Allostery in Drug Discovery

Informazioni relative al progetto

ALLODD

ID dell’accordo di sovvenzione: 956314

DOI

10.3030/956314

Progetto chiuso

Data della firma CE 28 Maggio 2021

Data di avvio 1 Settembre 2021

Data di completamento 31 Agosto 2025

Finanziato da

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Costo totale

€ 3 627 680,76

Contributo UE

€ 3 627 680,76

Coordinato da

IDRYMA IATROVIOLOGIKON EREUNON AKADEMIAS ATHINON
Greece

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

Other (1)

Supervisory Board and Governing Bodies of ALLODD

Websites, patent fillings, videos etc. (1)

Project Web presence (Website and Social Media)

Web presence Website and Social Media m3

Pubblicazioni

Peer reviewed articles (38)

Computational advances in discovering cryptic pockets for drug discovery

Autori: Martijn P. Bemelmans, Zoe Cournia, Kelly L. Damm-Ganamet, Francesco L. Gervasio, Vineet Pande
Pubblicato in: Current Opinion in Structural Biology, Numero 90, 2025, Pagina/e 102975, ISSN 0959-440X
Editore: Elsevier BV
DOI: 10.1016/j.sbi.2024.102975

Towards design of drugs and delivery systems with the Martini coarse-grained model

Autori: Lisbeth R. Kjølbye, Gilberto P. Pereira, Alessio Bartocci, Martina Pannuzzo, Simone Albani, Alessandro Marchetto, Brian Jiménez-García, Juliette Martin, Giulia Rossetti, Marco Cecchini, Sangwook Wu, Luca Monticelli, Paulo C. T. Souza
Pubblicato in: QRB Discovery, Numero 3, 2022, Pagina/e e19, ISSN 2633-2892
Editore: Cambridge University Press
DOI: 10.1017/qrd.2022.16

Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential

Autori: Sonja Peter, Lydia Siragusa, Morgan Thomas, Tommaso Palomba, Simon Cross, Noel M. O’Boyle, Dávid Bajusz, György G. Ferenczy, György M. Keserű, Giovanni Bottegoni, Brian Bender, Ijen Chen, Chris De Graaf
Pubblicato in: Journal of Chemical Information and Modeling, Numero 64, 2024, Pagina/e 8176-8192, ISSN 1549-9596
Editore: American Chemical Society
DOI: 10.1021/acs.jcim.4c00819

Functional modulation of PTH1R activation and signalling by RAMP2

Autori: Katarina Nemec, Hannes Schihada, Gunnar Kleinau, Ulrike Zabel, Eugene O. Grushevskyi, Patrick Scheerer, Martin J. Lohse, Isabella Maiellaro
Pubblicato in: Proceedings of the National Academy of Sciences of the United States of America, Numero Volume 119; Numero 32, 2022, Pagina/e e2122037119, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2122037119

Syntheses of differentially fluorinated triazole-based 1-deoxysphingosine analogues <i>en route</i> to SphK inhibitors

Autori: Adrià Cardona, Varbina Ivanova, Raúl Beltrán-Debón, Xavier Barril, Sergio Castillón, Yolanda Díaz, M. Isabel Matheu
Pubblicato in: Organic &amp; Biomolecular Chemistry, 2024, ISSN 1477-0520
Editore: Royal Society of Chemistry
DOI: 10.1039/d4ob01656d

Alchemical Free Energy Calculations on Membrane-Associated Proteins

Autori: Michail Papadourakis, Hryhory Sinenka, Pierre Matricon, Jérôme Hénin, Grace Brannigan, Laura Pérez-Benito, Vineet Pande, Herman van Vlijmen, Chris de Graaf, Francesca Deflorian, Gary Tresadern, Marco Cecchini, Zoe Cournia
Pubblicato in: Journal of Chemical Theory and Computation, Numero Volume 19; Numero 21, 2023, Pagina/e 7437–7458, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.3c00365

Mechanisms of thyrotropin receptor–mediated phenotype variability deciphered by gene mutations and M453T-knockin model

