{"entity": "researcher", "timestamp": "2026-08-09T07:02:37.693Z", "family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "affiliations": ["Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden.", "SciLifeLab, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6"}}, "publications": [{"entity": "publication", "iuid": "85de2289fd19407dad34e21e261cb987", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85de2289fd19407dad34e21e261cb987.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85de2289fd19407dad34e21e261cb987"}}, "title": "Detection and characterisation of ligand-induced conformational changes in acetylcholine binding proteins using biosensors and X-ray crystallography.", "authors": [{"family": "FitzGerald", "given": "Edward A", "initials": "EA", "orcid": "0000-0002-0603-1241", "researcher": {"href": "https://publications.scilifelab.se/researcher/66338852ec3d475380ba5bf6d50be1b7.json"}}, {"family": "Cederfelt", "given": "Daniela", "initials": "D"}, {"family": "Kovryzhenko", "given": "Daria", "initials": "D"}, {"family": "Boronat", "given": "Pierre", "initials": "P"}, {"family": "Lund", "given": "Bjarte Aarmo", "initials": "BA", "orcid": "0000-0001-9141-0555", "researcher": {"href": "https://publications.scilifelab.se/researcher/941bad0f031c47cea46b35bc049d778a.json"}}, {"family": "Dobritzsch", "given": "Doreen", "initials": "D"}, {"family": "Hennig", "given": "Sven", "initials": "S", "orcid": "0000-0002-8297-6845", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a64c0c8bf0e457d8251a98f54fc79df.json"}}, {"family": "Paseiro", "given": "Pablo Porragas", "initials": "PP"}, {"family": "de Esch", "given": "Iwan J P", "initials": "IJP"}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}], "type": "journal article", "published": "2025-10-01", "journal": {"title": "RSC Chem Biol", "issn": "2633-0679", "volume": "6", "issue": "10", "pages": "1625-1639", "issn-l": null}, "abstract": "Analysis of ligand-induced structural changes in proteins is challenging due to the lack of experimental methods suited for detection and characterisation of both ligand binding and induced structural changes. We have explored biosensors with different detection principles to study interactions between ligands and acetylcholine binding proteins (AChBPs), soluble homologues of Cys-loop ligand gated ion channels (LGICs) that undergo similar structural changes as LGICs upon ligand binding. X-ray crystallography was used to identify binding sites and establish if the detected conformational changes involved small changes in loop C or major structural changes in the pentamer associated with ion channel opening. Experiments were initially focused on ligands exhibiting complex surface plasmon resonance (SPR) biosensor sensorgrams or detected by second harmonic generation (SHG) biosensor analysis. Surface acoustic wave (SAW) and SHG biosensors confirmed that complexities in SPR data were indeed due to ligand-induced conformational changes. Grating coupled interferometry (GCI) biosensor sensorgrams were less complex, despite similar detection principles. switchSENSE biosensor analysis revealed that ligands resulted in either a compaction or expansion of the protein structure. X-ray crystallography of the protein-ligand complexes was only successful for 7 out of 12 ligands, despite nM-\u03bcM affinities. Crystals were not obtained for the two compounds shown by SHG analysis to induce large structural changes, while electron densities were not seen in the structures for some ligands. The work presented herein shows that several biosensor technologies have a unique capability to detect and discriminate binding and ligand induced conformational changes in proteins, also when interactions are rapid, weak and structural changes are small. However, they are complementary and provide different information.", "doi": "10.1039/d5cb00041f", "pmid": "40896114", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12394895"}, {"db": "pii", "key": "d5cb00041f"}], "notes": [], "created": "2025-11-18T22:03:28.805Z", "modified": "2025-11-18T22:03:29.261Z"}, {"entity": "publication", "iuid": "b180389c75874d4aa64b80bb8f0fcb9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b180389c75874d4aa64b80bb8f0fcb9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b180389c75874d4aa64b80bb8f0fcb9b"}}, "title": "Monitoring drug-target interactions through target engagement-mediated amplification on arrays and in situ.", "authors": [{"family": "Al-Amin", "given": "Rasel