Publications co-authored by SARomics Biostructures' team

Here, we show recent publications; please follow the links or scroll down for earlier publications. The PDB code, when present, reflects our contribution to the work.
The list represents just a tiny proportion of all projects handled at the company throughout the years. While some of the publications resulted from EU-funded projects in which SARomics Biostructures participated as an industrial partner, the majority are our customers' data, who kindly agreed to include our team members as co-authors. The customers own the data, and the decision to publish them belongs only to them.



Zetterberg FR, Diehl C, Håkansson M, Kahl-Knutson B, Leffler H, Nilsson UJ, Peterson K, Roper JA & Slack RJ (2023).
Discovery of Selective and Orally Available Galectin-1 Inhibitors
J. Med. Chem.

PDB entries:
8OJP - Human galectin 1 in complex with inhibitor (on hold until publication)

A new series of orally available α-d-galactopyranosides with high affinity and specificity toward galectin-1 have been discovered. High affinity and specificity were achieved by changing six-membered aryl-triazolyl substituents in a series of recently published galectin-3-selective α-d-thiogalactosides (e.g., GB1107 Kd galectin-1/3 3.7/0.037 μM) for five-membered heterocycles such as thiazoles. One compound, GB1490 (Kd galectin-1/3 0.4/2.7 μM), was selected for further characterization toward a panel of galectins showing a selectivity of 6- to 320-fold dependent on galectin. The X-ray structure of GB1490 bound to galectin-1 reveals the compound bound in a single conformation in the carbohydrate binding site.
Human galectin 1 in complex with inhibitor
Boonkrai C, Cotrone TS, Chaisuriyong W, Tantawichien T, Thisyakorn U, Fernandez S, Hunsawong T, Reed M, Wongtangprasert T, Audomsun T, Phakham T, Attakitbancha C, Saelao P, Focht D, Kimbung R, Welin M, Malik AA, Pisitkun T & Srisawat N (2023)
Efficacy of the combination of monoclonal antibodies against the SARS-CoV-2 Beta and Delta variants.
PLOS ONE 18(5): e0284173,

PDB entries:
8BSE- Crystal structure of SARS-COV-2 receptor binding domain (RBD) in complex with 1D1 Fab.
8BSF - Crystal structure of SARS-COV-2 receptor binding domain (RBD-beta variant) in complex with 3D2 Fab.

This study aimed to develop a monoclonal antibody against SARS-CoV-2 from B cells of recovered COVID-19 patients, which might have beneficial therapeutic purposes for COVID-19 patients. The authors generated human monoclonal antibodies (hmAbs) against the receptor binding domain (RBD) protein of SARS-CoV-2 using developed hybridoma technology. The isolated hmAbs against the RBD protein (wild-type) showed high binding activity and neutralized the interaction between the RBD and the cellular receptor angiotensin-converting enzyme 2 (ACE2) protein. Epitope binning and crystallography results displayed target epitopes of these antibodies in distinct regions beneficial in the mix as a cocktail.
SARS-COV-2 receptor binding domain (RBD) in complex with 1D1 Fab
Liu CY, Ahonen CL, Brown ME, Zhou L, Welin M, Krauland EM, Pejchal R, Widboom PF & Battles MB (2023).
Structure-based engineering of a novel CD3ε-targeting antibody for reduced polyreactivity
MAbs 15: 2189974-2189974.

PDB entries:
8F0L - Crystal Structure of the Human T cell Receptor CD3(EPSILON) N-Terminal Peptide Complexed with ADI-26906 FAB.