Autori: Kristiina Makkonen, Meeri Jännäri, Luís Crisóstomo, Matilda Kuusi, Konrad Patyra, Vladyslav Melnyk, Veli Linnossuo, Johanna Ojala, Rowmika Ravi, Christoffer Löf, Juho-Antti Mäkelä, Päivi Miettinen, Saila Laakso, Marja Ojaniemi, Jarmo Jääskeläinen, Markku Laakso, Filip Bossowski, Beata Sawicka, Karolina Stożek, Artur Bossowski, Gunnar Kleinau, Patrick Scheerer, null FinnGen, Mary Pat Re
Pubblicato in: JCI Insight, Numero 9, 2024, Pagina/e e167092, ISSN 2379-3708
Editore: American Society for Clinical of Investigation
DOI: 10.1172/jci.insight.167092

Machine learning approaches in predicting allosteric sites

Autori: Francho Nerín-Fonz, Zoe Cournia
Pubblicato in: Current Opinion in Structural Biology, Numero Volume 85, 2024, Pagina/e 102774, ISSN 0959-440X
Editore: Elsevier BV
DOI: 10.1016/j.sbi.2024.102774

Mechanistic insights into G-protein coupling with an agonist-bound G-protein-coupled receptor

Autori: Hossein Batebi, Guillermo Pérez-Hernández, Sabrina N. Rahman, Baoliang Lan, Antje Kamprad, Mingyu Shi, David Speck, Johanna K. S. Tiemann, Ramon Guixà-González, Franziska Reinhardt, Peter F. Stadler, Makaía M. Papasergi-Scott, Georgios Skiniotis, Patrick Scheerer, Brian K. Kobilka, Jesper M. Mathiesen, Xiangyu Liu, Peter W. Hildebrand
Pubblicato in: Nature Structural &amp; Molecular Biology, Numero 31, 2024, Pagina/e 1692-1701, ISSN 1545-9993
Editore: Nature Publishing Group
DOI: 10.1038/s41594-024-01334-2

ChemFlow_py: a flexible toolkit for docking and rescoring

Autori: Luca Monari, Katia Galentino, Marco Cecchini
Pubblicato in: Journal of Computer-Aided Molecular Design, Numero 37, 2023, Pagina/e 565-572, ISSN 0920-654X
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10822-023-00527-z

Is the Neuropeptide PEN a Ligand of GPR83?

Autori: Yvonne Giesecke, Vahid Asimi, Valentina Stulberg, Gunnar Kleinau, Patrick Scheerer, Beate Koksch, Carsten Grötzinger
Pubblicato in: International Journal of Molecular Sciences, Numero Volume 24; Numero 20, 2023, Pagina/e 15117, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms242015117

A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptor α1

Autori: Alessio Bartocci, Andrea Grazzi, Nour Awad, Pierre-Jean Corringer, Paulo C. T. Souza, Marco Cecchini
Pubblicato in: Nature Communications, Numero 15, 2024, Pagina/e 9040, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-024-53098-4

Allosteric antibodies: a novel paradigm in drug discovery

Autori: Léxane Fournier, Enrico Guarnera, Harald Kolmar, Stefan Becker
Pubblicato in: Trends in Pharmacological Sciences, 2024, ISSN 0165-6147
Editore: Elsevier BV
DOI: 10.1016/j.tips.2024.10.007

The role of G protein‐coupled receptors and their ligands in animal domestication

Autori: Gunnar Kleinau, Bice Chini, Leif Andersson, Patrick Scheerer
Pubblicato in: Animal Genetics, Numero 55, 2024, Pagina/e 893-906, ISSN 0268-9146
Editore: Blackwell Publishing Inc.
DOI: 10.1111/age.13476

Intramolecular activity regulation of adhesion GPCRs in light of recent structural and evolutionary information

Autori: Gunnar Kleinau, Amal Hassan Ali, Franziska Wiechert, Michal Szczepek, Andrea Schmidt, Christian M.T. Spahn, Ines Liebscher, Torsten Schöneberg, Patrick Scheerer
Pubblicato in: Pharmacological Research, Numero Volume 197, 2023, Pagina/e 106971, ISSN 1043-6618
Editore: Academic Press
DOI: 10.1016/j.phrs.2023.106971