A", "initials": "RA", "orcid": "0000-0002-0762-9034", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c8aeb2e9852413c832cf1a05be12d2f.json"}}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "Abdurakhmanov", "given": "Eldar", "initials": "E"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Arng\u00e5rden", "given": "Linda", "initials": "L"}, {"family": "Blokzijl", "given": "Andries", "initials": "A"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "Hammond", "given": "Maria", "initials": "M"}, {"family": "L\u00f6nn", "given": "Peter", "initials": "P"}, {"family": "Haybaeck", "given": "Johannes", "initials": "J"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M"}, {"family": "Jensen", "given": "Annika Jenmalm", "initials": "AJ"}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}, {"family": "Artursson", "given": "Per", "initials": "P"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2022-12-09", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "50", "issue": "22", "pages": "e129"}, "abstract": "Drugs are designed to bind their target proteins in physiologically relevant tissues and organs to modulate biological functions and elicit desirable clinical outcomes. Information about target engagement at cellular and subcellular resolution is therefore critical for guiding compound optimization in drug discovery, and for probing resistance mechanisms to targeted therapies in clinical samples. We describe a target engagement-mediated amplification (TEMA) technology, where oligonucleotide-conjugated drugs are used to visualize and measure target engagement in situ, amplified via rolling-circle replication of circularized oligonucleotide probes. We illustrate the TEMA technique using dasatinib and gefitinib, two kinase inhibitors with distinct selectivity profiles. In vitro binding by the dasatinib probe to arrays of displayed proteins accurately reproduced known selectivity profiles, while their differential binding to fixed adherent cells agreed with expectations from expression profiles of the cells. We also introduce a proximity ligation variant of TEMA to selectively investigate binding to specific target proteins of interest. This form of the assay serves to improve resolution of binding to on- and off-target proteins. In conclusion, TEMA has the potential to aid in drug development and clinical routine by conferring valuable insights in drug-target interactions at spatial resolution in protein arrays, cells and in tissues.", "doi": "10.1093/nar/gkac842", "pmid": "36189884", "labels": {"Autoimmunity and Serology Profiling": "Service", "Chemical Biology Consortium Sweden": "Collaborative", "Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9825164"}, {"db": "pii", "key": "6746875"}, {"db": "figshare", "key": "10.6084/m9.figshare.21107641.v1"}], "notes": [], "created": "2022-11-14T10:15:15.724Z", "modified": "2025-10-17T13:05:07.711Z"}, {"entity": "publication", "iuid": "5e158581154f4197b92e3232f7b464c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e158581154f4197b92e3232f7b464c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e158581154f4197b92e3232f7b464c5"}}, "title": "Sensitive Protein Detection Using Site-Specifically Oligonucleotide-Conjugated Nanobodies.", "authors": [{"family": "Al-Amin", "given": "Rasel A", "initials": "RA", "orcid": "0000-0002-0762-9034", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c8aeb2e9852413c832cf1a05be12d2f.json"}}, {"family": "Muthelo", "given": "Phathutshedzo M", "initials": "PM"}, {"family": "Abdurakhmanov", "given": "Eldar", "initials": "E"}, {"family": "Vincke", "given": "C\u00e9cile", "initials": "C"}, {"family": "Amin", "given": "Shahnaz P", "initials": "SP"}, {"family": "Muyldermans", "given": "Serge", "initials": "S", "orcid": "0000-0002-3678-3575", "researcher": {"href": "https://publications.scilifelab.se/researcher/089816af6f59476f8dee9b0d68f641b7.json"}}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2022-07-19", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "94", "issue": "28", "pages": "10054-10061", "issn-l": "0003-2700"}, "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.", "doi": "10.1021/acs.analchem.2c00584", "pmid": "35786874", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9310004"}], "notes": [], "created": "2022-11-24T22:42:08.768Z", "modified": "2025-10-17T13:05:07.754Z"}, {"entity": "publication", "iuid": "7628290a41184ddf88a208637257ac06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7628290a41184ddf88a208637257ac06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7628290a41184ddf88a208637257ac06"}}, "title": "Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses.", "authors": [{"family": "Luttens", "given": "Andreas", "initials": "A", "orcid": "0000-0003-2915-7901", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d46047fab4247caaeecf31be6da987f.json"}}, {"family": "Gullberg", "given": "Hjalmar", "initials": "H"}, {"family": "Abdurakhmanov", "given": "Eldar", "initials": "E"}, {"family": "Vo", "given": "Duy