM-1 s-1, k d = 1 s-1). X-ray crystallography of two of the fragments confirmed their binding at a previously described conformationally dynamic site, corresponding to the regulatory site of LGICs. These results reveal that SHG has the sensitivity to identify fragments that induce conformational changes in a protein. A selection of fragment hits with a response profile different to known LGIC regulators was characterized and confirmed to bind to dynamic regions of the protein.
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Affiliation(s)
- Edward A FitzGerald
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
- Beactica Therapeutics Virdings allé 2 Uppsala 754 40 Sweden
| | | | - Pierre Boronat
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Daniela Cederfelt
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | - Mia Abramsson
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | | | - Jacqueline E van Muijlwijk-Koezen
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Iwan J P de Esch
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Doreen Dobritzsch
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | - Tracy Young
- Biodesy, Inc. 170 Harbor Way South San Francisco 94080 CA USA
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
- Science for Life Laboratory, Uppsala University Sweden
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8
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Encarnação JC, Napolitano V, Opassi G, Danielson UH, Dubin G, Popowicz GM, Munier-Lehmann H, Buijs J, Andersson K, Björkelund H. A real-time cell-binding assay reveals dynamic features of STxB-Gb3 cointernalization and STxB-mediated cargo delivery into cancer cells. FEBS Lett 2020; 594:2406-2420. [PMID: 32473599 DOI: 10.1002/1873-3468.13847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/16/2020] [Accepted: 05/19/2020] [Indexed: 12/17/2022]
Abstract
The interaction between the Shiga toxin B-subunit (STxB) and its globotriaosylceramide receptor (Gb3) has a high potential for being exploited for targeted cancer therapy. The primary goal of this study was to evaluate the capacity of STxB to carry small molecules and proteins as cargo into cells. For this purpose, an assay was designed to provide real-time information about the StxB-Gb3 interaction as well as the dynamics and mechanism of the internalization process. The assay revealed the ability to distinguish the process of binding to the cell surface from internalization and presented the importance of receptor and STxB clustering for internalization. The overall setup demonstrated that the binding mechanism is complex, and the concept of affinity is difficult to apply. Hence, time-resolved methods, providing detailed information about the interaction of STxB with cells, are critical for the optimization of intracellular delivery.
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Affiliation(s)
- João Crispim Encarnação
- Ridgeview Instruments AB, Uppsala, Sweden.,Department of Immunology, Pathology and Genetics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Valeria Napolitano
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Giulia Opassi
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | | | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie, Technische Universität München, Garching, Germany
| | - Hélène Munier-Lehmann
- Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR3523, Paris, France
| | - Jos Buijs
- Ridgeview Instruments AB, Uppsala, Sweden.,Department of Immunology, Pathology and Genetics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Karl Andersson
- Ridgeview Instruments AB, Uppsala, Sweden.,Department of Immunology, Pathology and Genetics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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9
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Fuchs PÖ, Calitz C, Pavlović N, Binet F, Solbak SMØ, Danielson UH, Kreuger J, Heindryckx F, Gerwins P. Fibrin fragment E potentiates TGF-β-induced myofibroblast activation and recruitment. Cell Signal 2020; 72:109661. [PMID: 32334027 DOI: 10.1016/j.cellsig.2020.109661] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/19/2020] [Accepted: 04/20/2020] [Indexed: 02/07/2023]
Abstract
Fibrin is an essential constituent of the coagulation cascade, and the formation of hemostatic fibrin clots is central to wound healing. Fibrin clots are over time degraded into fibrin degradation products as the injured tissue is replaced by granulation tissue. Our goal was to study the role of the fibrin degradation product fragment E (FnE) in fibroblast activation and migration. We present evidence that FnE is a chemoattractant for fibroblasts and that FnE can potentiate TGF-β-induced myofibroblast formation. FnE forms a stable complex with αVβ3 integrin, and the integrin β3 subunit is required both for FnE-induced fibroblast migration and for potentiation of TGF-β-induced myofibroblast formation. Finally, subcutaneous infusion of FnE in mice results in a fibrotic response in the hypodermis. These results support a model where FnE released from clots in wounded tissue promote wound healing and fibrosis by both recruitment and activation of fibroblasts. Fibrin fragment E could thus represent a therapeutic target for treatment of pathological fibrosis.
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Affiliation(s)
- Peder Öhman Fuchs
- Dept. of Medical Cell Biology, Uppsala University, P.O. Box 571, SE-751 23 Uppsala, Sweden
| | - Carlemi Calitz
- Dept. of Medical Cell Biology, Uppsala University, P.O. Box 571, SE-751 23 Uppsala, Sweden
| | - Nataša Pavlović
- Dept. of Medical Cell Biology, Uppsala University, P.O. Box 571, SE-751 23 Uppsala, Sweden
| | - François Binet
- Dept. of Medical Cell Biology, Uppsala University, P.O. Box 571, SE-751 23 Uppsala, Sweden
| | | | - U Helena Danielson
- Dept. of Chemistry-BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden; Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Johan Kreuger
- Dept. of Medical Cell Biology, Uppsala University, P.O. Box 571, SE-751 23 Uppsala, Sweden
| | - Femke Heindryckx
- Dept. of Medical Cell Biology, Uppsala University, P.O. Box 571, SE-751 23 Uppsala, Sweden.
| | - Pär Gerwins
- Dept. of Medical Cell Biology, Uppsala University, P.O. Box 571, SE-751 23 Uppsala, Sweden; Dept. of Radiology, Uppsala University Hospital, SE-751 85 Uppsala, Sweden
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10
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Yang J, Talibov VO, Peintner S, Rhee C, Poongavanam V, Geitmann M, Sebastiano MR, Simon B, Hennig J, Dobritzsch D, Danielson UH, Kihlberg J. Macrocyclic Peptides Uncover a Novel Binding Mode for Reversible Inhibitors of LSD1. ACS Omega 2020; 5:3979-3995. [PMID: 32149225 PMCID: PMC7057333 DOI: 10.1021/acsomega.9b03493] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) is an epigenetic enzyme which regulates the methylation of Lys4 of histone 3 (H3) and is overexpressed in certain cancers. We used structures of H3 substrate analogues bound to LSD1 to design macrocyclic peptide inhibitors of LSD1. A linear, Lys4 to Met-substituted, 11-mer (4) was identified as the shortest peptide distinctly interacting with LSD1. It was evolved into macrocycle 31, which was >40 fold more potent (K i = 2.3 μM) than 4. Linear and macrocyclic peptides exhibited unexpected differences in structure-activity relationships for interactions with LSD1, indicating that they bind LSD1 differently. This was confirmed by the crystal structure of 31 in complex with LSD1-CoREST1, which revealed a novel binding mode at the outer rim of the LSD1 active site and without a direct interaction with FAD. NMR spectroscopy of 31 suggests that macrocyclization restricts its solution ensemble to conformations that include the one in the crystalline complex. Our results provide a solid basis for the design of optimized reversible LSD1 inhibitors.
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Affiliation(s)
- Jie Yang
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - Vladimir O. Talibov
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - Stefan Peintner
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - Claire Rhee
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | | | - Matthis Geitmann
- Beactica
AB, Uppsala Business Park, Virdings allé 2, SE-75450 Uppsala, Sweden
| | | | - Bernd Simon
- Structural
and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Janosch Hennig
- Structural
and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Doreen Dobritzsch
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - U. Helena Danielson
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
- Science
for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jan Kihlberg
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
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11
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Opassi G, Nordström H, Lundin A, Napolitano V, Magari F, Dzus T, Klebe G, Danielson UH. Establishing Trypanosoma cruzi farnesyl pyrophosphate synthase as a viable target for biosensor driven fragment-based lead discovery. Protein Sci 2020; 29:991-1003. [PMID: 31994261 PMCID: PMC7096706 DOI: 10.1002/pro.3834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022]
Abstract
Procedures for producing and exploring Trypanosoma cruzi farnesyl pyrophosphate synthase (tcFPPS) for surface plasmon resonance (SPR) biosensor‐driven fragment‐based discovery have been established. The method requires functional sensor surfaces with high sensitivity for extended times and appropriate controls. Initial problems with protein stability and lack of useful reference compounds motivated optimization of experimental procedures and conditions. The improved methods enabled the production of pure, folded and dimeric protein, and identified procedures for storage and handling. A new coupled enzymatic assay, using luciferase for detection of pyrophosphate, was developed and used to confirm that the purified enzyme was active after purification and storage. It also confirmed that sensor surfaces prepared with structurally intact protein was active. An SPR‐biosensor assay for fragment library screening and hit confirmation was developed. A thermal shift assay was used in parallel. A library of 90 fragments was efficiently screened by both assays at a single concentration in the presence and absence of the catalytic cofactor Mg2+. Hits were selected on the basis of response levels or ΔTm > 1°C and selectivity for tcFPPS in the presence of Mg2+. Characterization of hits by SPR showed that all had low affinities and the relationships between steady‐state responses and concentrations were not sufficiently hyperbolic for determination of KD‐values. Instead, ranking could be performed from the slope of the linear relationship at low concentrations. This pilot screen confirms that the procedures developed herein enables SPR‐biosensor driven fragment‐based discovery of leads targeting tcFPPS, despite the lack of a reference compound. Significance Statement To enable the discovery of drugs, it is essential to have access to relevant forms of the target protein and valid biochemical methods for studying the protein and effects of compounds that may be evolved into drugs. We have established methods for the discovery of drugs for treatment of American Trypanosomiasis (Chagas disease), using farnesyl pyrophosphate synthase from Trypanosoma cruzi as a target.