Effect of Water Networks On Ligand Binding: Computational Predictions vs Experiments

Autori: Tibor Viktor Szalai, Dávid Bajusz, Rita Börzsei, Balázs Zoltán Zsidó, Janez Ilaš, György G. Ferenczy, Csaba Hetényi, György M. Keserű
Pubblicato in: Journal of Chemical Information and Modeling, Numero 64, 2024, Pagina/e 8980-8998, ISSN 1549-9596
Editore: American Chemical Society
DOI: 10.1021/acs.jcim.4c01291

SH2db, an information system for the SH2 domain

Autori: Dávid Bajusz, Gáspár Pándy-Szekeres, Ágnes Takács, Elvin D de Araujo, György M Keserű
Pubblicato in: Nucleic Acids Research, Numero Volume 51; Numero W1, 2023, Pagina/e W542–W552, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkad420

Evaluation of Pharmacological Rescue of Melanocortin-4 Receptor Nonsense Mutations by Aminoglycoside

Autori: Friederike Höpfner, Sarah Paisdzior, Nanina Reininghaus, Iqra Sohail, Patrick Scheerer, Paolo Annibale, Heike Biebermann, Peter Kühnen
Pubblicato in: Life, Numero Volume 12; Numero 11, 2022, Pagina/e 1793, ISSN 2075-1729
Editore: MDPI
DOI: 10.3390/life12111793

Fucosyl glycosides for DC-SIGN targeting: Fucosylation strategies, synthesis and binding studies of model compounds

Autori: Rohit Chavan, Jonathan Lefèbre, Kateřina Jochová, Hana Dvořáková, Christoph Rademacher, Petra Ménová
Pubblicato in: Bioorganic &amp; Medicinal Chemistry, Numero 123, 2025, Pagina/e 118164, ISSN 0968-0896
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.bmc.2025.118164

Structural Basis for Highly Selective Class II Alpha Phosphoinositide-3-Kinase Inhibition

Autori: Murat Kücükdisli, Hassen Bel-Abed, Davide Cirillo, Wen-Ting Lo, Nina-Louisa Efrém, André Horatscheck, Liudmila Perepelittchenko, Polina Prokofeva, Theresa A. L. Ehret, Silke Radetzki, Martin Neuenschwander, Edgar Specker, Guillaume Médard, Susanne Müller, Stephanie Wilhelm, Bernhard Kuster, Jens Peter von Kries, Volker Haucke, Marc Nazaré
Pubblicato in: Journal of Medicinal Chemistry, Numero Volume 66; Numero 20, 2023, Pagina/e 14278-14302, ISSN 0022-2623
Editore: American Chemical Society
DOI: 10.1021/acs.jmedchem.3c01319

A platform for the early selection of non-competitive antibody-fragments from yeast surface display libraries

Autori: Léxane Fournier, Deniz Demir, Desislava Elter, Lukas Pekar, Harald Kolmar, Lars Toleikis, Stefan Becker
Pubblicato in: Biological Chemistry, 2024, ISSN 1431-6730
Editore: Walter de Gruyter GmbH & Co. KG
DOI: 10.1515/hsz-2024-0102

Mapping protein binding sites by photoreactive fragment pharmacophores

Autori: Péter Ábrányi-Balogh, Dávid Bajusz, Zoltán Orgován, Aaron B. Keeley, László Petri, Nikolett Péczka, Tibor Viktor Szalai, Gyula Pálfy, Márton Gadanecz, Emma K. Grant, Tímea Imre, Tamás Takács, Ivan Ranđelović, Marcell Baranyi, András Marton, Gitta Schlosser, Qirat F. Ashraf, Elvin D. de Araujo, Tamás Karancsi, László Buday, József Tóvári, András Perczel, Jacob T. Bush, Györ
Pubblicato in: Communications Chemistry, Numero 7, 2024, Pagina/e 168, ISSN 2399-3669
Editore: Macmillan Publishers Ltd part of Springer Nature
DOI: 10.1038/s42004-024-01252-w