Duc", "initials": "DD"}, {"family": "Akaberi", "given": "Dario", "initials": "D", "orcid": "0000-0002-9595-9796", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f2dffc1327b471fa84256a7837344f1.json"}}, {"family": "Talibov", "given": "Vladimir O", "initials": "VO"}, {"family": "Nekhotiaeva", "given": "Natalia", "initials": "N"}, {"family": "Vangeel", "given": "Laura", "initials": "L"}, {"family": "De Jonghe", "given": "Steven", "initials": "S", "orcid": "0000-0002-3872-6558", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fbacfdaac194a87b975bf65cab9bfc4.json"}}, {"family": "Jochmans", "given": "Dirk", "initials": "D"}, {"family": "Krambrich", "given": "Janina", "initials": "J"}, {"family": "Tas", "given": "Ali", "initials": "A"}, {"family": "Lundgren", "given": "Bo", "initials": "B"}, {"family": "Gravenfors", "given": "Ylva", "initials": "Y", "orcid": "0000-0001-6025-4908", "researcher": {"href": "https://publications.scilifelab.se/researcher/deff200706ca4ee4be00bb8122de0c7b.json"}}, {"family": "Craig", "given": "Alexander J", "initials": "AJ"}, {"family": "Atilaw", "given": "Yoseph", "initials": "Y"}, {"family": "Sandstr\u00f6m", "given": "Anja", "initials": "A"}, {"family": "Moodie", "given": "Lindon W K", "initials": "LWK", "orcid": "0000-0002-9500-4535", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9377be68ffc416690153f44ab45de21.json"}}, {"family": "Lundkvist", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "van Hemert", "given": "Martijn J", "initials": "MJ"}, {"family": "Neyts", "given": "Johan", "initials": "J"}, {"family": "Lennerstrand", "given": "Johan", "initials": "J"}, {"family": "Kihlberg", "given": "Jan", "initials": "J", "orcid": "0000-0002-4205-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9805d4f39cc48f79a6e6ba076917021.json"}}, {"family": "Sandberg", "given": "Kristian", "initials": "K", "orcid": "0000-0002-6395-6590", "researcher": {"href": "https://publications.scilifelab.se/researcher/2747d3fe7810406fafc429d9e66225ef.json"}}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}, {"family": "Carlsson", "given": "Jens", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7d91087358e46e38bb1b7110dc0b214.json"}}], "type": "journal article", "published": "2022-02-23", "journal": {"title": "J. Am. Chem. Soc.", "issn": "1520-5126", "issn-l": "0002-7863", "volume": "144", "issue": "7", "pages": "2905-2920"}, "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.", "doi": "10.1021/jacs.1c08402", "pmid": "35142215", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Chemical Biology Consortium Sweden": "Service", "Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8848513"}], "notes": [], "created": "2022-03-23T14:12:50.377Z", "modified": "2025-10-17T13:05:07.806Z"}, {"entity": "publication", "iuid": "cdb649940de34aaf9bd52daedf59043f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cdb649940de34aaf9bd52daedf59043f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cdb649940de34aaf9bd52daedf59043f"}}, "title": "Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase.", "authors": [{"family": "Talibov", "given": "Vladimir O", "initials": "VO", "orcid": "0000-0002-1135-2744", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2cdaf464ed342d695baf33c19690518.json"}}, {"family": "Fabini", "given": "Edoardo", "initials": "E", "orcid": "0000-0001-8688-2208", "researcher": {"href": "https://publications.scilifelab.se/researcher/388d219ceead49ae9b2ebe5a22af582c.json"}}, {"family": "FitzGerald", "given": "Edward A", "initials": "EA", "orcid": "0000-0002-0603-1241", "researcher": {"href": "https://publications.scilifelab.se/researcher/66338852ec3d475380ba5bf6d50be1b7.json"}}, {"family": "Tedesco", "given": "Daniele", "initials": "D", "orcid": "0000-0003-2585-7791", "researcher": {"href": "https://publications.scilifelab.se/researcher/2eb39e0e14fe43e5aa6a8be62c5373bf.json"}}, {"family": "Cederfeldt", "given": "Daniela", "initials": "D"}, {"family": "Talu", "given": "Martin J", "initials": "MJ"}, {"family": "Rachman", "given": "Moira