Allostery in Drug Discovery

Project Information

ALLODD

Grant agreement ID: 956314

DOI

10.3030/956314

Project closed

EC signature date 28 May 2021

Start date 1 September 2021

End date 31 August 2025

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 3 627 680,76

EU contribution

€ 3 627 680,76

Coordinated by

IDRYMA IATROVIOLOGIKON EREUNON AKADEMIAS ATHINON
Greece

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

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

Publications

Peer reviewed articles (38)

Computational advances in discovering cryptic pockets for drug discovery

Author(s): Martijn P. Bemelmans, Zoe Cournia, Kelly L. Damm-Ganamet, Francesco L. Gervasio, Vineet Pande
Published in: Current Opinion in Structural Biology, Issue 90, 2025, Page(s) 102975, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2024.102975

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

Author(s): 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
Published in: QRB Discovery, Issue 3, 2022, Page(s) e19, ISSN 2633-2892
Publisher: Cambridge University Press
DOI: 10.1017/qrd.2022.16

Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential

Author(s): 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
Published in: Journal of Chemical Information and Modeling, Issue 64, 2024, Page(s) 8176-8192, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.4c00819

Functional modulation of PTH1R activation and signalling by RAMP2

Author(s): Katarina Nemec, Hannes Schihada, Gunnar Kleinau, Ulrike Zabel, Eugene O. Grushevskyi, Patrick Scheerer, Martin J. Lohse, Isabella Maiellaro
Published in: Proceedings of the National Academy of Sciences of the United States of America, Issue Volume 119; Issue 32, 2022, Page(s) e2122037119, ISSN 0027-8424
Publisher: 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

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

Alchemical Free Energy Calculations on Membrane-Associated Proteins

Author(s): 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
Published in: Journal of Chemical Theory and Computation, Issue Volume 19; Issue 21, 2023, Page(s) 7437–7458, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.3c00365

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

Author(s): 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
Published in: JCI Insight, Issue 9, 2024, Page(s) e167092, ISSN 2379-3708
Publisher: American Society for Clinical of Investigation
DOI: 10.1172/jci.insight.167092

Machine learning approaches in predicting allosteric sites

Author(s): Francho Nerín-Fonz, Zoe Cournia
Published in: Current Opinion in Structural Biology, Issue Volume 85, 2024, Page(s) 102774, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2024.102774

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

Author(s): 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
Published in: Nature Structural &amp; Molecular Biology, Issue 31, 2024, Page(s) 1692-1701, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-024-01334-2

ChemFlow_py: a flexible toolkit for docking and rescoring

Author(s): Luca Monari, Katia Galentino, Marco Cecchini
Published in: Journal of Computer-Aided Molecular Design, Issue 37, 2023, Page(s) 565-572, ISSN 0920-654X
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10822-023-00527-z

Is the Neuropeptide PEN a Ligand of GPR83?

Author(s): Yvonne Giesecke, Vahid Asimi, Valentina Stulberg, Gunnar Kleinau, Patrick Scheerer, Beate Koksch, Carsten Grötzinger
Published in: International Journal of Molecular Sciences, Issue Volume 24; Issue 20, 2023, Page(s) 15117, ISSN 1422-0067
Publisher: 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

Author(s): Alessio Bartocci, Andrea Grazzi, Nour Awad, Pierre-Jean Corringer, Paulo C. T. Souza, Marco Cecchini
Published in: Nature Communications, Issue 15, 2024, Page(s) 9040, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-53098-4

Allosteric antibodies: a novel paradigm in drug discovery

Author(s): Léxane Fournier, Enrico Guarnera, Harald Kolmar, Stefan Becker
Published in: Trends in Pharmacological Sciences, 2024, ISSN 0165-6147
Publisher: Elsevier BV
DOI: 10.1016/j.tips.2024.10.007

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

Author(s): Gunnar Kleinau, Bice Chini, Leif Andersson, Patrick Scheerer
Published in: Animal Genetics, Issue 55, 2024, Page(s) 893-906, ISSN 0268-9146
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/age.13476

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

Author(s): Gunnar Kleinau, Amal Hassan Ali, Franziska Wiechert, Michal Szczepek, Andrea Schmidt, Christian M.T. Spahn, Ines Liebscher, Torsten Schöneberg, Patrick Scheerer
Published in: Pharmacological Research, Issue Volume 197, 2023, Page(s) 106971, ISSN 1043-6618
Publisher: Academic Press
DOI: 10.1016/j.phrs.2023.106971

