Suades A, Qureshi A, McComas S, Coinçon M, Rudling A, Chatzikyriakidou Y, Landreh M, Carlsson J & Drew D (2023) Establishing mammalian GLUT kinetics and lipid composition influences in a reconstituted-liposome system. Nat Commun 14, 4070. DOI: 10.1038/s41467-023-39711-y
Matricon P, Anh TN. Nguyen A, Vo D, Baltos J, Jaiteh M, Luttens A, Kampen S, Christopoulos A, Kihlberg J, May L, Carlsson J (2023) Structure-based virtual screening discovers potent and selective adenosine A1 receptor antagonists. Eur. J. Med. Chem. 115419. DOI: 10.1016/j.ejmech.2023.115419
,, , , , , , , , , , , , Angew. Chem. Int. Ed. e202218959. DOI: 10.1002/anie.202218959
Kampen S, Rodríguez D, Jørgensen M, Kruszyk-Kujawa M, Huang X, Collins Jr. M, Boyle N, Maurel D, Rudling D, Lebon G & Carlsson J (2022) Structure-based Discovery of Negative Allosteric Modulators of the Metabotrpic Glutamate Receptor 5. ACS Chem. Biol. 17 (10), 2744-2752. DOI: 10.1021/acschembio.2c00234
Romero-Fernandez W, Taura JJ, Crans RAJ, Lopez-Cano M, Fores-Pons R, Narváez M, Carlsson J, Ciruela F, Fuxe K & Borroto-Escuela DO (2022) The mGlu5 Receptor Protomer-Mediated Dopamine D2 Receptor Trans-Inhibition Is Dependent on the Adenosine A2A Receptor Protomer: Implications for Parkinson’s Disease. Mol. Neurobiol. https://link.springer.com/article/10.1007/s12035-022-02946-9
Luttens A, Gullberg H, Abdurakhmanov, Vo DD, Akaberi D, Talibov VO, Nekhotiaeva N, Vangeel L, De Jonghe D, 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 (2022) Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses. J. Am. Chem. Soc. 144(7):2905–2920. DOI: 10.1021/jacs.1c08402.
Begnini F, Geschwindner S, Johansson P, Wissler L, Lewis RJ, Danelius E, Luttens A, Matricon P, Carlsson J, Lenders S, König B, Friedel A, Sjö P, Schiesser S & Kihlberg J (2022) Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1–Nrf2 Protein–Protein Interaction. J. Med. Chem. 65(4):3473–3517. DOI: 10.1021/acs.jmedchem.1c01975.
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Matricon P, Duy Duc Vo, Gao Z, Kihlberg J, Jacobson KA & Carlsson J (2021) Fragment-based design of selective GPCR ligands guided by free energy simulations. Chem. Commun. 57:12305-12308. DOI: 10.1039/D1CC03202J.
Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ & Shoichet BK (2021) A practical guide to large-scale docking. Nat. Protoc. 16:4799–4832. DOI: 10.1038/s41596-021-00597-z.
Draper-Joyce CJ, Bhola R, Wang J, Bhattarai A, Nguyen ATN, Cowie-Kent I, O’Sullivan K, Chia LY, Venugopal H, Valant C, Thal DM, Wootten D, Panel N, Carlsson J, Christie MJ, White PJ, Scammells P, May LT, Sexton PM, Danev R, Miao Y, Glukhova A, Imlach WL & Christopoulos A (2021) Positive Allosteric Mechanisms of Adenosine A1 Receptor-Mediated Analgesia. Nature 597(7877):571–576. DOI: https://doi.org/10.1038/s41586-021-03897-2.
Kampen S, Duc Vo D, Zhang X, Panel N, Yang Y, Jaiteh M, Matricon P, Svenningsson, P, Brea J, Loza MI, Kihlberg J & Carlsson J (2021) Structure‐guided Design of G Protein‐coupled Receptor Polypharmacology. Angew. Chem. 60(33):18022-18030. DOI: 10.1002/anie.202101478.
Kapla J, Rodríguez Espigares I, Ballante F, Selent J & Carlsson J (2021) Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models? PLoS Comput. Biol. 17(5):e1008936. DOI: 10.1371/journal.pcbi.1008936.