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Affiliation(s)
- Giulia Opassi
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Helena Nordström
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden.,SciLifeLab, Uppsala, Sweden
| | | | - Valeria Napolitano
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa, Krakow, Poland
| | - Francesca Magari
- Institut für Pharmazeutische Chemie, Phillips-Universität Marburg, Marburg, Germany
| | - Tom Dzus
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Phillips-Universität Marburg, Marburg, Germany
| | - U Helena Danielson
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden.,SciLifeLab, Uppsala, Sweden
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12
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Xu X, Makaraviciute A, Abdurakhmanov E, Wermeling F, Li S, Danielson UH, Nyholm L, Zhang Z. Estimating Detection Limits of Potentiometric DNA Sensors Using Surface Plasmon Resonance Analyses. ACS Sens 2020; 5:217-224. [PMID: 31833355 DOI: 10.1021/acssensors.9b02086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
As the signals of potentiometric-based DNA ion-selective field effect transistor (ISFET) sensors differ largely from report to report, a systematic revisit to this method is needed. Herein, the hybridization of the target and the probe DNA on the sensor surface and its dependence on the surface probe DNA coverage and the ionic strength were systematically investigated by surface plasmon resonance (SPR). The maximum potentiometric DNA hybridization signal that could be registered by an ISFET sensor was estimated based on the SPR measurements, without considering buffering effects from any side interaction on the sensing electrode. We found that under physiological solutions (200 to 300 mM ionic strength), the ISFET sensor could not register the DNA hybridization events on the sensor surface due to Debye screening. Lowering the salt concentration to enlarge the Debye length would at the same time reduce the surface hybridization efficiency, thus suppressing the signal. This adverse effect of low salt concentration on the hybridization efficiency was also found to be more significant on the surface with higher probe coverage due to steric hindrance. With the method of diluting buffer, the maximum potentiometric signal generated by the DNA hybridization was estimated to be only around 120 mV with the lowest detection limit of 30 nM, occurring on a surface with optimized probe coverage and in the tris buffer with 10 mM NaCl. An alternative method would be to achieve high-efficiency hybridization in the buffer with high salt concentration (1 M NaCl) and then to perform potentiometric measurements in the buffer with low salt concentration (1 mM NaCl). Based on the characterization of the stability of the hybridized DNA duplexes on the sensor surface in low salt concentration buffer solutions, the estimated maximum potentiometric signal could be significantly higher using the alternative method. The lowest detection limit for this alternative method was estimated to be around 0.6 nM. This work can serve as an important quantitative reference for potentiometric DNA sensors.
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Affiliation(s)
- Xingxing Xu
- Division of Solid-State Electronics, Department of Engineering Sciences, Ångström Laboratory, Uppsala University, P.O. Box 534, SE-751 21 Uppsala, Sweden
| | - Asta Makaraviciute
- Division of Solid-State Electronics, Department of Engineering Sciences, Ångström Laboratory, Uppsala University, P.O. Box 534, SE-751 21 Uppsala, Sweden
| | - Eldar Abdurakhmanov
- Department of Chemistry-BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Fredrik Wermeling
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | - Shiyu Li
- Division of Solid-State Electronics, Department of Engineering Sciences, Ångström Laboratory, Uppsala University, P.O. Box 534, SE-751 21 Uppsala, Sweden
| | - U. Helena Danielson
- Department of Chemistry-BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Leif Nyholm
- Department of Chemistry-Ångström Laboratory, Uppsala University, P.O. Box 538, SE-751 21 Uppsala, Sweden
| | - Zhen Zhang
- Division of Solid-State Electronics, Department of Engineering Sciences, Ångström Laboratory, Uppsala University, P.O. Box 534, SE-751 21 Uppsala, Sweden
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13
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Pandya NJ, Seeger C, Babai N, Gonzalez-Lozano MA, Mack V, Lodder JC, Gouwenberg Y, Mansvelder HD, Danielson UH, Li KW, Heine M, Spijker S, Frischknecht R, Smit AB. Noelin1 Affects Lateral Mobility of Synaptic AMPA Receptors. Cell Rep 2019; 24:1218-1230. [PMID: 30067977 PMCID: PMC6088136 DOI: 10.1016/j.celrep.2018.06.102] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/26/2018] [Accepted: 06/26/2018] [Indexed: 11/24/2022] Open
Abstract
Lateral diffusion on the neuronal plasma membrane of the AMPA-type glutamate receptor (AMPAR) serves an important role in synaptic plasticity. We investigated the role of the secreted glycoprotein Noelin1 (Olfactomedin-1 or Pancortin) in AMPAR lateral mobility and its dependence on the extracellular matrix (ECM). We found that Noelin1 interacts with the AMPAR with high affinity, however, without affecting rise- and decay time and desensitization properties. Noelin1 co-localizes with synaptic and extra-synaptic AMPARs and is expressed at synapses in an activity-dependent manner. Single-particle tracking shows that Noelin1 reduces lateral mobility of both synaptic and extra-synaptic GluA1-containing receptors and affects short-term plasticity. While the ECM does not constrain the synaptic pool of AMPARs and acts only extrasynaptically, Noelin1 contributes to synaptic potentiation by limiting AMPAR mobility at synaptic sites. This is the first evidence for the role of a secreted AMPAR-interacting protein on mobility of GluA1-containing receptors and synaptic plasticity. Noelin1 interacts with high affinity to AMPA receptors (AMPARs) Noelin1 is secreted upon cellular stimulation (Extra)synaptic AMPAR mobility, but not channel properties, are affected by Noelin1 Reducing synaptic AMPAR lateral mobility by Noelin1 limits synaptic plasticity
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Affiliation(s)
- Nikhil J Pandya
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Christian Seeger
- Beactica AB, Virdings allé 2, 754 50 Uppsala, Sweden; Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Norbert Babai
- Department of Biology, Animal Physiology, Friedrich Alexander University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Miguel A Gonzalez-Lozano
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Volker Mack
- Department of CNS Diseases Research, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach (an der Riss), Germany
| | - Johannes C Lodder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Yvonne Gouwenberg
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - U Helena Danielson
- Beactica AB, Virdings allé 2, 754 50 Uppsala, Sweden; Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Martin Heine
- Research Group Molecular Physiology, Leibniz Institute for Neurobiology, Brenneckestrasse 6, 39118 Magdeburg, Germany
| | - Sabine Spijker
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands.
| | - Renato Frischknecht
- Department of Biology, Animal Physiology, Friedrich Alexander University Erlangen-Nürnberg, 91058 Erlangen, Germany; Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Brenneckestrasse 6, 39118 Magdeburg, Germany
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands.
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14
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Xu X, Makaraviciute A, Kumar S, Wen C, Sjödin M, Abdurakhmanov E, Danielson UH, Nyholm L, Zhang Z. Structural Changes of Mercaptohexanol Self-Assembled Monolayers on Gold and Their Influence on Impedimetric Aptamer Sensors. Anal Chem 2019; 91:14697-14704. [PMID: 31650834 DOI: 10.1021/acs.analchem.9b03946] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Despite a large number of publications describing biosensors based on electrochemical impedance spectroscopy (EIS), little attention has been paid to the stability and reproducibility issues of the sensor interfaces. In this work, the stability and reproducibility of faradaic EIS analyses on the aptamer/mercaptohexanol (MCH) self-assembled monolayer (SAM)-functionalized gold surfaces in ferri- and ferrocyanide solution were systematically evaluated prior to and after the aptamer-probe DNA hybridization. It is shown that the EIS data exhibited significant drift, and this significantly affected the reproducibility of the EIS signal of the hybridization. As a result, no significant difference between the charge transfer resistance (RCT) changes induced by the aptamer-target DNA hybridization and that caused by the drift could be identified. A conditioning of the electrode in the measurement solution for more than 12 h was required to reach a stable RCT baseline prior to the aptamer-probe DNA hybridization. The monitored drift in RCT and double layer capacitance during the conditioning suggests that the MCH SAM on the gold surface reorganized to a thinner but more closely packed layer. We also observed that the hot binding buffer used in the following aptamer-probe DNA hybridization process could induce additional MCH and aptamer reorganization, and thus further drift in RCT. As a result, the RCT change caused by the aptamer-probe DNA hybridization was less than that caused by the hot binding buffer (blank control experiment). Therefore, it is suggested that the use of high temperature in the EIS measurement should be carefully evaluated or avoided. This work provides practical guidelines for the EIS measurements. Moreover, because SAM-functionalized gold electrodes are widely used in biosensors, for example, DNA sensors, an improved understanding of the origin of the observed drift is very important for the development of well-functioning and reproducible biosensors.