Structure of the actively translating plant 80S ribosome at 2.2 Å resolution

Autori: Julia Smirnova, Justus Loerke, Gunnar Kleinau, Andrea Schmidt, Jörg Bürger, Etienne H. Meyer, Thorsten Mielke, Patrick Scheerer, Ralph Bock, Christian M. T. Spahn, Reimo Zoschke
Pubblicato in: Nature Plants, Numero Volume 9, 2023, Pagina/e 987–1000, ISSN 2055-0278
Editore: Nature Portfolio
DOI: 10.1038/s41477-023-01407-y

Molecular Effects of Auto-Antibodies on Angiotensin II Type 1 Receptor Signaling and Cell Proliferation

Autori: Aurélie Philippe, Gunnar Kleinau, Jason Jannis Gruner, Sumin Wu, Daniel Postpieszala, David Speck, Harald Heidecke, Simon J. Dowell, Gabriela Riemekasten, Peter W. Hildebrand, Julian Kamhieh-Milz, Rusan Catar, Michal Szczepek, Duska Dragun, Patrick Scheerer
Pubblicato in: International Journal of Molecular Sciences, Numero Volume 23; Numero 7, 2022, Pagina/e 3984, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23073984

Discovery of potent allosteric antibodies inhibiting EGFR

Autori: Léxane Fournier, Lukas Pekar, Birgitta Leuthner, Harald Kolmar, Lars Toleikis, Stefan Becker
Pubblicato in: mAbs, Numero 16, 2024, Pagina/e 2406548, ISSN 1942-0870
Editore: Landes Bioscience
DOI: 10.1080/19420862.2024.2406548

Electrophilic MiniFrags Revealed Unprecedented Binding Sites for Covalent HDAC8 Inhibitors

Autori: Aaron B. Keeley, Aleksandra Kopranovic, Vincenzo Di Lorenzo, Péter Ábrányi-Balogh, Niklas Jänsch, Linh N. Lai, László Petri, Zoltán Orgován, Daniel Pölöske, Anna Orlova, András György Németh, Charlotte Desczyk, Tímea Imre, Dávid Bajusz, Richard Moriggl, Franz-Josef Meyer-Almes, György M. Keserü
Pubblicato in: Journal of Medicinal Chemistry, Numero 67, 2024, Pagina/e 572-585, ISSN 0022-2623
Editore: American Chemical Society
DOI: 10.1021/acs.jmedchem.3c01779

Evolutionary analyses reveal immune cell receptor GPR84 as a conserved receptor for bacteria-derived molecules

Autori: Amadeus Samuel Schulze, Gunnar Kleinau, Rosanna Krakowsky, David Rochmann, Ranajit Das, Catherine L. Worth, Petra Krumbholz, Patrick Scheerer, Claudia Stäubert
Pubblicato in: iScience, Numero Volume 25; Numero 10, 2022, Pagina/e 105087, ISSN 2589-0042
Editore: Cell Press
DOI: 10.1016/j.isci.2022.105087

Aryl fucosides: synthesis and evaluation of their binding affinity towards the DC-SIGN receptor

Autori: Rohit Chavan, Maurice Besch, Jonathan Lefèbre, Christoph Rademacher, Petra Ménová
Pubblicato in: Organic &amp; Biomolecular Chemistry, 2025, ISSN 1477-0520
Editore: Royal Society of Chemistry
DOI: 10.1039/d5ob00472a

Glycomimetics for the inhibition and modulation of lectins

Autori: Steffen Leusmann, Petra Ménová, Elena Shanin, Alexander Titz, Christoph Rademacher
Pubblicato in: Chemical Society Reviews, Numero Volume 52, 2023, Pagina/e 3663-3740, ISSN 0306-0012
Editore: Royal Society of Chemistry
DOI: 10.1039/d2cs00954d

AI-based identification of therapeutic agents targeting GPCRs: introducing ligand type classifiers and systems biology

Autori: Jonas Goßen, Rui Pedro Ribeiro, Dirk Bier, Bernd Neumaier, Paolo Carloni, Alejandro Giorgetti, Giulia Rossetti
Pubblicato in: Chemical Science, Numero Volume 14, 2023, Pagina/e 8651-8661, ISSN 2041-6520
Editore: Royal Society of Chemistry
DOI: 10.1039/d3sc02352d

Exploring Chemical Spaces in the Billion Range: Is Docking a Computational Alternative to DNA-Encoded Libraries?