M", "initials": "MM", "orcid": "0000-0003-3671-8885", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1f1b1f3345049d18bc74b87122ef7f9.json"}}, {"family": "Mihalic", "given": "Filip", "initials": "F"}, {"family": "Manoni", "given": "Elisabetta", "initials": "E"}, {"family": "Naldi", "given": "Marina", "initials": "M", "orcid": "0000-0003-4468-2974", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e95a716834e4fbe86fa28fd0fde8f4a.json"}}, {"family": "Sanese", "given": "Paola", "initials": "P"}, {"family": "Forte", "given": "Giovanna", "initials": "G"}, {"family": "Lepore Signorile", "given": "Martina", "initials": "M"}, {"family": "Barril", "given": "Xavier", "initials": "X"}, {"family": "Simone", "given": "Cristiano", "initials": "C"}, {"family": "Bartolini", "given": "Manuela", "initials": "M", "orcid": "0000-0002-2890-3856", "researcher": {"href": "https://publications.scilifelab.se/researcher/10a0e31d3d414cf6a0b274e0a7495d32.json"}}, {"family": "Dobritzsch", "given": "Doreen", "initials": "D"}, {"family": "Del Rio", "given": "Alberto", "initials": "A", "orcid": "0000-0002-1890-6797", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b547aaccb804575b09a0ded5282f7c8.json"}}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}], "type": "journal article", "published": "2021-05-04", "journal": {"title": "ChemBioChem", "issn": "1439-7633", "volume": "22", "issue": "9", "pages": "1597-1608", "issn-l": "1439-4227"}, "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 \u03bcM, 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 \u03bcM). 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.", "doi": "10.1002/cbic.202000736", "pmid": "33400854", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8248052"}], "notes": [], "created": "2021-12-08T12:06:32.774Z", "modified": "2025-10-17T13:05:07.894Z"}, {"entity": "publication", "iuid": "4e30c827221d45299555816bce6ebaf2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e30c827221d45299555816bce6ebaf2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e30c827221d45299555816bce6ebaf2"}}, "title": "Discovery of fragments inducing conformational effects in dynamic proteins using a second-harmonic generation biosensor", "authors": [{"family": "FitzGerald", "given": "Edward A", "initials": "EA", "orcid": "0000-0002-0603-1241", "researcher": {"href": "https://publications.scilifelab.se/researcher/66338852ec3d475380ba5bf6d50be1b7.json"}}, {"family": "Butko", "given": "Margaret T", "initials": "MT"}, {"family": "Boronat", "given": "Pierre", "initials": "P"}, {"family": "Cederfelt", "given": "Daniela", "initials": "D"}, {"family": "Abramsson", "given": "Mia", "initials": "M", "orcid": "0000-0002-8184-0145", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b13d2ef38bf49d386f12ad170ae939d.json"}}, {"family": "Ludviksdottir", "given": "Hildur", "initials": "H"}, {"family": "van Muijlwijk-Koezen", "given": "Jacqueline E", "initials": "JE"}, {"family": "de Esch", "given": "Iwan J P", "initials": "IJP"}, {"family": "Dobritzsch", "given": "Doreen", "initials": "D"}, {"family": "Young", "given": "Tracy", "initials": "T"}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}], "type": "journal-article", "published": "2021-00-00", "journal": {"title": "RSC Adv.", "issn": "2046-2069", "issn-l": "2046-2069", "volume": "11", "issue": "13", "pages": "7527-7537"}, "abstract": null, "doi": "10.1039/d0ra09844b", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Service", "Drug Discovery and Development": null}, "xrefs": [], "notes": [], "created": "2021-12-02T12:28:50.784Z", "modified": "2025-10-17T13:05:07.930Z"}, {"entity": "publication", "iuid": "0da0ae4f148b4c269b2e050772b012bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0da0ae4f148b4c269b2e050772b012bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0da0ae4f148b4c269b2e050772b012bc"}}, "title": "Establishing Trypanosoma cruzi farnesyl pyrophosphate synthase as a viable target for biosensor driven fragment-based lead discovery.", "authors": [{"family": "Opassi", "given": "Giulia", "initials": "G"}, {"family": "Nordstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Lundin", "given": "Arne", "initials": "A"}, {"family": "Napolitano", "given": "Valeria", "initials": "V"}, {"family": "Magari", "given": "Francesca", "initials": "F"}, {"family": "Dzus", "given": "Tom", "initials": "T"}, {"family": "Klebe", "given": "Gerhard", "initials": "G", "orcid": "0000-0003-0177-537X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6afa0eddded142f2a16043d896012024.json"}}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}], "type": "journal article", "published": "2020-04-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "29", "issue": "4", "pages": "991-1003", "issn-l": "0961-8368"}, "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 \u0394T m > 1\u00b0C 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.", "doi": "10.1002/pro.3834", "pmid": "31994261", "labels": {"Drug Discovery and Development": null}, "xrefs": [{"db": "pmc", "key": "PMC7096706"}], "notes": [], "created": "2020-12-04T23:38:48.809Z", "modified": "2025-10-17T13:05:08.047Z"}, {"entity": "publication", "iuid": "7aa9a011dfae4264bb5ed7dbf3b4c135", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7aa9a011dfae4264bb5ed7dbf3b4c135.