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Affiliation(s)
| | | | - Shalen Kumar
- School of Biological Sciences , Victoria University of Wellington , Wellington 6140 , New Zealand.,AuramerBio Limited, Callaghan Innovation Quarter , 69 Seaview Road , Gracefield, Lower Hutt 5010 , New Zealand
| | | | | | - Eldar Abdurakhmanov
- Department of Chemistry-BMC and Science for Life Laboratory , Uppsala University , P.O. Box 576, Uppsala SE-751 23 , Sweden
| | - U Helena Danielson
- Department of Chemistry-BMC and Science for Life Laboratory , Uppsala University , P.O. Box 576, Uppsala SE-751 23 , Sweden
| | - Leif Nyholm
- Department of Chemistry, The Ångström Laboratory , Uppsala University , P.O. Box 538, Uppsala SE-751 21 , Sweden
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15
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Fabini E, Talibov VO, Mihalic F, Naldi M, Bartolini M, Bertucci C, Del Rio A, Danielson UH. Unveiling the Biochemistry of the Epigenetic Regulator SMYD3. Biochemistry 2019; 58:3634-3645. [PMID: 31389685 DOI: 10.1021/acs.biochem.9b00420] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SET and MYND domain-containing protein 3 (SMYD3) is a lysine methyltransferase that plays a central role in a variety of cancer diseases, exerting its pro-oncogenic activity by methylation of key proteins, of both nuclear and cytoplasmic nature. However, the role of SMYD3 in the initiation and progression of cancer is not yet fully understood and further biochemical characterization is required to support the discovery of therapeutics targeting this enzyme. We have therefore developed robust protocols for production, handling, and crystallization of SMYD3 and biophysical and biochemical assays for clarification of SMYD3 biochemistry and identification of useful lead compounds. Specifically, a time-resolved biosensor assay was developed for kinetic characterization of SMYD3 interactions. Functional differences in SMYD3 interactions with its natural small molecule ligands SAM and SAH were revealed, with SAM forming a very stable complex. A variety of peptides mimicking putative substrates of SMYD3 were explored in order to expose structural features important for recognition. The interaction between SMYD3 and some peptides was influenced by SAM. A nonradioactive SMYD3 activity assay using liquid chromatography-mass spectrometry (LC-MS) analysis explored substrate features of importance also for methylation. Methylation was notable only toward MAP kinase kinase kinase 2 (MAP3K2_K260)-mimicking peptides, although binary and tertiary complexes were detected also with other peptides. The analysis supported a random bi-bi mechanistic model for SMYD3 methyltransferase catalysis. Our work unveiled complexities in SMYD3 biochemistry and resulted in procedures suitable for further studies and identification of novel starting points for design of effective and specific leads for this potential oncology target.
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Affiliation(s)
- Edoardo Fabini
- Department of Pharmacy and Biotechnology , Alma Mater Studiorum University of Bologna , Bologna , Italy.,Institute of Organic Synthesis and Photoreactivity (ISOF) , National Research Council (CNR) , Bologna , Italy
| | | | - Filip Mihalic
- Department of Chemistry - BMC , Uppsala University , Uppsala , Sweden
| | - Marina Naldi
- Department of Pharmacy and Biotechnology , Alma Mater Studiorum University of Bologna , Bologna , Italy.,Center for Applied Biomedical Research (C.R.B.A.) , S. Orsola-Malpighi Hospital , Bologna , Italy
| | - Manuela Bartolini
- Department of Pharmacy and Biotechnology , Alma Mater Studiorum University of Bologna , Bologna , Italy
| | - Carlo Bertucci
- Department of Pharmacy and Biotechnology , Alma Mater Studiorum University of Bologna , Bologna , Italy
| | - Alberto Del Rio
- Institute of Organic Synthesis and Photoreactivity (ISOF) , National Research Council (CNR) , Bologna , Italy.,Innovamol Consulting Srl , Modena , Italy
| | - U Helena Danielson
- Department of Chemistry - BMC , Uppsala University , Uppsala , Sweden.,Science for Life Laboratory , Uppsala University , Uppsala , Sweden
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16
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Belfrage AK, Abdurakhmanov E, Åkerblom E, Brandt P, Alogheli H, Neyts J, Danielson UH, Sandström A. Pan-NS3 protease inhibitors of hepatitis C virus based on an R3-elongated pyrazinone scaffold. Eur J Med Chem 2018; 148:453-464. [DOI: 10.1016/j.ejmech.2018.02.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 01/20/2018] [Accepted: 02/10/2018] [Indexed: 02/07/2023]
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17
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Linkuvienė V, Talibov VO, Danielson UH, Matulis D. Introduction of Intrinsic Kinetics of Protein–Ligand Interactions and Their Implications for Drug Design. J Med Chem 2018; 61:2292-2302. [DOI: 10.1021/acs.jmedchem.7b01408] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, Vilnius, LT-10257, Lithuania
| | - Vladimir O. Talibov
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, SE-751 23, Sweden
| | - U. Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, SE-751 23, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, SE-751 23, Sweden
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, Vilnius, LT-10257, Lithuania
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18
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Solbak SMØ, Abdurakhmanov E, Vedeler A, Danielson UH. Characterization of interactions between hepatitis C virus NS5B polymerase, annexin A2 and RNA - effects on NS5B catalysis and allosteric inhibition. Virol J 2017; 14:236. [PMID: 29228983 PMCID: PMC5725786 DOI: 10.1186/s12985-017-0904-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/27/2017] [Indexed: 12/12/2022] Open
Abstract
Background Direct acting antivirals (DAAs) provide efficient hepatitis C virus (HCV) therapy and clearance for a majority of patients, but are not available or effective for all patients. They risk developing HCV-induced hepatocellular carcinoma (HCC), for which the mechanism remains obscure and therapy is missing. Annexin A2 (AnxA2) has been reported to co-precipitate with the non-structural (NS) HCV proteins NS5B and NS3/NS4A, indicating a role in HCC tumorigenesis and effect on DAA therapy. Methods Surface plasmon resonance biosensor technology was used to characterize direct interactions between AnxA2 and HCV NS5B, NS3/NS4 and RNA, and the subsequent effects on catalysis and inhibition. Results No direct interaction between AnxA2 and NS3/NS4A was detected, while AnxA2 formed a slowly dissociating, high affinity (KD = 30 nM), complex with NS5B, decreasing its catalytic activity and affinity for the allosteric inhibitor filibuvir. The RNA binding of the two proteins was independent and AnxA2 and NS5B interacted with different RNAs in ternary complexes of AnxA2:NS5B:RNA, indicating specific preferences. Conclusions The complex interplay revealed between NS5B, AnxA2, RNA and filibuvir, suggests that AnxA2 may have an important role for the progression and treatment of HCV infections and the development of HCC, which should be considered also when designing new allosteric inhibitors. Electronic supplementary material The online version of this article (10.1186/s12985-017-0904-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara M Ø Solbak
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | - Anni Vedeler
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden. .,Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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19
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Nosrati M, Solbak S, Nordesjö O, Nissbeck M, Dourado DFAR, Andersson KG, Housaindokht MR, Löfblom J, Virtanen A, Danielson UH, Flores SC. Insights from engineering the Affibody-Fc interaction with a computational-experimental method. Protein Eng Des Sel 2017; 30:593-601. [DOI: 10.1093/protein/gzx023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/12/2017] [Indexed: 01/25/2023] Open
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20
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Seeger C, Talibov VO, Danielson UH. Biophysical analysis of the dynamics of calmodulin interactions with neurogranin and Ca 2+ /calmodulin-dependent kinase II. J Mol Recognit 2017; 30. [PMID: 28449373 PMCID: PMC5518211 DOI: 10.1002/jmr.2621] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/26/2016] [Accepted: 02/06/2017] [Indexed: 01/17/2023]
Abstract
Calmodulin (CaM) functions depend on interactions with CaM‐binding proteins, regulated by
Ca2+. Induced structural changes influence the affinity, kinetics, and specificities of the interactions. The dynamics of CaM interactions with neurogranin (Ng) and the CaM‐binding region of
Ca2+/calmodulin‐dependent kinase II (CaMKII290−309) have been studied using biophysical methods. These proteins have opposite
Ca2+ dependencies for CaM binding. Surface plasmon resonance biosensor analysis confirmed that
Ca2+ and CaM interact very rapidly, and with moderate affinity (
KDSPR=3μM). Calmodulin‐CaMKII290−309 interactions were only detected in the presence of
Ca2+, exhibiting fast kinetics and nanomolar affinity (
KDSPR=7.1nM). The CaM–Ng interaction had higher affinity under
Ca2+‐depleted (
KDSPR=480nM,k1=3.4×105M−1s−1 and k−1 = 1.6 × 10−1s−1) than
Ca2+‐saturated conditions (
KDSPR=19μM). The IQ motif of Ng (Ng27−50) had similar affinity for CaM as Ng under
Ca2+‐saturated conditions (
KDSPR=14μM), but no interaction was seen under
Ca2+‐depleted conditions. Microscale thermophoresis using fluorescently labeled CaM confirmed the surface plasmon resonance results qualitatively, but estimated lower affinities for the Ng (
KDMST=890nM) and CaMKII290−309(
KDMST=190nM) interactions. Although CaMKII290−309 showed expected interaction characteristics, they may be different for full‐length CaMKII. The data for full‐length Ng, but not Ng27−50, agree with the current model on Ng regulation of
Ca2+/CaM signaling.
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Affiliation(s)
- Christian Seeger
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.,Beactica AB, Uppsala, Sweden
| | | | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.,Beactica AB, Uppsala, Sweden.,Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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21
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Saupe F, Reichel M, Huijbers EJM, Femel J, Markgren PO, Andersson CE, Deindl S, Danielson UH, Hellman LT, Olsson AK. Development of a novel therapeutic vaccine carrier that sustains high antibody titers against several targets simultaneously. FASEB J 2016; 31:1204-1214. [PMID: 27993994 DOI: 10.1096/fj.201600820r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 12/06/2016] [Indexed: 01/10/2023]
Abstract
With the aim to improve the efficacy of therapeutic vaccines that target self-antigens, we have developed a novel fusion protein vaccine on the basis of the C-terminal multimerizing end of the variable lymphocyte receptor B (VLRB), the Ig equivalent in jawless fishes. Recombinant vaccines were produced in Escherichia coli by fusing the VLRB sequence to 4 different cancer-associated target molecules. The anti-self-immune response generated in mice that were vaccinated with VLRB vaccines was compared with the response in mice that received vaccines that contained bacterial thioredoxin (TRX), previously identified as an efficient carrier. The anti-self-Abs were analyzed with respect to titers, binding properties, and duration of response. VLRB-vaccinated mice displayed a 2- to 10-fold increase in anti-self-Ab titers and a substantial decrease in Abs against the foreign part of the fusion protein compared with the response in TRX-vaccinated mice (P < 0.01). VLRB-generated Ab response had duration similar to the corresponding TRX-generated Abs, but displayed a higher diversity in binding characteristics. Of importance, VLRB vaccines could sustain an immune response against several targets simultaneously. VLRB vaccines fulfill several key criteria for an efficient therapeutic vaccine that targets self-antigens as a result of its small size, its multimerizing capacity, and nonexposed foreign sequences in the fusion protein.-Saupe, F., Reichel, M., Huijbers, E. J. M., Femel, J., Markgren, P.-O., Andersson, C. E., Deindl, S., Danielson, U. H., Hellman, L. T., Olsson, A.-K. Development of a novel therapeutic vaccine carrier that sustains high antibody titers against several targets simultaneously.