Fleetwood O, Carlsson J & Delemotte L (2021) Identification of ligand-specific G-protein coupled receptor states and prediction of downstream efficacy via data-driven modeling. eLife 10:e60715. DOI: 10.7554/eLife.60715
Matricon P, Suresh RR, Gao ZG, Panel N, Jacobson KA & Carlsson J (2020) Ligand design by targeting a binding site water. Chem. Sci. 12:960-968. DOI: 10.1039/D0SC04938G
Rodríguez-Espigares I, Torrens-Fontanals M, Tiemann JKS, Aranda-García D, Ramírez-Anguita JM, Stepniewski TM, Worp N, Varela-Rial A, Morales-Pastor A, Medel-Lacruz B, Pándy-Szekeres G, Mayol E, Giorgino T, Carlsson J, Deupi X, Filipek S, Filizola M, Gómez-Tamayo JC, Gonzalez A, Gutierrez-de-Teran H, Jiménez-Rosés M, Jespers W, Kapla J, Khelashvili G, Kolb P, Latek D, Marti-Solano M, Matricon P, Matsoukas MT, Miszta P, Olivella M, Perez-Benito L, Provasi D, Ríos S, Torrecillas IR, Sallander J, Sztyler A, Vasile S, Weinstein H, Zachariae U, Hildebrand PW, De Fabritiis G, Sanz F, Gloriam DE, Cordomi A & Guixà-González R & Selent J (2020) GPCRmd uncovers the dynamics of the 3D-GPCRome. Nat. Methods, 8:777-787. DOI: 10.1038/s41592-020-0884-y
Jacobson KA, Gao ZG, Matricon P, Eddy MT & Carlsson J (2020) Adenosine A2A receptor antagonists: from caffeine to selective non-xanthines. Br. J. Pharmacol., 2020:1-16. DOI: 10.1111/bph.15103
Sommer ME, Selent J, Carlsson J, De Graaf C, Gloriam DE, Keseru GM, Kosloff M, Mordalski S, Rizk A, Rosenkilde MM, Sotelo E, Tiemann JKS, Tobin A, Vardjan N, Waldhoer M & Kolb P (2020) The European Research Network on Signal Transduction (ERNEST): toward a multidimensional holistic understanding of G protein-coupled receptor signalling. ACS Pharmacol. Transl. Sci., 3:361-370. DOI: 10.1021/acsptsci.0c00024
M. Jaiteh, I. Rodríguez-Espigares, J. Selent & J. Carlsson (2020) Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity. PLoS Comput. Biol., 16:3 DOI: 10.1371/journal.pcbi.1007680
Fleetwood O, Matricon P, Carlsson J & Delemotte L (2019) Energy landscapes reveal agonist’s control of GPCR activation via microswitches. Biochemistry, 59:880-891 DOI: 10.1021/acs.biochem.9b00842
Ballante F, Rudling A, Zeifman A, Luttens A, Vo DD, Irwin J J, Kihlberg J, Brea J M, Loza M I, & Carlsson J (2020) Docking finds GPCR ligands in dark chemical matter. J. Med. Chem., 63:613–620 DOI: 10.1021/acs.jmedchem.9b01560
Wright SC, Kozielewicz P, Kowalski-Jahn M, Petersen J, Bowin C-F, Slodkowicz G, Marti-Solano M, Rodríguez D , Hot B, Okashah N, Strakova K, Valnohova J, Babu MM, Lambert NA, Carlsson J & Schulte G (2019) A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection. Nature Communications, 10:667. DOI:10.1038/s41467-019-08630-2
Wright S C, Cañizal M C A, Benkel T, Simon K, Le Gouill C, Matricon P, Namkung Y, Lukasheva V, König G M, Laporte S A, Carlsson J, Kostenis E, Bouvier M, Schulte G, Hoffmann C (2018) FZD5 is a Gαq-coupled receptor that exhibits the functional hallmarks of prototypical GPCRs. SCI. SIGNAL. 11 (559). DOI: 10.1126/scisignal.aar5536
Kennedy A J, Ballante F , Johansson J R, Milligan G, Sundström L, Nordqvist A & Carlsson J (2018) Structural Characterization of Agonist Binding to Protease-Activated Receptor 2 through Mutagenesis and Computational Modeling. ACS Pharmacology & Translational Science 1 (2), 119-133. DOI: 10.1021/acsptsci.8b00019
Borroto-Escuela D O, Rodríguez D, Romero-Fernandez W, Kapla J, Jaiteh M, Ranganathan A, Lazarova T, Fuxe K & Carlsson J (2018) Mapping the interface of a GPCR dimer: A structural model of the A2A adenosine and D2 dopamine receptor heteromer. Front. Pharmacol. DOI:10.3389/fphar.2018.00829
Lundgren AK C, Sjöstrand D, Biner O, Bennett M, Rudling A , Johansson A, Brzezinski P, Carlsson J , Von Ballmoos C & Högbom M (2018) Scavenging of superoxide by a membrane-bound superoxide oxidase. Nature Chemical Biology. DOI: 10.1038/s41589-018-0072-x