Bispecific antibodies continue to represent a growth area for antibody therapeutics, with roughly a third of molecules in clinical development being T-cell engagers that use an anti-CD3 binding arm. Using insights from the crystal structure of anti-Hu/Cy CD3 antibody ADI- 26906 in complex with CD3ε and antibody engineering using a yeast-based platform, the authors have derived high-affinity CD3 antibody variants with very low polyreactivity and significantly improved biophysical developability. Comparison of these variants with CD3 antibodies in the clinic (as part of bi- or multi- specifics) shows that affinity for CD3 is correlated with polyreactivity. The engineered CD3 antibodies break this correlation, forming a broad affinity range with no to low polyreactivity. Such antibodies will enable bispecifics with improved pharmacokinetic and safety profiles and suggest engineering solutions that will benefit the large and growing sector of T-cell engagers.
Structure of the Human T cell Receptor CD3(EPSILON) N-Terminal Peptide Complexed with ADI-26906 FA
Simon IA, Bjørn-Yoshimoto WE, Harpsøe K, Iliadis S, Svensson B, Jensen AA, Gloriam DE (2023).
Ligand selectivity hotspots in serotonin GPCRs.
Trenda Pharm. Sci. 44, 978-990.

Serotonin is a neurotransmitter involved in the regulation of numerous physiological processes. Its action is also modulated by drugs in the treatment of schizophrenia, depression, migraine, and obesity. However, these drugs typically have adverse effects caused by promiscuous binding across 12 serotonin and more than 20 homologous receptors. This review maps 19 ‘selectivity hotspots’, that are non-conserved binding site residues that control selectivity via favorable target interactions or repulsive ‘off-target’ contacts. It also reviews functional rationale from observed ligand-binding affinities and mutagenesis effects.
serotonin GPCR binding hotspots

Earlier publications

  • 2022

    Maurer MF, Lewis JL, Ardour D, Gudgeon CJ, Chandrasekaran S, Mudri S, Kleist, KN, Navas C, Wolfson MF, Rixon MW, Swanson R, Dillon SR, Levin SD, Kimbung YR, Akutsu M, Logan DT, Walse B, Swiderek K & Peng SL (2022). The engineered CD80 variant fusion therapeutic davoceticept combines checkpoint antagonism with conditional CD28 co-stimulation for anti-tumor immunity.
    Nature Commun. 13, 1790. doi: 10.1038/s41467-022-29286-5

    Ahlqvist J, Linares-Pastén JA, Håkansson M, Jasilonis A, Kwiatkow K, Fridjonsson, OH, Kaczarowska, A-K, Dabrowski, S, Aevarsson, A, Hreggvidsson, GO, Al-Karadaghi S, Kaczorowska, T, Nordberg Karlsson E. (2022).
    Crystal structure and initial characterization of a novel archeal-like Holiday junction-resolving enzyme from Thermus thermophilus phage Tth 15-6.
    Acta Cryst. D78, 1384-1398.

    Dandare SU, Håkansson M, Svensson LA, Timson DJ, Allen CRC (2022).
    Expression, purification and crystallization of a novel metagenome-derived salicylaldehyde dehydrogenase from Apline soil.
    Acta Crystallographic Secition F: Structural Biology Communications 78 (4).

    Kirk, NS, Chen Q, Wu YG, Asante, AL, Hu H, Espinosa JF, Martínez-Olid F, Margetts MB, Faiz A. Mohammed FA, Kiselyov VV, Barrett DG & Lawrence MC (2022)
    Activation of the human insulin receptor by non-insulin-related peptides.
    Nat Commun 13, 5695.
    The authors acknowledge Carl Diehl for his contribution to the NMR part of the work.
  • 2021
  • 2020-2019
    Nyerges A, et al. and Welin M, Kimbung R, Focht D, Peterlin Mašič L, and Pal C. (2020). Rational design of balanced dual-targeting antibiotics with limited resistance.
    PLoS Biol 18(10):e3000819.

    Karczewski J, Krasucki S P, Asare-Okai P N,
    Diehl C, Friedman A, Brown C M, Maezato Y, and Streatfield S J. (2020). Isolation, Characterization and Structure Elucidation of a Novel Lantibiotic From Paenibacillus sp.
    Front. Microbiol. 24.

    Sanchez-Fernandez A,
    Diehl C, Houston J E, Leung A E, Tellam J P, Rogers S E, Prevost S, Ulvenlund S, Sjögren H, and Wahlgren M. (2020). An integrative toolbox to unlock the structure and dynamics of protein–surfactant complexes.
    Nanoscale Adv 2, 4011-4023.