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Affiliation(s)
- Falk Saupe
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Matthias Reichel
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elisabeth J M Huijbers
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Julia Femel
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per-Olof Markgren
- Department of Chemistry-BMC, Biomedical Center, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - C Evalena Andersson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - U Helena Danielson
- Department of Chemistry-BMC, Biomedical Center, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars T Hellman
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna-Karin Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden;
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22
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Renaud JP, Chung CW, Danielson UH, Egner U, Hennig M, Hubbard RE, Nar H. Biophysics in drug discovery: impact, challenges and opportunities. Nat Rev Drug Discov 2016; 15:679-98. [PMID: 27516170 DOI: 10.1038/nrd.2016.123] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past 25 years, biophysical technologies such as X-ray crystallography, nuclear magnetic resonance spectroscopy, surface plasmon resonance spectroscopy and isothermal titration calorimetry have become key components of drug discovery platforms in many pharmaceutical companies and academic laboratories. There have been great improvements in the speed, sensitivity and range of possible measurements, providing high-resolution mechanistic, kinetic, thermodynamic and structural information on compound-target interactions. This Review provides a framework to understand this evolution by describing the key biophysical methods, the information they can provide and the ways in which they can be applied at different stages of the drug discovery process. We also discuss the challenges for current technologies and future opportunities to use biophysical methods to solve drug discovery problems.
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Affiliation(s)
- Jean-Paul Renaud
- NovAliX, Boulevard Sébastien Brant, 67405 Illkirch Cedex, France.,Institut de Génétique et Biologie Moléculaire et Cellulaire, CNRS UMR7104/INSERM U964/Université de Strasbourg, 1 rue Laurent Fries - BP10142, 67404 Illkirch Cedex, France.,RiboStruct, 15 rue Neuve, 67540 Ostwald, France
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - U Helena Danielson
- Department of Chemistry - BMC and Science for Life Laboratory, Drug Discovery &Development Platform, Uppsala University, SE-751 05 Uppsala, Sweden.,Beactica AB, Uppsala Business Park, 754 50 Uppsala, Sweden
| | - Ursula Egner
- Bayer Pharma AG, Müllerstrasse 178, 13353 Berlin, Germany
| | - Michael Hennig
- Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland.,leadXpro AG, PARK INNOVAARE, CH-5234 Villigen, Switzerland
| | - Roderick E Hubbard
- University of York, Heslington, York, YO10 5DD, UK.,Vernalis (R&D), Granta Park, Cambridge, CB21 6GB, UK
| | - Herbert Nar
- Boehringer Ingelheim GmbH &Co. KG, Birkendorfer Strasse 65, 88400 Biberach, Germany
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23
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Belfrage AK, Abdurakhmanov E, Kerblom E, Brandt P, Oshalim A, Gising J, Skogh A, Neyts J, Danielson UH, Sandström A. Discovery of pyrazinone based compounds that potently inhibit the drug-resistant enzyme variant R155K of the hepatitis C virus NS3 protease. Bioorg Med Chem 2016; 24:2603-20. [PMID: 27160057 DOI: 10.1016/j.bmc.2016.03.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 01/15/2023]
Abstract
Herein, we present the design and synthesis of 2(1H)-pyrazinone based HCV NS3 protease inhibitors with variations in the C-terminus. Biochemical evaluation was performed using genotype 1a, both the wild-type and the drug resistant enzyme variant, R155K. Surprisingly, compounds without an acidic sulfonamide retained good inhibition, challenging our previous molecular docking model. Moreover, selected compounds in this series showed nanomolar potency against R155K NS3 protease; which generally confer resistance to all HCV NS3 protease inhibitors approved or in clinical trials. These results further strengthen the potential of this novel substance class, being very different to the approved drugs and clinical candidates, in the development of inhibitors less sensitive to drug resistance.
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Affiliation(s)
- Anna Karin Belfrage
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, Box 574, SE-75123 Uppsala, Sweden
| | - Eldar Abdurakhmanov
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - Eva Kerblom
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, Box 574, SE-75123 Uppsala, Sweden
| | - Peter Brandt
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, Box 574, SE-75123 Uppsala, Sweden
| | - Anna Oshalim
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, Box 574, SE-75123 Uppsala, Sweden
| | - Johan Gising
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, Box 574, SE-75123 Uppsala, Sweden
| | - Anna Skogh
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, Box 574, SE-75123 Uppsala, Sweden
| | - Johan Neyts
- Rega Institute, Department of Microbiology and Immunology, University of Leuven, B-3000 Leuven, Belgium
| | - U Helena Danielson
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - Anja Sandström
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, Box 574, SE-75123 Uppsala, Sweden.
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24
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Talibov VO, Linkuvienė V, Matulis D, Danielson UH. Kinetically Selective Inhibitors of Human Carbonic Anhydrase Isozymes I, II, VII, IX, XII, and XIII. J Med Chem 2016; 59:2083-93. [PMID: 26805033 DOI: 10.1021/acs.jmedchem.5b01723] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
To get a better understanding of the possibility of developing selective carbonic anhydrase (CA) inhibitors, interactions between 17 benzenesulphonamide ligands and 6 human CAs (full-length CA I, II, VII, and XIII and catalytic domains of CA IX and XII) were characterized using surface plasmon resonance and fluorescent-based thermal shift assays. Kinetics revealed that the strongest binders had subnanomolar affinities with low dissociation rates (i.e., kd values around 1 × 10(-3) s(-1)) or were essentially irreversible. Chemodynamic analysis of the interactions highlighted an intrinsic mechanism of the CA-sulphonamide interaction kinetics and showed that slow dissociation rates were mediated by large hydrophobic contacts. The studied inhibitors demonstrated a high cross-reactivity within the protein family. However, according to chemical phylogenetic analysis developed for kinetic data, several ligands were found to be selective against certain CA isozymes, indicating that it should be possible to develop selective CA inhibitors suitable for clinical use.
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Affiliation(s)
- Vladimir O Talibov
- Department of Chemistry - BMC, Uppsala University , Box 576, Uppsala SE-751 23, Sweden
| | - Vaida Linkuvienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University , V.A. Graičiu̅no 8, Vilnius LT-02241, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University , V.A. Graičiu̅no 8, Vilnius LT-02241, Lithuania
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University , Box 576, Uppsala SE-751 23, Sweden.,Science for Life Laboratory, Uppsala University , Uppsala SE-751 23, Sweden
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25
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Huang HH, Seeger C, Danielson UH, Lindblad P. Analysis of the leakage of gene repression by an artificial TetR-regulated promoter in cyanobacteria. BMC Res Notes 2015; 8:459. [PMID: 26387086 PMCID: PMC4575469 DOI: 10.1186/s13104-015-1425-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 09/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is a need for strong and tightly regulated promoters to construct more reliable and predictable genetic modules for synthetic biology and metabolic engineering. For this reason we have previously constructed a TetR regulated L promoter library for the cyanobacterium Synechocystis PCC 6803. In addition to the L03 promoter showing wide dynamic range of transcriptional regulation, we observed the L09 promoter as unique in high leaky gene expression under repressed conditions. In the present study, we attempted to identify the cause of L09 promoter leakage. TetR binding to the promoter was studied by theoretical simulations of DNA breathing dynamics and by surface plasmon resonance (SPR) biosensor technology to analyze the kinetics of the DNA-protein interactions. RESULTS DNA breathing dynamics of a promoter was computed with the extended nonlinear Peyrard-Bishop-Dauxois mesoscopic model to yield a DNA opening probability profile at a single nucleotide resolution. The L09 promoter was compared to the L10, L11, and L12 promoters that were point-mutated and different in repressed promoter strength. The difference between DNA opening probability profiles is trivial on the TetR binding site. Furthermore, the kinetic rate constants of TetR binding, as measured by SPR biosensor technology, to the respective promoters are practically identical. This suggests that a trivial difference in probability as low as 1 × 10(-4) cannot lead to detectable variations in the DNA-protein interactions. Higher probability at the downstream region of transcription start site of the L09 promoter compared to the L10, L11, and L12 promoters was observed. Having practically the same kinetics of binding to TetR, the leakage problem of the L09 promoter might be due to enhanced RNA Polymerase (RNAP)-promoter interactions in the downstream region. CONCLUSIONS Both theoretical and experimental analyses of the L09 promoter's leakage problem exclude a mechanism of reduced TetR binding but instead suggest enhanced RNAP binding. These results assist in creating more tightly regulated promoters for realizing synthetic biology and metabolic engineering in biotechnological applications.
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Affiliation(s)
- Hsin-Ho Huang
- Department of Chemistry - Ångström, Science for Life Laboratory, Microbial Chemistry, Uppsala University, P.O. Box 523, 751 20, Uppsala, Sweden.
| | - Christian Seeger
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, 751 23, Uppsala, Sweden.
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, 751 23, Uppsala, Sweden.
| | - Peter Lindblad
- Department of Chemistry - Ångström, Science for Life Laboratory, Microbial Chemistry, Uppsala University, P.O. Box 523, 751 20, Uppsala, Sweden.