Jaiteh M , Zeifman A , Saarinen M, Svenningsson P, Brea J M, Loza M I & Carlsson J (2018) Docking screens for dual inhibitors of disparate drug targets for Parkinson’s disease. J. Med. Chem., 61 (12): 5269-5278
Rudling A , Orro A & Carlsson J (2018) Prediction of ordered water molecules in protein binding sites from molecular dynamics simulations: The impact of ligand binding on hydration networks. J. Chem. Inf. Model., 58 (2): 350-361
Rudling A , Gustafsson R, Almlöf I, Homan E, Scobie M, Warpman Berglund U, Helleday T, Stenmark P & Carlsson J (2017) Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space. J Med Chem, 60:8160–8169
Männel B, Jaiteh M, Zeifman A, Randakova A, Möller D, Hübner H, Gmeiner P & Carlsson J (2017) Structure-Guided Screening for Functionally Selective D2 Dopamine Receptor Ligands from a Virtual Chemical Library. ACS Chem. Biol., 12:2652–2661
Petersen J, Wright SC, Rodríguez D, Matricon P, Lahav N, Vromen A, Assaf Friedler, Strömqvist J, Wennmalm S, Carlsson J & Schulte G (2017) Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling. Nature Communications 8, 226
Matricon P, Ranganathan A, Warnick E, Gao ZG, Rudling A, Lambertucci C, Marucci G, Ezzati A, Jaiteh M, Dal Ben D, Jacobson KA & Carlsson J (2017) Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A 2A adenosine receptor binding site. Scientific Reports, 7:6398
Strakovaa K, Matricon P, Yokota C, Arthofer E, Bernatik O, Rodríguez D, Arenas E, Carlsson J, Bryja V, Schulte G (2017) The tyrosine Y250 2.39 in Frizzled 4 defines a conserved motif important for structural integrity of the receptor and recruitment of Disheveled. Cellular Signalling, 38:85-96
Ranganathan A, Rodríguez D, Carlsson J (2017) Structure-Based Discovery of GPCR Ligands from Crystal Structures and Homology Models. Topics in Medicinal Chemistry, pp 1-35.
Borroto-Escuela D, Carlsson J, Ambrogini P, Narváez M, Wydra K, Tarakanov A, Li X, Millón C, Ferraro L, Cuppini R, Tanganelli S, Liu F, Filip M, Diaz-Cabiale Z, Fuxe K (2017) Understanding the Role of GPCR Heteroreceptor Complexes in Modulating the Brain Networks in Health and Disease. Frontiers in Cellular Neuroscience, 11, 1.
Ranganathan A, Heine P, Rudling A, Plückthun A, Kummer L, Carlsson J (2016) Ligand discovery for a peptide-binding GPCR by structure-based screening of fragment- and lead-like chemical libraries. ACS Chem. Biol., 12:735–745
Rodríguez D, Chakraborty S, Warnick E, Crane S, Gao ZG, O’Connor R, Jacobson KA and Carlsson J (2016) Structure-Based Screening of Uncharted Chemical Space for Atypical Adenosine Receptor Agonists. ACS Chem. Biol., 11:2763-2772
Ranganathan A, Stoddart LA, Hill SJ and Carlsson J (2015) Fragment-based discovery of subtype selective adenosine receptor ligands from homology models. J Med Chem, 58:9578-9590
Lam VM, Rodríguez D, Zhang T, Koh EJ, Carlsson J and Salahpour A (2015) Discovery of Trace Amine-Associated Receptor 1 Ligands by Molecular Docking Screening against a Homology Model. Med. Chem. Comm., 6:2216-2223
Rodríguez D, Ranganathan A, and Carlsson J (2015) Discovery of GPCR Ligands by Molecular Docking Screening: Novel Opportunities Provided by Crystal Structures. Curr Top Med Chem, 2484-2503.
Rodríguez D, Gao ZG, Moss SM, Jacobson KA., and Carlsson J (2015) Molecular docking screening using agonist-bound GPCR structures: Probing the A2A adenosine receptor. J Chem Inf Model, 54:2004-2021.
Ranganathan A, Dror RO, and Carlsson J (2014) Insights into the Role of Asp79 2.50 in beta 2 Adrenergic Receptor Activation from Molecular Dynamics Simulations. Biochemistry, 53:7283-7296.
Rodríguez D, Ranganathan A, and Carlsson J (2014) Strategies for improved modeling of GPCR-drug complexes: blind predictions of serotonin receptors bound to ergotamine. J Chem Inf Model, 54:2004-2021.