    Schneider, P.,
    Welin, M., Svensson, B., Walse, B. and Schneider, G. (2020). Virtual screening and design with machine intelligence applied to Pim‐1 kinase inhibitors.
    Mol. Inf., 39, 2000109.

    Telzerow A, Paris J,
    Håkansson M, González‐Sabín J, Ríos‐Lombardía N, Gröger H, Morís F, Schürmann M, Schwab H, Steiner K. (2020). Expanding the Toolbox of R‐Selective Amine Transaminases by Identification and Characterization of New Members.
    ChemBioChem 2020 21, 1–12.

    Ladds M J G W, Popova G, Pastor-Fernández A, Kannan S, van Leeuwen I M M,
    Håkansson M, Walse B, Tholander F, Ravi Bhatia, Verma C S, Lane D P, Laín S. (2020). Exploitation of dihydroorotate dehydrogenase (DHODH) and p53 activation as therapeutic targets: A case study in polypharmacology.
    J Biol Chem 295, 17935-17949.

    Shilova A, Lebrette H, Aurelius, O, Nan J,
    Welin M, Kovacic R, Ghosh S, Safari C, Friel R J, Milas M, Matej Z, Högbom M, Brändén G, Kloos M, Shoeman R L, Doak B, Ursby, T M. Håkansson T M, Logan D T, and Mueller U. (2020). Current status and future opportunities for serial crystallography at MAX IV Laboratory
    J. Synchrotron Rad. 27, 1095-1102.

    Plotka M, Szadkowska M,
    Håkansson M, Kovačič R, Al-Karadaghi S, Walse B, Werbowy O, Kaczorowska A-K, and Kaczorowski T. (2020). Molecular Characterization of a Novel Lytic Enzyme LysC from Clostridium intestinale URNW and Its Antibacterial Activity Mediated by Positively Charged N-Terminal Extension.
    Int J Mol Sci. 21, 4894;

    Baggio C, Udompholkul P, Gambini L, Jossart J, Salem AF,
    Håkansson M, Perry JJP, Pellecchia M. (2020). N-locking stabilization of covalent helical peptides: Application to Bfl-1 antagonists.
    Chem Biol Drug Des. 95, 412-426.
    doi: 10.1111/cbdd.13661

    Telzerow A, Paris J,
    Håkansson M, Gonzalez-Sabin J, Rios-Lombardía N, Schrmann M, Grger H, Morís F, Kourist R, Schwab H and Steiner K (2019). Amine Transaminase from Exophiala Xenobiotica - Crystal Structure and Engineering of a Fold IV Transaminase that Naturally Converts Biaryl Ketones.
    ACS Catal. 9, 1140−1148.

    Dahlqvist A, Mandal S, Peterson K,
    Håkansson M, Logan DT, Zetterberg FR, Leffler H, Nilsson UJ (2019). 3-Substituted 1-Naphthamidomethyl-C-galactosyls Interact with Two Unique Sub-sites for High-Affinity and High-Selectivity Inhibition of Galectin-3.
    Molecules. 24 (24), 4554.

    Ruggieri F, Campillo-Brocal JC, Chen S, Humble MS,
    Walse B, Logan DT, Berglund P (2019). Insight into the dimer dissociation process of the Chromobacterium violaceum (S)-selective amine transaminase.
    Sci Rep. 9, 16946. DOI: 10.1093/nar/25.17.3389

    Freitag-Pohl S, Jasilionis A,
    Håkansson M, Svensson LA, Kovačič R, Welin M, Watzlawick H, Wang L, Altenbuchner J, Płotka M, Kaczorowska AK, Kaczorowski T, Nordberg Karlsson E, Al-Karadaghi S, Walse B, Aevarsson A, Pohl E (2019). Crystal structures of the Bacillus subtilis prophage lytic cassette proteins XepA and YomS.
    Acta Crystallogr D Struct Biol., 75(Pt 11):1028-1039.

    Korkmaz B, Lesner A, Wysocka M, Gieldon A,
    Håkansson M, Gauthier F, Logan DT, Jenne DE, Lauritzen C, Pedersen J (2019). Structure-based design and in vivo anti-arthritic activity evaluation of a potent dipeptidyl cyclopropyl nitrile inhibitor of cathepsin C.
    Biochem Pharmacol. 164, 349-367.