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26
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Anscombe E, Meschini E, Mora-Vidal R, Martin MP, Staunton D, Geitmann M, Danielson UH, Stanley WA, Wang LZ, Reuillon T, Golding BT, Cano C, Newell DR, Noble MEM, Wedge SR, Endicott JA, Griffin RJ. Identification and Characterization of an Irreversible Inhibitor of CDK2. Chem Biol 2015; 22:1159-64. [PMID: 26320860 PMCID: PMC4579270 DOI: 10.1016/j.chembiol.2015.07.018] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/02/2015] [Accepted: 07/24/2015] [Indexed: 01/04/2023]
Abstract
Irreversible inhibitors that modify cysteine or lysine residues within a protein kinase ATP binding site offer, through their distinctive mode of action, an alternative to ATP-competitive agents. 4-((6-(Cyclohexylmethoxy)-9H-purin-2-yl)amino)benzenesulfonamide (NU6102) is a potent and selective ATP-competitive inhibitor of CDK2 in which the sulfonamide moiety is positioned close to a pair of lysine residues. Guided by the CDK2/NU6102 structure, we designed 6-(cyclohexylmethoxy)-N-(4-(vinylsulfonyl)phenyl)-9H-purin-2-amine (NU6300), which binds covalently to CDK2 as shown by a co-complex crystal structure. Acute incubation with NU6300 produced a durable inhibition of Rb phosphorylation in SKUT-1B cells, consistent with it acting as an irreversible CDK2 inhibitor. NU6300 is the first covalent CDK2 inhibitor to be described, and illustrates the potential of vinyl sulfones for the design of more potent and selective compounds.
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Affiliation(s)
- Elizabeth Anscombe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Elisa Meschini
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Regina Mora-Vidal
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Mathew P Martin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - David Staunton
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - U Helena Danielson
- Beactica AB, Box 567, 751 22 Uppsala, Sweden; Department of Chemistry-BMC, Uppsala University, 751 23 Uppsala, Sweden
| | - Will A Stanley
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Lan Z Wang
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Tristan Reuillon
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Bernard T Golding
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - Celine Cano
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - David R Newell
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Martin E M Noble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Stephen R Wedge
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Roger J Griffin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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27
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Koos B, Cane G, Grannas K, Löf L, Arngården L, Heldin J, Clausson CM, Klaesson A, Hirvonen MK, de Oliveira FMS, Talibov VO, Pham NT, Auer M, Danielson UH, Haybaeck J, Kamali-Moghaddam M, Söderberg O. Proximity-dependent initiation of hybridization chain reaction. Nat Commun 2015; 6:7294. [PMID: 26065580 PMCID: PMC4490387 DOI: 10.1038/ncomms8294] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/24/2015] [Indexed: 11/09/2022] Open
Abstract
Sensitive detection of protein interactions and post-translational modifications of native proteins is a challenge for research and diagnostic purposes. A method for this, which could be used in point-of-care devices and high-throughput screening, should be reliable, cost effective and robust. To achieve this, here we design a method (proxHCR) that combines the need for proximal binding with hybridization chain reaction (HCR) for signal amplification. When two oligonucleotide hairpins conjugated to antibodies bind in close proximity, they can be activated to reveal an initiator sequence. This starts a chain reaction of hybridization events between a pair of fluorophore-labelled oligonucleotide hairpins, generating a fluorescent product. In conclusion, we show the applicability of the proxHCR method for the detection of protein interactions and posttranslational modifications in microscopy and flow cytometry. As no enzymes are needed, proxHCR may be an inexpensive and robust alternative to proximity ligation assays. Proximity ligation assays are a sensitive method for detecting protein interactions, but require the addition of enzymes. Here the authors introduce proxHCR, an enzyme-free method of detecting interactions in close proximity by inducing a hybribization chain reaction (HCR) of fluorescently labelled oligonucleotides.
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Affiliation(s)
- Björn Koos
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Gaëlle Cane
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Karin Grannas
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Liza Löf
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Linda Arngården
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Johan Heldin
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Carl-Magnus Clausson
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Axel Klaesson
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - M Karoliina Hirvonen
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Felipe M S de Oliveira
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Vladimir O Talibov
- Department of Chemistry-BMC, Box 256, Uppsala University, SE-75123 Uppsala, Sweden
| | - Nhan T Pham
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, C H Waddington Building, Max Born Cresent, Kings Buildings, Edinburgh EH9 3BF, UK
| | - Manfred Auer
- School of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, C H Waddington Building, Max Born Cresent, Kings Buildings, Edinburgh EH9 3BF, UK
| | - U Helena Danielson
- Department of Chemistry-BMC, Box 256, Uppsala University, SE-75123 Uppsala, Sweden
| | - Johannes Haybaeck
- Institute of Pathology, Medical University of Graz, A-8036 Graz, Austria
| | - Masood Kamali-Moghaddam
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
| | - Ola Söderberg
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical center, Husargatan 3, Box 815, SE-75108 Uppsala, Sweden
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Spurny R, Debaveye S, Farinha A, Veys K, Vos AM, Gossas T, Atack J, Bertrand S, Bertrand D, Danielson UH, Tresadern G, Ulens C. Molecular blueprint of allosteric binding sites in a homologue of the agonist-binding domain of the α7 nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A 2015; 112:E2543-52. [PMID: 25918415 PMCID: PMC4434711 DOI: 10.1073/pnas.1418289112] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The α7 nicotinic acetylcholine receptor (nAChR) belongs to the family of pentameric ligand-gated ion channels and is involved in fast synaptic signaling. In this study, we take advantage of a recently identified chimera of the extracellular domain of the native α7 nicotinic acetylcholine receptor and acetylcholine binding protein, termed α7-AChBP. This chimeric receptor was used to conduct an innovative fragment-library screening in combination with X-ray crystallography to identify allosteric binding sites. One allosteric site is surface-exposed and is located near the N-terminal α-helix of the extracellular domain. Ligand binding at this site causes a conformational change of the α-helix as the fragment wedges between the α-helix and a loop homologous to the main immunogenic region of the muscle α1 subunit. A second site is located in the vestibule of the receptor, in a preexisting intrasubunit pocket opposite the agonist binding site and corresponds to a previously identified site involved in positive allosteric modulation of the bacterial homolog ELIC. A third site is located at a pocket right below the agonist binding site. Using electrophysiological recordings on the human α7 nAChR we demonstrate that the identified fragments, which bind at these sites, can modulate receptor activation. This work presents a structural framework for different allosteric binding sites in the α7 nAChR and paves the way for future development of novel allosteric modulators with therapeutic potential.
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Affiliation(s)
- Radovan Spurny
- Laboratory of Structural Neurobiology, Katholieke Universiteit Leuven, Leuven B-3000, Belgium
| | - Sarah Debaveye
- Laboratory of Structural Neurobiology, Katholieke Universiteit Leuven, Leuven B-3000, Belgium
| | - Ana Farinha
- Laboratory of Structural Neurobiology, Katholieke Universiteit Leuven, Leuven B-3000, Belgium
| | | | - Ann M Vos
- Discovery Sciences, Janssen Research and Development, Beerse B-2340, Belgium
| | | | - John Atack
- Translational Drug Discovery Group, University of Sussex, BN1 9QJ Brighton, United Kingdom
| | | | | | - U Helena Danielson
- Beactica AB, SE-752 37 Uppsala, Sweden; Department of Chemistry, Uppsala Biomedical Center, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Gary Tresadern
- Discovery Sciences, Janssen Research and Development, Beerse B-2340, Belgium
| | - Chris Ulens
- Laboratory of Structural Neurobiology, Katholieke Universiteit Leuven, Leuven B-3000, Belgium;
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29
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Lampa A, Alogheli H, Ehrenberg AE, Åkerblom E, Svensson R, Artursson P, Danielson UH, Karlén A, Sandström A. Vinylated linear P2 pyrimidinyloxyphenylglycine based inhibitors of the HCV NS3/4A protease and corresponding macrocycles. Bioorg Med Chem 2014; 22:6595-6615. [PMID: 25456385 DOI: 10.1016/j.bmc.2014.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/04/2014] [Accepted: 10/09/2014] [Indexed: 10/24/2022]
Abstract
With three recent market approvals and several inhibitors in advanced stages of development, the hepatitis C virus (HCV) NS3/4A protease represents a successful target for antiviral therapy against hepatitis C. As a consequence of dealing with viral diseases in general, there are concerns related to the emergence of drug resistant strains which calls for development of inhibitors with an alternative binding-mode than the existing highly optimized ones. We have previously reported on the use of phenylglycine as an alternative P2 residue in HCV NS3/4A protease inhibitors. Herein, we present the synthesis, structure-activity relationships and in vitro pharmacokinetic characterization of a diverse series of linear and macrocyclic P2 pyrimidinyloxyphenylglycine based inhibitors. With access to vinyl substituents in P3, P2 and P1' positions an initial probing of macrocyclization between different positions, using ring-closing metathesis (RCM) could be performed, after addressing some synthetic challenges. Biochemical results from the wild type enzyme and drug resistant variants (e.g., R155 K) indicate that P3-P1' macrocyclization, leaving the P2 substituent in a flexible mode, is a promising approach. Additionally, the study demonstrates that phenylglycine based inhibitors benefit from p-phenylpyrimidinyloxy and m-vinyl groups as well as from the combination with an aromatic P1 motif with alkenylic P1' elongations. In fact, linear P2-P1' spanning intermediate compounds based on these fragments were found to display promising inhibitory potencies and drug like properties.