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7aa9a011dfae4264bb5ed7dbf3b4c135"}}, "title": "Estimating Detection Limits of Potentiometric DNA Sensors Using Surface Plasmon Resonance Analyses.", "authors": [{"family": "Xu", "given": "Xingxing", "initials": "X", "orcid": "0000-0002-1769-4382", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0585b665e994ac5990b4911b0cc5cfa.json"}}, {"family": "Makaraviciute", "given": "Asta", "initials": "A"}, {"family": "Abdurakhmanov", "given": "Eldar", "initials": "E"}, {"family": "Wermeling", "given": "Fredrik", "initials": "F"}, {"family": "Li", "given": "Shiyu", "initials": "S", "orcid": "0000-0003-4948-8353", "researcher": {"href": "https://publications.scilifelab.se/researcher/eaafe0529dbc46fb904b20cb943dad09.json"}}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}, {"family": "Nyholm", "given": "Leif", "initials": "L", "orcid": "0000-0001-9292-016X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7be3793cb034f04a7303a3ba8d0d4bf.json"}}, {"family": "Zhang", "given": "Zhen", "initials": "Z", "orcid": "0000-0003-4317-9701", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84c807f13484a2abf4ab92ab77e37ec.json"}}], "type": "journal article", "published": "2020-01-24", "journal": {"title": "ACS Sens.", "issn": "2379-3694", "issn-l": "2379-3694", "volume": "5", "issue": "1", "pages": "217-224"}, "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.", "doi": "10.1021/acssensors.9b02086", "pmid": "31833355", "labels": {"Drug Discovery and Development": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-01-07T13:59:48.906Z", "modified": "2025-10-17T13:05:08.079Z"}, {"entity": "publication", "iuid": "8ccac0ee2a5541a0a004b8a69d5dc52d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ccac0ee2a5541a0a004b8a69d5dc52d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ccac0ee2a5541a0a004b8a69d5dc52d"}}, "title": "Structural Changes of Mercaptohexanol Self-Assembled Monolayers on Gold and Their Influence on Impedimetric Aptamer Sensors.", "authors": [{"family": "Xu", "given": "Xingxing", "initials": "X", "orcid": "0000-0002-1769-4382", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0585b665e994ac5990b4911b0cc5cfa.json"}}, {"family": "Makaraviciute", "given": "Asta", "initials": "A", "orcid": "0000-0003-3843-7198", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f14031ff310417f9af2b54cc63b905d.json"}}, {"family": "Kumar", "given": "Shalen", "initials": "S"}, {"family": "Wen", "given": "Chenyu", "initials": "C", "orcid": "0000-0003-4395-7905", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2fdf123d31543d2a22fb1eaee3eab0d.json"}}, {"family": "Sj\u00f6din", "given": "Martin", "initials": "M", "orcid": "0000-0003-4126-4347", "researcher": {"href": "https://publications.scilifelab.se/researcher/3abc615673734cadbacd8e6ed1de8829.json"}}, {"family": "Abdurakhmanov", "given": "Eldar", "initials": "E"}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}, {"family": "Nyholm", "given": "Leif", "initials": "L", "orcid": "0000-0001-9292-016X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7be3793cb034f04a7303a3ba8d0d4bf.json"}}, {"family": "Zhang", "given": "Zhen", "initials": "Z", "orcid": "0000-0003-4317-9701", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84c807f13484a2abf4ab92ab77e37ec.json"}}], "type": "journal article", "published": "2019-11-19", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "91", "issue": "22", "pages": "14697-14704", "issn-l": "0003-2700"}, "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.", "doi": "10.1021/acs.analchem.9b03946", "pmid": "31650834", "labels": {"Drug Discovery and Development": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-01-07T14:01:17.339Z", "modified": "2025-10-17T13:05:08.088Z"}, {"entity": "publication", "iuid": "88a29e62c4c244569384139a55139f86", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88a29e62c4c244569384139a55139f86.