    Kracht ON, Correia Cordeiro RS,
    Håkansson M, Stockmann J, Sander D, Bandow J, Senges CHR, Logan DT, Kourist R (2019). Discovery of three novel sesquiterpene synthases from Streptomyces chartreusis NRRL 3882 and crystal structure of an α-eudesmol synthase.
    J Biotechnol. 297, 71-77.

    Casaletto JB, Geddie ML, Abu-Yousif AO, Masson K, Fulgham A, Boudot A, Maiwald T, Kearns JD, Kohli N, Su S, Razlog M, Raue A, Kalra A, Håkansson M, Logan DT, Welin M, Chattopadhyay S, Harms BD, Nielsen UB, Schoeberl B, Lugovskoy AA, MacBeath G (2019). MM-131, a bispecific anti-Met/EpCAM mAb, inhibits HGF-dependent and HGF-independent Met signaling through concurrent binding to EpCAM.
    Proc Natl Acad Sci U S A 116, 7533-7542.

  • 2018-2017
    Ruggieri F, van Langen LM, Logan DT, Walse B, Berglund P. (2018). Transaminase-Catalyzed Racemization with Potential for Dynamic Kinetic Resolutions.
    ChemCatChem, 10, 1-8.

    Gustafsson NMS, Färnegårdh K, Bonagas N, Ninou AH, Groth P, Wiita E, Jönsson M,
    Hallberg K, Lehto J, Pennisi R, Martinsson J, Norström C, Hollers J, Schultz J, Andersson M, Markova N, Marttila P, Kim B, Norin M, Olin T, Helleday T (2018). Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination.
    Nat Commun. 9, 3872. DOI: 10.1038/s41467-018-06287-x

    Abdillahi SM, Maaß T, Kasetty G, Strömstedt AA, Baumgarten M, Tati R, Nordin SL,
    Walse B, Wagener R, Schmidtchen A, Mörgelin M (2018)
    Collagen VI Contains Multiple Host Defense Peptides with Potent In Vivo Activity.
    J Immunol., 201, 1007-1020.

    Ladds MJGW, van Leeuwen IMM, Drummond CJ, Chu S, Healy AR, Popova G, Pastor Fernández A, Mollick T, Darekar S, Sedimbi SK, Nekulova M, Sachweh MCC, Campbell J, Higgins M, Tuck C, Popa M, Safont MM, Gelebart P, Fandalyuk Z, Thompson AM, Svensson R, Gustavsson AL, Johansson L, Färnegårdh K, Yngve U, Saleh A, Haraldsson M, D'Hollander ACA, Franco M, Zhao Y,
    Håkansson M, Walse B, Larsson K, Peat EM, Pelechano V, Lunec J, Vojtesek B, Carmena M, Earnshaw WC, McCarthy AR, Westwood NJ, Arsenian-Henriksson M, Lane DP, Bhatia R, McCormack E, Laín S. A (2018). A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage.
    Nat Commun. 9, 1107. DOI: 10.1038/s41467-018-03441-3

    Andersen MCF, Boos I, Kinnaert C, Awan SI, Pedersen HL, Kračun SK, Lanz G,Rydahl MG, Kjærulff L,
    Håkansson M, Kimbung R, Logan DT, Gotfredsen CH, Willats WGT, Clausen MH (2018). Synthesis of branched and linear 1,4-linked galactan oligosaccharides.
    Org Biomol Chem. 16, 1157-1162. DOI: 10.1039/c7ob03035e

    Peterson K, Kumar R, Stenström O, Verma P, Verma PR,
    Håkansson M, Kahl-Knutsson B, Zetterberg F, Leffler H, Akke M, Logan DT, Nilsson UJ (2018). Systematic tuning of fluoro-galectin-3 interactions provides thiodigalactoside derivatives with single digit nM affinity and high selectivity.
    J Med Chem 61, 1164–1175. DOI: 10.1021/acs.jmedchem.7b01626.