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Affiliation(s)
- Anna Lampa
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Hiba Alogheli
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Angelica E Ehrenberg
- Department of Chemistry-BMC, Uppsala University, BMC, Box 576, SE-751 23 Uppsala, Sweden
| | - Eva Åkerblom
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Richard Svensson
- Department of Pharmacy, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden; The Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Uppsala University, A Node of the Chemical Biology Consortium Sweden (CBCS), Box 580, SE-751 23 Uppsala, Sweden
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden; The Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Uppsala University, A Node of the Chemical Biology Consortium Sweden (CBCS), Box 580, SE-751 23 Uppsala, Sweden
| | - U Helena Danielson
- Department of Chemistry-BMC, Uppsala University, BMC, Box 576, SE-751 23 Uppsala, Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Anja Sandström
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden.
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Lampa AK, Bergman SM, Gustafsson SS, Alogheli H, Åkerblom EB, Lindeberg GG, Svensson RM, Artursson P, Danielson UH, Karlén A, Sandström A. Novel Peptidomimetic Hepatitis C Virus NS3/4A Protease Inhibitors Spanning the P2-P1' Region. ACS Med Chem Lett 2014; 5:249-54. [PMID: 24900813 DOI: 10.1021/ml400217r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/02/2013] [Indexed: 02/06/2023] Open
Abstract
Herein, novel hepatitis C virus NS3/4A protease inhibitors based on a P2 pyrimidinyloxyphenylglycine in combination with various regioisomers of an aryl acyl sulfonamide functionality in P1 are presented. The P1' 4-(trifluoromethyl)phenyl side chain was shown to be particularly beneficial in terms of inhibitory potency. Several inhibitors with K i-values in the nanomolar range were developed and included identification of promising P3-truncated inhibitors spanning from P2-P1'. Of several different P2 capping groups that were evaluated, a preference for the sterically congested Boc group was revealed. The inhibitors were found to retain inhibitory potencies for A156T, D168V, and R155K variants of the protease. Furthermore, in vitro pharmacokinetic profiling showed several beneficial effects on metabolic stability as well as on apparent intestinal permeability from both P3 truncation and the use of the P1' 4-(trifluoromethyl)phenyl side chain.
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Affiliation(s)
- Anna K. Lampa
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Sara M. Bergman
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Sofia S. Gustafsson
- Department of Chemistry−BMC, Uppsala University, BMC, Box 576, SE-751 23 Uppsala,
Sweden
| | - Hiba Alogheli
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Eva B. Åkerblom
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Gunnar G. Lindeberg
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Richard M. Svensson
- Department of Pharmacy, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden
- The Uppsala University Drug
Optimization and Pharmaceutical Profiling Platform, Uppsala University, a Node of the Chemical Biology Consortium
Sweden (CBCS), Box 580, SE-751 23 Uppsala, Sweden
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden
- The Uppsala University Drug
Optimization and Pharmaceutical Profiling Platform, Uppsala University, a Node of the Chemical Biology Consortium
Sweden (CBCS), Box 580, SE-751 23 Uppsala, Sweden
| | - U. Helena Danielson
- Department of Chemistry−BMC, Uppsala University, BMC, Box 576, SE-751 23 Uppsala,
Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
| | - Anja Sandström
- Department of Medicinal Chemistry,
Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
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Svahn Gustafsson S, Ehrenberg A, Schmuck B, Anwar MI, Danielson UH. Identification of weak points of hepatitis C virus NS3 protease inhibitors using surface plasmon resonance biosensor-based interaction kinetic analysis and genetic variants. J Med Chem 2014; 57:1802-11. [PMID: 24512311 DOI: 10.1021/jm401690f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To aid the design of next generation hepatitis C virus (HCV) drugs, the kinetics of the interactions between NS3 protease inhibitors and enzyme from genotypes 1a, 1b, and 3a have been characterized. The linear mechanism-based inhibitors VX-950 (telaprevir) and SCH 503034 (boceprevir) benefited from covalent adduct formation. However, the apparent affinities were rather weak (VX-950, K(D)* of 340, 8.5, and 1000 nM for genotypes 1a, 1b and 3a, respectively; SCH 503034, K(D)* of 90 and 3.9 nM for 1b and 3a, respectively). The non-mechanism-based macrocyclic inhibitors BILN-2016 (ciluprevir) and ITMN-191 (danoprevir) had faster association and slower dissociation kinetics, indicating that rigidification is kinetically favorable. ITMN-191 had nanomolar affinities for all genotypes (K(D)* of 0.13, 1.6, and 0.52 nM), suggesting that a broad spectrum drug is conceivable. The data show that macrocyclic scaffolds and mechanism-based inhibition are advantageous but that there is considerable room for improvement of the kinetics of HCV protease targeted drugs.
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Ehrenberg AE, Schmuck B, Anwar MI, Gustafsson SS, Stenberg G, Danielson UH. Accounting for strain variations and resistance mutations in the characterization of hepatitis C NS3 protease inhibitors. J Enzyme Inhib Med Chem 2014; 29:868-76. [PMID: 24517372 DOI: 10.3109/14756366.2013.864651] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
CONTEXT Natural strain variation and rapid resistance development makes development of broad spectrum hepatitis C virus (HCV) drugs very challenging and evaluation of inhibitor selectivity and resistance must account for differences in the catalytic properties of enzyme variants. OBJECTIVE To understand how to study selectivity and relationships between efficacy and genotype or resistant mutants for NS3 protease inhibitors. MATERIALS AND METHODS The catalytic properties of NS3 protease from genotypes 1a, 1b and 3a, and their sensitivities to four structurally and mechanistically different NS3 protease inhibitors have been analysed under different experimental conditions. RESULTS The optimisation of buffer conditions for each protease variant enabled the comparison of their catalytic properties and sensitivities to the inhibitors. All inhibitors were most effective against genotype 1a protease, with VX-950 having the broadest selectivity. DISCUSSION AND CONCLUSION A new strategy for evaluation of inhibitors relevant for the discovery of broad spectrum HCV drugs was established.
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Sussman F, Villaverde MC, Domínguez JL, Danielson UH. On the active site protonation state in aspartic proteases: implications for drug design. Curr Pharm Des 2013; 19:4257-75. [PMID: 23170891 DOI: 10.2174/1381612811319230009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 11/19/2012] [Indexed: 11/22/2022]
Abstract
Aspartic proteases (AP) are a family of important hydrolytic enzymes in medicinal chemistry, since many of its members have become therapeutical targets for a wide variety of diseases from AIDS to Alzheimer. The enzymatic activity of these proteins is driven by the Asp dyad, a pair of active site Asp residues that participate in the hydrolysis of peptides. Hence, the protonation state of these and other acidic residues present in these enzymes determines the catalytic rate and the affinity for an inhibitor at a given pH. In the present work we have reviewed the effect of the protonation states of the titratable residues in AP's both on catalysis and inhibition in this family of enzymes. The first section focuses on the details of the catalytic reaction mechanism picture brought about by a large number of kinetic, crystallographic and computational chemistry analyses. The results indicate that although the mechanism is similar in both retroviral and eukaryotic enzymes, there are some clear differences. For instance, while in the former family branch the binding of the substrate induces a mono-ionic charge state for the Asp dyad, this charge state seems to be already present in the unbound state of the eukaryotic enzymes. In this section we have explored as well the possible existence of low barrier hydrogen bonds (LBHB's) in the enzymatic path. Catalytic rate enhancement in AP's could in part be explained by the lowering of the barrier for proton transfer in a hydrogen bond from donor to acceptor, which is a typical feature of LBHB's. Review of the published work indicates that the experimental support for this type of bonds is rather scarce and it may be more probable in the first stages of the hydrolytic mechanism in retroviral proteases. The second section deals with the effect of active site protonation state on inhibitor binding. The design of highly potent AP inhibitors, that could be the basis for drug leads require a deep knowledge of the protonation state of the active site residues induced by their presence. This vital issue has been tackled by experimental techniques like NMR, X-ray crystallography, calorimetric and binding kinetic techniques. Recently, we have developed a protocol that combines monitoring the pH effect on binding affinities by SPR methods and rationalization of the results by molecular mechanics based calculations. We have used this combined method on BACE-1 and HIV-1 PR, two important therapeutic targets. Our calculations are able to reproduce the inhibitor binding trends to either enzyme upon a pH increase. The results indicate that inhibitors that differ in the Asp dyad binding fragments will present different binding affinity trends upon a pH increase. Our calculations have enabled us to predict the protonation states at different pH values that underlie the above mentioned trends. We have found out that these results have many implications not only for in silico hit screening campaigns aimed at finding high affinity binders, but also (in the case of BACE-1) for the discovery of cell active compounds.
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Affiliation(s)
- Fredy Sussman
- Departamento de Quimica Organica, Facultad de Quimica, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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Manfroni G, Cannalire R, Barreca ML, Kaushik-Basu N, Leyssen P, Winquist J, Iraci N, Manvar D, Paeshuyse J, Guhamazumder R, Basu A, Sabatini S, Tabarrini O, Danielson UH, Neyts J, Cecchetti V. The versatile nature of the 6-aminoquinolone scaffold: identification of submicromolar hepatitis C virus NS5B inhibitors. J Med Chem 2013; 57:1952-63. [PMID: 24131104 DOI: 10.1021/jm401362f] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have previously reported that the 6-aminoquinolone chemotype is a privileged scaffold to obtain antibacterial and antiviral agents. Herein we describe the design, synthesis, and enzymatic and cellular characterization of new 6-aminoquinolone derivatives as potent inhibitors of NS5B polymerase, an attractive and viable therapeutic target to develop safe anti-HCV agents. The 6-amino-7-[4-(2-pyridinyl)-1-piperazinyl]quinolone derivative 8 proved to be the best compound of this series, exhibiting an IC50 value of 0.069 μM against NS5B polymerase and selective antiviral effect (EC50 = 3.03 μM) coupled with the absence of any cytostatic effect (CC50 > 163 μM; SI > 54) in Huh 9-13 cells carrying a HCV genotype 1b, as measured by MTS assay. These results indicate that the 6-aminoquinolone scaffold is worthy of further investigation in the context of NS5B-targeted HCV drug discovery programs.