Autori: Levente M. Mihalovits, Tibor V. Szalai, Dávid Bajusz, György M. Keserű
Pubblicato in: Journal of Chemical Information and Modeling, Numero 64, 2024, Pagina/e 8963-8979, ISSN 1549-9596
Editore: American Chemical Society
DOI: 10.1021/acs.jcim.4c00803

Secondary sites of the C-type lectin-like fold

Autori: Jonathan Lefèbre, Torben Falk, Yunzhan Ning, Christoph Rademacher
Pubblicato in: Chemistry: A European Journal, Numero Volume 30; Numero 30, 2024, Pagina/e e202400660, ISSN 0947-6539
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/chem.202400660

A Setmelanotide-like Effect at MC4R Is Achieved by MC4R Dimer Separation

Autori: Nanina Reininghaus, Sarah Paisdzior, Friederike Höpfner, Sabine Jyrch, Cigdem Cetindag, Patrick Scheerer, Peter Kühnen, Heike Biebermann
Pubblicato in: Biomolecules, Numero Volume 12; Numero 8, 2022, Pagina/e 1119, ISSN 2218-273X
Editore: MDPI
DOI: 10.3390/biom12081119

Identification of the Allosteric Binding Site for Thiazolopyrimidine on the C-Type Lectin Langerin

Autori: Hengxi Zhang, Carlos Modenutti, Yelha Phani Kumar Nekkanti, Maxime Denis, Iris A. Bermejo, Jonathan Lefèbre, Kateryna Che, Dongyoon Kim, Marten Kagelmacher, Dennis Kurzbach, Marc Nazaré, Christoph Rademacher
Pubblicato in: ACS Chemical Biology, Numero Volume 17; Numero 10, 2022, Pagina/e 2728–2733, ISSN 1554-8929
Editore: American Chemical Society
DOI: 10.1021/acschembio.2c00626

The orchestrated signaling by PI3Kα and PTEN at the membrane interface

Autori: Danai Maria Kotzampasi, Kyriaki Premeti, Alexandra Papafotika, Vasiliki Syropoulou, Savvas Christoforidis, Zoe Cournia, George Leondaritis
Pubblicato in: Computational and Structural Biotechnology Journal, Numero Volume 20, 2022, Pagina/e 5607-5621, ISSN 2001-0370
Editore: Elsevier
DOI: 10.1016/j.csbj.2022.10.007

ChemFlow─From 2D Chemical Libraries to Protein–Ligand Binding Free Energies

Autori: Diego E. Barreto Gomes, Katia Galentino, Marion Sisquellas, Luca Monari, Cédric Bouysset, Marco Cecchini
Pubblicato in: Journal of Chemical Information and Modeling, Numero Volume 63; Numero 2, 2023, Pagina/e 407–411, ISSN 1549-9596
Editore: American Chemical Society
DOI: 10.1021/acs.jcim.2c00919

Angiotensin and Endothelin Receptor Structures With Implications for Signaling Regulation and Pharmacological Targeting

Autori: David Speck, Gunnar Kleinau, Michal Szczepek, Dennis Kwiatkowski, Rusan Catar, Aurélie Philippe, Patrick Scheerer
Pubblicato in: Frontiers in Endocrinology, Numero Volume 13, 2022, Pagina/e 880002, ISSN 1664-2392
Editore: Frontiers Media
DOI: 10.3389/fendo.2022.880002

Enhancing NK cell-mediated tumor killing of B7-H6+ cells with bispecific antibodies targeting allosteric sites of NKp30

Autori: Léxane Fournier, Paul Arras, Lukas Pekar, Harald Kolmar, Stefan Zielonka, Lars Toleikis, Stefan Becker
Pubblicato in: Molecular Therapy: Oncology, Numero 33, 2024, Pagina/e 200917, ISSN 2950-3299
Editore: Elsevier Inc.
DOI: 10.1016/j.omton.2024.200917