    Zetterberg FR, Peterson K, Johnsson R, Brimert T,
    Håkansson M, Logan DT, Leffler H, Nilsson UJ (2018). Monosaccharide derivatives with low nM lectin affinity and high selectivity based on combined fluorine-amide, phenyl-arginine, sulfur-π, and halogen bond interactions.
    ChemMedChem 13, 133-137. DOI: 10.1002/cmdc.201700744.

    Takemoto Y, Slough DP, Meinke G, Katnik C, Graziano ZA, Chidipi B, Reiser M, Alhadidy MM, Ramirez R, Salvador-Montañés O, Ennis S, Guerrero-Serna G, Haburcak M,
    Diehl C, Cuevas J, Jalife J, Bohm A, Lin YS, Noujaim SF (2017). Structural basis for the antiarrhythmic blockade of a potassium channel with a small molecule.
    FASEB J pii: fj.201700349R. DOI: 10.1096/fj.201700349R.

    Anderson LC,
    Håkansson M, Walse B and Nilsson CL (2017). Intact Protein Analysis at 21 Tesla and X-Ray Crystallography Define Structural Differences in Single Amino Acid Variants of Human Mitochondrial Branched-Chain Amino Acid Aminotransferase 2 (BCAT2).
    J Am Soc Mass Spectrom 28, 1796-1804. DOI: 10.1007/s13361-017-1705-0

    Walse B, Turnbull AP and Boyd SM (2017). Tailoring Hit Identification and Qualification Methods for Targeting Protein–Protein Interactions.
    In Applied Biophysics for Drug Discovery (Huddler, D. and Zartler, E.R., ed.) pp. 29-59, John Wiley & Sons, Inc, Hoboken, NJ, USA.

    Noresson AL, Aurelius O, Öberg CT, Engström O, Sundin AP, Håkansson M, Stenström O, Akke M, Logan DT, Leffler H, Nilsson UJ (2017).
    Designing interactions by control of protein-ligand complex conformation: tuning arginine-arene interaction geometry for enhanced electrostatic protein-ligand interactions.
    Chem Sci. 9, 1014-1021. DOI: 10.1039/c7sc04749e
  • 2016-2015
    Nilsson LM, Green LC, Veppil Muralidharan S, Demir D, Welin M, Bhadury J, Logan D, Walse B and Nilsson JA (2016). Cancer differentiating agent hexamethylene bisacetamide inhibits BET bromodomain proteins.
    Cancer Res. 76, 2376-2383. DOI: 10.1158/0008-5472.CAN-15-2721

    Badarau A, Rouha H, Malafa S, Battles MB, Walker L, Nielson N, Dolezilkova I, Teubenbacher A, Banerjee S, Maierhofer B, Weber S, Stulik L,
    Logan DT, Welin M, Mirkina I, Pleban C, Zauner G, Gross K, Jägerhofer M, Magyarics Z & Nagy E (2016). Context matters: The importance of dimerization-induced conformation of the LukGH leukocidin of Staphylococcus aureus for the generation of neutralizing antibodies.
    MAbs. 8, 1347-1360. DOI: 10.1080/19420862.2016.1215791

    Badarau A, Rouha H, Malafa S, Logan DT, Håkansson M, Stulik L, Dolezilkova I, Teubenbacher A, Gross K, Maierhofer B, Weber S, Jägerhofer M, Hoffmann D, Nagy E (2015). Structure-Function Analysis of Heterodimer Formation, Oligomerization, and Receptor Binding of the Staphylococcus aureus Bi-component Toxin LukGH.
    J. Biol. Chem. 290, 142-156. DOI: 10.1074/jbc.M114.598110

    Rodrigues T, Reker, D,
    Welin M, Caldera M, Brunner C, Gabernet G,Schneider P, Walse B and Schneider G (2015). De Novo Fragment Design for Drug Discovery and Chemical Biology.
    Angewandte Chemie International Edition, DOI: 10.1002/anie.201508055.