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Affiliation(s)
- Giuseppe Manfroni
- Dipartimento di Chimica e Tecnologia del Farmaco, Università degli Studi di Perugia , Via del Liceo 1, 06123 Perugia, Italy
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Gising J, Belfrage AK, Alogheli H, Ehrenberg A, Åkerblom E, Svensson R, Artursson P, Karlén A, Danielson UH, Larhed M, Sandström A. Achiral pyrazinone-based inhibitors of the hepatitis C virus NS3 protease and drug-resistant variants with elongated substituents directed toward the S2 pocket. J Med Chem 2013; 57:1790-801. [PMID: 23517538 DOI: 10.1021/jm301887f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Herein we describe the design, synthesis, inhibitory potency, and pharmacokinetic properties of a novel class of achiral peptidomimetic HCV NS3 protease inhibitors. The compounds are based on a dipeptidomimetic pyrazinone glycine P3P2 building block in combination with an aromatic acyl sulfonamide in the P1P1' position. Structure-activity relationship data and molecular modeling support occupancy of the S2 pocket from elongated R(6) substituents on the 2(1H)-pyrazinone core and several inhibitors with improved inhibitory potency down to Ki = 0.11 μM were identified. A major goal with the design was to produce inhibitors structurally dissimilar to the di- and tripeptide-based HCV protease inhibitors in advanced stages of development for which cross-resistance might be an issue. Therefore, the retained and improved inhibitory potency against the drug-resistant variants A156T, D168V, and R155K further strengthen the potential of this class of inhibitors. A number of the inhibitors were tested in in vitro preclinical profiling assays to evaluate their apparent pharmacokinetic properties. The various R(6) substituents were found to have a major influence on solubility, metabolic stability, and cell permeability.
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Affiliation(s)
- Johan Gising
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden
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36
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Barreca ML, Manfroni G, Leyssen P, Winquist J, Kaushik-Basu N, Paeshuyse J, Krishnan R, Iraci N, Sabatini S, Tabarrini O, Basu A, Danielson UH, Neyts J, Cecchetti V. Structure-based discovery of pyrazolobenzothiazine derivatives as inhibitors of hepatitis C virus replication. J Med Chem 2013; 56:2270-82. [PMID: 23409936 DOI: 10.1021/jm301643a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The NS5B RNA-dependent RNA polymerase is an attractive target for the development of novel and selective inhibitors of hepatitis C virus replication. To identify novel structural hits as anti-HCV agents, we performed structure-based virtual screening of our in-house library followed by rational drug design, organic synthesis, and biological testing. These studies led to the identification of pyrazolobenzothiazine scaffold as a suitable template for obtaining novel anti-HCV agents targeting the NS5B polymerase. The best compound of this series was the meta-fluoro-N-1-phenyl pyrazolobenzothiazine derivative 4a, which exhibited an EC50 = 3.6 μM, EC90 = 25.6 μM, and CC50 > 180 μM in the Huh 9-13 replicon system, thus providing a good starting point for further hit evolution.
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Affiliation(s)
- Maria Letizia Barreca
- Dipartimento di Chimica e Tecnologia del Farmaco, Sezione di Chimica Farmaceutica II, Università degli Studi di Perugia, Via del Liceo 1, 06123 Perugia, Italy.
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Seeger C, Gorny X, Reddy PP, Seidenbecher C, Danielson UH. Kinetic and mechanistic differences in the interactions between caldendrin and calmodulin with AKAP79 suggest different roles in synaptic function. J Mol Recognit 2013; 25:495-503. [PMID: 22996592 DOI: 10.1002/jmr.2215] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The kinetic and mechanistic details of the interaction between caldendrin, calmodulin and the B-domain of AKAP79 were determined using a biosensor-based approach. Caldendrin was found to compete with calmodulin for binding at AKAP79, indicating overlapping binding sites. Although the AKAP79 affinities were similar for caldendrin (K(D) = 20 nM) and calmodulin (K(D) = 30 nM), their interaction characteristics were different. The calmodulin interaction was well described by a reversible one-step model, but was only detected in the presence of Ca(2+). Caldendrin interacted with a higher level of complexity, deduced to be an induced fit mechanism with a slow relaxation back to the initial encounter complex. It interacted with AKAP79 also in the absence of Ca(2+), but with different kinetic rate constants. The data are consistent with a similar initial Ca(2+)-dependent binding step for the two proteins. For caldendrin, a second Ca(2+)-independent rearrangement step follows, resulting in a stable complex. The study shows the importance of establishing the mechanism and kinetics of protein-protein interactions and that minor differences in the interaction of two homologous proteins can have major implications in their functional characteristics. These results are important for the further elucidation of the roles of caldendrin and calmodulin in synaptic function.
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38
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Winquist J, Geschwindner S, Xue Y, Gustavsson L, Musil D, Deinum J, Danielson UH. Identification of structural-kinetic and structural-thermodynamic relationships for thrombin inhibitors. Biochemistry 2013; 52:613-26. [PMID: 23290007 DOI: 10.1021/bi301333z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To improve our understanding of drug-target interactions, we explored the effect of introducing substituted amine residues with increased chain length in the P3 residue of the thrombin inhibitor melagatran. Inhibition, kinetic, and thermodynamic data obtained via stopped-flow spectroscopy (SF), isothermal microcalorimetry (ITC), and surface plasmon resonance (SPR) biosensor analysis were interpreted with the help of X-ray crystal structures of the enzyme-inhibitor complexes. The association rate became faster when the lipophilicity of the inhibitors was increased. This was coupled to an increased enthalpic component and a corresponding decreased entropic component. The dissociation rates were reduced with an increase in chain length, with only a smaller increase and a decrease in the enthalpic and entropic components, respectively. Overall, the affinity increased with an increase in chain length, with similar changes in the enthalpic and entropic components. ITC analysis confirmed the equilibrium data from SPR analysis, showing that the interaction of melagatran was the most enthalpy-driven interaction. Structural analysis of the thrombin-inhibitor complex showed that the orientation of the P1 and P2 parts of the molecules was very similar, but that there were significant differences in the interaction between the terminal part of the P3 side chain and the binding pocket. A combination of charge repulsion, H-bonds, and hydrophobic interactions could be used to explain the observed kinetic and thermodynamic profiles for the ligands. In conclusion, changes in the structure of a lead compound can have significant effects on its interaction with the target that translate directly into kinetic and thermodynamic effects. In contrast to what may be intuitively expected, hydrogen bond formation and breakage are not necessarily reflected in enthalpy gains and losses, respectively.
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Affiliation(s)
- Johan Winquist
- Department of Chemistry-BMC, Uppsala University, SE-751 23 Uppsala, Sweden
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Gossas T, Nordström H, Xu MH, Sun ZH, Lin GQ, Wallberg H, Danielson UH. The advantage of biosensor analysis over enzyme inhibition studies for slow dissociating inhibitors – characterization of hydroxamate-based matrix metalloproteinase-12 inhibitors. Med Chem Commun 2013. [DOI: 10.1039/c2md20268a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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40
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Seeger C, Christopeit T, Fuchs K, Grote K, Sieghart W, Danielson UH. Histaminergic pharmacology of homo-oligomeric β3 γ-aminobutyric acid type A receptors characterized by surface plasmon resonance biosensor technology. Biochem Pharmacol 2012; 84:341-51. [DOI: 10.1016/j.bcp.2012.04.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 04/01/2012] [Accepted: 04/09/2012] [Indexed: 12/12/2022]
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41
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Gorny X, Mikhaylova M, Seeger C, Reddy PP, Reissner C, Schott BH, Helena Danielson U, Kreutz MR, Seidenbecher C. AKAP79/150 interacts with the neuronal calcium-binding protein caldendrin. J Neurochem 2012; 122:714-26. [PMID: 22693956 DOI: 10.1111/j.1471-4159.2012.07828.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The A kinase-anchoring protein AKAP79/150 is a postsynaptic scaffold molecule and a key regulator of signaling events. At the postsynapse it coordinates phosphorylation and dephosphorylation of receptors via anchoring kinases and phosphatases near their substrates. Interactions between AKAP79 and two Ca(2+) -binding proteins caldendrin and calmodulin have been investigated here. Calmodulin is a known interaction partner of AKAP79/150 that has been shown to regulate activity of the kinase PKC in a Ca(2+) -dependent manner. Pull-down experiments and surface plasmon resonance biosensor analyses have been used here to demonstrate that AKAP79 can also interact with caldendrin, a neuronal calcium-binding protein implicated in regulation of Ca(2+) -influx and release. We demonstrate that calmodulin and caldendrin compete for a partially overlapping binding site on AKAP79 and that their binding is differentially dependent on calcium. Therefore, this competition is regulated by calcium levels. Moreover, both proteins have different binding characteristics suggesting that the two proteins might play complementary roles. The postsynaptic enrichment, the complex binding mechanism, and the competition with calmodulin, makes caldendrin an interesting novel player in the signaling toolkit of the AKAP interactome.