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88a29e62c4c244569384139a55139f86"}}, "title": "Introduction of Intrinsic Kinetics of Protein-Ligand Interactions and Their Implications for Drug Design.", "authors": [{"family": "Linkuvien\u0117", "given": "Vaida", "initials": "V"}, {"family": "Talibov", "given": "Vladimir O", "initials": "VO"}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}, {"family": "Matulis", "given": "Daumantas", "initials": "D", "orcid": "0000-0002-6178-6276", "researcher": {"href": "https://publications.scilifelab.se/researcher/3907523345b74f5482633a8b0b5cfa2b.json"}}], "type": "journal article", "published": "2018-03-22", "journal": {"title": "J. Med. Chem.", "issn": "1520-4804", "volume": "61", "issue": "6", "pages": "2292-2302", "issn-l": "0022-2623"}, "abstract": "Structure-kinetic relationship analyses and identification of dominating interactions for optimization of lead compounds should ideally be based on intrinsic rate constants instead of the more easily accessible observed kinetic constants, which also account for binding-linked reactions. The intrinsic rate constants for sulfonamide inhibitors and pharmacologically relevant isoforms of carbonic anhydrase were determined by a novel surface plasmon resonance (SPR) biosensor-based approach, using chemodynamic analysis of binding-linked pH-dependent effects. The observed association rates ( k aobs) were pH-dependent and correlated with the fraction of deprotonated inhibitor and protonated zinc-bound water molecule. The intrinsic association rate constants ( kaintr) were pH independent and higher than kaobs. By contrast, the observed and intrinsic dissociation rate constants were identical and pH-independent, demonstrating that the observed association and dissociation mechanisms are inherently different. A model accounting for the differences between intrinsic and observed rate constants was developed, useful also for other interactions with binding-linked protonation reactions.", "doi": "10.1021/acs.jmedchem.7b01408", "pmid": "29466001", "labels": {"Drug Discovery and Development": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-31T10:45:17.535Z", "modified": "2025-10-17T13:05:08.470Z"}, {"entity": "publication", "iuid": "d16c2a4a4c114d26aed8e150867bcbbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d16c2a4a4c114d26aed8e150867bcbbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d16c2a4a4c114d26aed8e150867bcbbb"}}, "title": "Proximity-dependent initiation of hybridization chain reaction.", "authors": [{"family": "Koos", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Cane", "given": "Ga\u00eblle", "initials": "G"}, {"family": "Grannas", "given": "Karin", "initials": "K"}, {"family": "L\u00f6f", "given": "Liza", "initials": "L"}, {"family": "Arng\u00e5rden", "given": "Linda", "initials": "L"}, {"family": "Heldin", "given": "Johan", "initials": "J", "orcid": "0000-0002-0915-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a546798d014cd3a44537ae5db9f889.json"}}, {"family": "Clausson", "given": "Carl-Magnus", "initials": "CM"}, {"family": "Klaesson", "given": "Axel", "initials": "A"}, {"family": "Hirvonen", "given": "M Karoliina", "initials": "MK"}, {"family": "de Oliveira", "given": "Felipe M S", "initials": "FM", "orcid": "0000-0001-6074-7462", "researcher": {"href": "https://publications.scilifelab.se/researcher/e21dfb5c78b94f9f8631d4bdba6cf9e6.json"}}, {"family": "Talibov", "given": "Vladimir O", "initials": "VO", "orcid": "0000-0002-1135-2744", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2cdaf464ed342d695baf33c19690518.json"}}, {"family": "Pham", "given": "Nhan T", "initials": "NT"}, {"family": "Auer", "given": "Manfred", "initials": "M"}, {"family": "Danielson", "given": "U Helena", "initials": "UH", "orcid": "0000-0003-2728-0340", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2bf7dffedf44237807c23718c72efa6.json"}}, {"family": "Haybaeck", "given": "Johannes", "initials": "J", "orcid": "0000-0001-5518-3359", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7ed164711b3491489b91d7ecc35f63b.json"}}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O", "orcid": "0000-0003-2883-1925", "researcher": {"href": "https://publications.scilifelab.se/researcher/68df823efa304c0b9962684ac1515808.json"}}], "type": "journal article", "published": "2015-06-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "6", "pages": "7294", "issn-l": "2041-1723"}, "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.", "doi": "10.1038/ncomms8294", "pmid": "26065580", "labels": {"PLA and Single Cell Proteomics": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC4490387"}, {"db": "pii", "key": "ncomms8294"}], "notes": [], "created": "2023-06-16T12:43:37.596Z", "modified": "2023-06-16T12:44:14.437Z"}]}