    Fisher SZ, von Schantz L,
    Håkansson M, Logan DT & Ohlin M. (2015). Neutron Crystallographic Studies Reveal Hydrogen Bond and Water-Mediated Interactions between a Carbohydrate-Binding Module and Its Bound Carbohydrate Ligand.
    Biochemistry 54, 6435-6438. DOI: 10.1021/acs.biochem.5b01058

    Jong-Eun Kim, Joe Eun Son, Hyein Jeong, Dong Joon Kim, Sang Gwon Seo, Eunjung Lee, Tae Gyu Lim, Jong Rhan Kim, Yengo Raymond
    Kimbung, Hanyong Chen, Ann M. Bode, Ki Won Lee and Zigang Dong (2015). A Novel Cinnamon-Related Natural Product with Pim-1 Inhibitory Activity Inhibits Leukemia and Skin Cancer.
    Cancer Res. 75, 2716-2728.
    doi: 10.1158/0008-5472.CAN-14-3655
  • 2014-2012
    von Schantz L, Håkansson M, Logan DT, Nordberg-Karlsson E and Ohlin M (2014). Carbohydrate binding module recognition of xyloglucan defined by polar contacts with branching xyloses and CH-π interactions.
    Proteins, 82, 3466-75.

    Turnbull AP, Boyd SM & Walse B (2014). Fragment-based drug discovery and protein-protein interactions.
    Res. Rep Biochem. 4, 13-26.

    Lolli ML, Ducime A, Federico, A Pippione AC, Sainas S, Barge A, Martina K, Boschi D, Lupino E, Piccinini M, Kubbutat M, Schächtele C, Contreras JM, Morice C, Sussman J, Peleg J, Walse B and Al-Kadaraghi S (2014). Towards a Bioisosteric Alkaest: application to the bioisosteric modulation of IMD-0354.
    In: Book of Abstracts. p. 234, Lisbon, Portugal, September 7-11.
    See poster…

    Saraboji K,
    Håkansson M, Genheden S, Diehl C, Qvist J, Weininger U, Nilsson UJ, Leffler H, Ryde U, Akke M & Logan DT. (2012). The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics.
    Biochemistry 2012, 51:296-306.

    Humble MS, Cassimjee KE,
    Håkansson, M, Kimbung YR, Walse B, Abedi V, Federsel H-J, Berglund P & Logan DT (2012). Crystal structures of the Chromobacterium violaceum ω-transaminase reveal major structural rearrangements upon binding of coenzyme PLP.
    FEBS J., 279, 779-792.

    von Schantz, L.,
    Håkansson, M., Logan, D.T., Walse, B., Osterlin, J., Nordberg-Karlsson, E. and Ohlin, M. (2012). Structural basis for carbohydrate-binding specificity -a comparative assessment of two engineered carbohydrate-binding modules.
    Glycobiology, 22, 948-961.

    Boyd SM, Turnbull AP and
    Walse B (2012). Fragment library design considerations.
    WIREs Comput. Mol. Sci., 2, 868-885.
  • 2011-2009
    Kasetty G, Papareddy P, Kalle M, Rydengård V, Walse B, Svensson B, Mörgelin M, Malmsten M & Schmidtchen A (2011). The C-terminal sequence of several human serine proteases encodes host defense functions.
    J Innate Immun. 3, 471-482.

    Svensson SL, Pasupuleti M, Walse B, Malmsten M, Mörgelin M, Sjögren C, Olin AI, Collin M, Schmidtchen A, Palmer R & Egesten A (2010). Midkine and pleiotrophin have bactericidal properties: preserved antibacterial activity in a family of heparin-binding growth factors during evolution.
    J Biol Chem. 285, 16105-16115.

    Diehl C, Engström O, Delaine T, Håkansson M, Genheden S, Modig K, Leffler H, Ryde U, Nilsson UJ & Akke M (2010). Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3.
    J Am Chem Soc. 132, 14577-1489.

    Fritzson I, Svensson B, Al-Karadaghi S, Walse B, Wellmar U, Nilsson UJ, da Graça Thrige D & Jönsson S. (2010).
    Inhibition of human DHODH by 4-hydroxycoumarins, fenamic acids, and N-(alkylcarbonyl)anthranilic acids identified by structure-guided fragment selection.
    ChemMedChem. 5, 608-617.