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Affiliation(s)
- Xenia Gorny
- Leibniz Institute for Neurobiology, Magdeburg, Germany
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Gossas T, Vrang L, Henderson I, Sedig S, Sahlberg C, Lindström E, Danielson UH. Aliskiren displays long-lasting interactions with human renin. Naunyn Schmiedebergs Arch Pharmacol 2011; 385:219-24. [PMID: 22193701 DOI: 10.1007/s00210-011-0718-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022]
Abstract
Aliskiren is a selective renin inhibitor recently approved for use in hypertension. Efficacy duration appears longer than what would be expected based on its circulating half-life. The aim was therefore to characterize the kinetics of the interaction between aliskiren and renin. The interaction was evaluated in three assays and compared with two other renin inhibitors including remikiren. First, the inhibition of recombinant human renin was assessed by monitoring the cleavage of fluorescent substrate. Second, human plasma renin activity (PRA) was monitored by measuring generated angiotensin I over 1 h in the presence or absence of inhibitor. Finally, the affinity, association and dissociation rate constants were determined by using a surface plasmon resonance (SPR) biosensor assay. Aliskiren and remikiren were found to be equipotent inhibitors of recombinant renin activity (K(i) ≤ 0.04 nM) while compound 1 displayed a K (i) value of 1 nM. PRA was efficiently inhibited by both aliskiren and remikiren with IC₅₀ values of 0.2-0.3 nM. Remikiren and aliskiren also displayed long-lasting interactions with immobilized renin having k (off) values of 0.18 and 0.11 × 10⁻³ s⁻¹ respectively. These dissociation rate constants corresponded to residence times of 1.5 and 2.5 h, respectively, while compound 1 had a residence time lasting only 3 min. It is therefore concluded that the long-lasting interaction between aliskiren and human renin may contribute to the 24 h anti-hypertensive effect seen in clinical trials and possibly also to target-mediated drug disposition.
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Affiliation(s)
- Thomas Gossas
- Department of Biochemistry and Organic Chemistry, BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
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Christopeit T, Stenberg G, Gossas T, Nyström S, Baraznenok V, Lindström E, Danielson UH. A surface plasmon resonance-based biosensor with full-length BACE1 in a reconstituted membrane. Anal Biochem 2011; 414:14-22. [PMID: 21382336 DOI: 10.1016/j.ab.2011.02.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 02/17/2011] [Accepted: 02/27/2011] [Indexed: 10/18/2022]
Abstract
A surface plasmon resonance (SPR) biosensor-based assay for membrane-embedded full-length BACE1 (β-site amyloid precursor protein cleaving enzyme 1), a drug target for Alzheimer's disease, has been developed. It allows the analysis of interactions with the protein in its natural lipid membrane environment. The enzyme was captured via an antibody recognizing a C-terminal His6 tag, after which a lipid membrane was reconstituted on the chip using a brain lipid extract. The interaction between the enzyme and several inhibitors confirmed that the surface was functional. It had slightly different interaction characteristics as compared with a reference surface with immobilized ectodomain BACE1 but had the same inhibitor characteristic pH effect. The possibility of studying interactions with BACE1 under more physiological conditions than assays using truncated enzyme or conditions dictated by high enzyme activity is expected to increase our understanding of the role of BACE1 in Alzheimer's disease and contribute to the discovery of clinically efficient BACE1 inhibitors. The strategy exploited in the current study can be adapted to other membrane-bound drug targets by selecting suitable capture antibodies and lipid mixtures for membrane reconstitution.
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Affiliation(s)
- Tony Christopeit
- Department of Biochemistry and Organic Chemistry, Uppsala University, Sweden
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Gustafsson SS, Vrang L, Terelius Y, Danielson UH. Quantification of interactions between drug leads and serum proteins by use of “binding efficiency”. Anal Biochem 2011; 409:163-75. [DOI: 10.1016/j.ab.2010.10.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 10/20/2010] [Accepted: 10/21/2010] [Indexed: 12/20/2022]
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Tegler LT, Nonglaton G, Büttner F, Caldwell K, Christopeit T, Danielson UH, Fromell K, Gossas T, Larsson A, Longati P, Norberg T, Ramapanicker R, Rydberg J, Baltzer L. Powerful protein binders from designed polypeptides and small organic molecules--a general concept for protein recognition. Angew Chem Int Ed Engl 2011; 50:1823-7. [PMID: 21328648 DOI: 10.1002/anie.201005059] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 12/12/2010] [Indexed: 11/07/2022]
Affiliation(s)
- Lotta T Tegler
- Department of Biochemistry and Organic Chemistry, Uppsala University, P.O. Box 576, 75123 Uppsala, Sweden
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Tegler LT, Nonglaton G, Büttner F, Caldwell K, Christopeit T, Danielson UH, Fromell K, Gossas T, Larsson A, Longati P, Norberg T, Ramapanicker R, Rydberg J, Baltzer L. Powerful Protein Binders from Designed Polypeptides and Small Organic Molecules-A General Concept for Protein Recognition. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Brandt P, Geitmann M, Danielson UH. Deconstruction of non-nucleoside reverse transcriptase inhibitors of human immunodeficiency virus type 1 for exploration of the optimization landscape of fragments. J Med Chem 2011; 54:709-18. [PMID: 21207958 DOI: 10.1021/jm101052g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This study has taken a closer look at the theoretical basis for protein-fragment interactions. The approach involved the deconstruction of 3 non-nucleoside inhibitors of HIV-1 reverse transcriptase and investigation of the interaction between 21 substructures and the enzyme. It focused on the concept of ligand efficiency and showed that ligand independent free energy fees (ΔG(ind)) are crucial for the understanding of the binding affinities of fragments. A value of 7.0 kcal mol(-1) for the ΔG(ind) term is shown to be a lower limit for the NNRTI binding pocket of HIV-1 RT. The addition of the ΔG(ind) term to the dissociation free energy in the calculation of a corrected ligand efficiency, in combination with the lack of an efficient ligand binding hot spot in the NNIBP, fully explains the existence of nonbinding NNRTI substructures. By applying the concept to a larger set of ligands, we could define a binding site profile that indicates the absence of an efficient fragment binding hot spot but an efficient binding of full-sized NNRTIs. The analysis explains some of the challenges in identifying fragments against flexible targets involving conformational changes and how fragments may be prioritized.
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Geitmann M, Elinder M, Seeger C, Brandt P, de Esch IJP, Danielson UH. Identification of a novel scaffold for allosteric inhibition of wild type and drug resistant HIV-1 reverse transcriptase by fragment library screening. J Med Chem 2011; 54:699-708. [PMID: 21207961 DOI: 10.1021/jm1010513] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A novel scaffold inhibiting wild type and drug resistant variants of human immunodeficiency virus type 1 reverse transcriptase (HIV-1RT) has been identified in a library consisting of 1040 fragments. The fragments were significantly different from already known non-nucleoside reverse transcriptase inhibitors (NNRTIs), as indicated by a Tversky similarity analysis. A screening strategy involving SPR biosensor-based interaction analysis and enzyme inhibition was used. Primary biosensor-based screening, using short concentration series, was followed by analysis of nevirapine competition and enzyme inhibition, thus identifying inhibitory fragments binding to the non-nucleoside reverse transcriptase inhibitor (NNRTI) binding site. Ten hits were discovered, and their affinities and resistance profiles were evaluated with wild type and three drug resistant enzyme variants (K103N, Y181C, and L100I). One fragment exhibited submillimolar K(D) and IC(50) values against all four tested enzyme variants. A substructure comparison between the fragment and 826 structurally diverse published NNRTIs confirmed that the scaffold was novel. The fragment is a bromoindanone with a ligand efficiency of 0.42 kcal/mol(-1).
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Elinder M, Geitmann M, Gossas T, Källblad P, Winquist J, Nordström H, Hämäläinen M, Danielson UH. Experimental Validation of a Fragment Library for Lead Discovery Using SPR Biosensor Technology. ACTA ACUST UNITED AC 2010; 16:15-25. [DOI: 10.1177/1087057110389038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A new fragment library for lead discovery has been designed and experimentally validated for use in surface plasmon resonance (SPR) biosensor-based screening. The 930 compounds in the library were selected from 4.6 million commercially available compounds using a series of physicochemical and medicinal chemistry filters. They were screened against 3 prototypical drug targets: HIV-1 protease, thrombin and carbonic anhydrase, and a nontarget: human serum albumin. Compound solubility was not a problem under the conditions used for screening. The high sensitivity of the sensor surfaces allowed the detection of interactions for 35% to 97% of the fragments, depending on the target protein. None of the fragments was promiscuous (i.e., interacted with a stoichiometry ≥5:1 with all 4 proteins), and only 2 compounds dissociated slowly from all 4 proteins. The use of several targets proved valuable since several compounds would have been disqualified from the library on the grounds of promiscuity if fewer target proteins had been used. The experimental procedure allowed an efficient evaluation and exploration of the new fragment library and confirmed that the new library is suitable for SPR biosensor-based screening.
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Affiliation(s)
- Malin Elinder
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
| | | | | | | | - Johan Winquist
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
| | - Helena Nordström
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
| | | | - U. Helena Danielson
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
- Beactica AB, Uppsala, Sweden
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Abstract
The transition from high throughput screening of collections of drug-like compounds to screening of fragment libraries via lower throughput methods with high sensitivity has revolutionized early drug discovery. It is highlighting the need for sensitive biophysical techniques for interaction analysis rather than high throughput methods. Biosensors with SPR detection are well suited for this novel scenario. In less than 20 years the technique has been launched, established and become a highly informative method for a variety of applications in drug discovery. It is no longer limited to the detection of proteins or other high molecular weight analytes, but the detection of weakly interacting fragments is now feasible. This paper discusses the theoretical and experimental limitations for such applications and reviews a number of successful studies in the area of fragment-based lead discovery that have recently been published. It can be anticipated that the evolution of this young technique will be significantly influenced by the requirements for efficient fragment-based lead discovery.
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Affiliation(s)
- U Helena Danielson
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden.
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