Kufareva I, Katritch V, Rodríguez D, Ranganathan A, Carlsson J & other GPCR Dock 2013 Participants; Stevens, R. C.; Abagyan, R. (2014) Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure, 22:1120-1139.
Rodríguez D, Brea J, Loza M I, Carlsson J (2014) Structure-based Discovery of Selective Serotonin 5-HT1B Receptor Ligands. Structure , 22:1140-1151.
Chen D, Ranganathan A, Ijzerman AP, Siegal G, Carlsson J (2013) Complementarity between in silico and biophysical screening approaches in fragment-based lead discovery against the A2A adenosine receptor. J Chem Inf Model 53(10):2701-14.
Heusser SA, Howard RJ, Borghese CM, Cullins MA, Broemstrup T, Lee US, Lindahl E, Carlsson J, Harris RA (2013) Functional validation of virtual screening for novel agents with general anesthetic action at ligand-gated ion channels. Mol Pharmacol 84:670-678.
Johansson A, Högbom M, Carlsson J, Gennis RB, Brzezinski P (2013) The role of aspartate 132 at the orifice of a proton pathway in Cytochrome c Oxidase. Proc Natl Acad Sci 110:8912-8917.
Benod C*, Carlsson J*, Uthayaruban R, Hwang P, Irwin JJ, Doak AK, Shoichet BK, Sablin EB, and Fletterick RJ (2013) Structure-based discovery of antagonists of nuclear receptor LRH-1, J Biol Chem 288:19830-44.
Johansson A, Carlsson J, Högbom M, Hosler JP, Gennis RB, and Brzezinski P (2013) Proton uptake and pKa changes in the uncoupled Asn139Cys variant of Cytochrome c Oxidase. Biochemistry 52:827-836.
Carlsson J, ToshDK, Phan K, Gao ZG, Jacobson KA (2012) Structure-activity relationships and molecular modeling of 1,2,4-triazoles as adenosine receptor antagonists. ACS Med Chem Lett, 3:715-720.
Carlsson J, Coleman RG, SetolaV, Irwin JJ, Fan H, Schlessinger A, Sali A, Roth BL, and Shoichet, BK (2011) Ligand discovery from a Dopamine D3 receptor homology model and crystal Structure. Nature Chemical Biology 7:769-778.
Kufareva I, Rueda M, Katritch V, Carlsson J and other participants of GPCR Dock 2010, Stevens R, Abagyan R. (2011) Status of GPCR modeling and docking as reflected by community wide GPCR Dock 2010 assessment, Structure, 19:1108-1126.
Carlsson J, Yoo L, Gao GZ, Irwin JI, Shoichet BK, and Jacobson KA (2010) Structure-based discovery of A2A adenosine receptor ligands. J Med Chem 53:3748-3755.
Carlsson J and Åqvist J (2009) Absolute hydration entropies of alkali metal ions from molecular dynamics simulations. J Phys Chem B 113:10255-10260.
Wallin G, Nervall M, Carlsson J, Boukharta L, and Åqvist J (2009) Charges for large scale binding free energy calculations with the linear interaction energy method. J. Chem. Theory Comput. 5:381-295.
Carlsson J, Boukharta L, and Åqvist J (2008) Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase. J Med Chem 51:2648-2656.
Nervall M, Hanspers P, Carlsson J, Boukharta L, and Åqvist J (2008) Predicting binding modes from free energy calculations. J Med Chem 51:2657-2667.
Henriksson LM, Unge T, Carlsson J, Åqvist J, Mowbray SL, and Jones TA (2007) Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem 282:19905-19916.
Almlöf M, Carlsson J, and Åqvist J (2007) Improving the accuracy of the linear interaction energy method for solvation free energies. J Chem Theory Comput 3:2162-2175.
Thomaeus A, Carlsson J, Åqvist J, and Widersten M (2007) Active site of epoxide hydrolases revisited: A noncanonical residue in potato StEH1 promotes both formation and breakdown of the alkylenzyme intermediate. Biochemistry 46:2466-2479.
Carlsson J, and Åqvist J (2006) Calculations of solute and solvent entropies from molecular dynamics simulations. Phys Chem Chem Phys 8:5385-5395.
Carlsson J, Ander M, Nervall M, and Åqvist J (2006) Continuum solvation models in the linear interaction energy method. J Phys Chem B 110:12034-12041.
Carlsson J, and Åqvist J (2005) Absolute and relative entropies from computer simulation with applications to ligand binding. J Phys Chem B 109:6448-6456.
Simonson T, Carlsson J, and Case DA (2004) Proton binding to proteins: pKa calculations with explicit and implicit solvent models. J Am Chem Soc 126:4167-4180.