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

Author(s): Tibor Viktor Szalai, Dávid Bajusz, Rita Börzsei, Balázs Zoltán Zsidó, Janez Ilaš, György G. Ferenczy, Csaba Hetényi, György M. Keserű
Published in: Journal of Chemical Information and Modeling, Issue 64, 2024, Page(s) 8980-8998, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.4c01291

SH2db, an information system for the SH2 domain

Author(s): Dávid Bajusz, Gáspár Pándy-Szekeres, Ágnes Takács, Elvin D de Araujo, György M Keserű
Published in: Nucleic Acids Research, Issue Volume 51; Issue W1, 2023, Page(s) W542–W552, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad420

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

Author(s): Friederike Höpfner, Sarah Paisdzior, Nanina Reininghaus, Iqra Sohail, Patrick Scheerer, Paolo Annibale, Heike Biebermann, Peter Kühnen
Published in: Life, Issue Volume 12; Issue 11, 2022, Page(s) 1793, ISSN 2075-1729
Publisher: MDPI
DOI: 10.3390/life12111793

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

Author(s): Rohit Chavan, Jonathan Lefèbre, Kateřina Jochová, Hana Dvořáková, Christoph Rademacher, Petra Ménová
Published in: Bioorganic &amp; Medicinal Chemistry, Issue 123, 2025, Page(s) 118164, ISSN 0968-0896
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.bmc.2025.118164

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

Author(s): 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
Published in: Journal of Medicinal Chemistry, Issue Volume 66; Issue 20, 2023, Page(s) 14278-14302, ISSN 0022-2623
Publisher: 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

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

Mapping protein binding sites by photoreactive fragment pharmacophores

Author(s): 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
Published in: Communications Chemistry, Issue 7, 2024, Page(s) 168, ISSN 2399-3669
Publisher: 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

Author(s): 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
Published in: Nature Plants, Issue Volume 9, 2023, Page(s) 987–1000, ISSN 2055-0278
Publisher: Nature Portfolio
DOI: 10.1038/s41477-023-01407-y

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

Author(s): 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
Published in: International Journal of Molecular Sciences, Issue Volume 23; Issue 7, 2022, Page(s) 3984, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23073984

Discovery of potent allosteric antibodies inhibiting EGFR

Author(s): Léxane Fournier, Lukas Pekar, Birgitta Leuthner, Harald Kolmar, Lars Toleikis, Stefan Becker
Published in: mAbs, Issue 16, 2024, Page(s) 2406548, ISSN 1942-0870
Publisher: Landes Bioscience
DOI: 10.1080/19420862.2024.2406548

Electrophilic MiniFrags Revealed Unprecedented Binding Sites for Covalent HDAC8 Inhibitors

Author(s): 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
Published in: Journal of Medicinal Chemistry, Issue 67, 2024, Page(s) 572-585, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.3c01779

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

Author(s): Amadeus Samuel Schulze, Gunnar Kleinau, Rosanna Krakowsky, David Rochmann, Ranajit Das, Catherine L. Worth, Petra Krumbholz, Patrick Scheerer, Claudia Stäubert
Published in: iScience, Issue Volume 25; Issue 10, 2022, Page(s) 105087, ISSN 2589-0042
Publisher: Cell Press
DOI: 10.1016/j.isci.2022.105087

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

Author(s): Rohit Chavan, Maurice Besch, Jonathan Lefèbre, Christoph Rademacher, Petra Ménová
Published in: Organic &amp; Biomolecular Chemistry, 2025, ISSN 1477-0520
Publisher: Royal Society of Chemistry
DOI: 10.1039/d5ob00472a

Glycomimetics for the inhibition and modulation of lectins

Author(s): Steffen Leusmann, Petra Ménová, Elena Shanin, Alexander Titz, Christoph Rademacher
Published in: Chemical Society Reviews, Issue Volume 52, 2023, Page(s) 3663-3740, ISSN 0306-0012
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2cs00954d

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

Author(s): Jonas Goßen, Rui Pedro Ribeiro, Dirk Bier, Bernd Neumaier, Paolo Carloni, Alejandro Giorgetti, Giulia Rossetti
Published in: Chemical Science, Issue Volume 14, 2023, Page(s) 8651-8661, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/d3sc02352d

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

Author(s): Levente M. Mihalovits, Tibor V. Szalai, Dávid Bajusz, György M. Keserű
Published in: Journal of Chemical Information and Modeling, Issue 64, 2024, Page(s) 8963-8979, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.4c00803

Secondary sites of the C-type lectin-like fold

Author(s): Jonathan Lefèbre, Torben Falk, Yunzhan Ning, Christoph Rademacher
Published in: Chemistry: A European Journal, Issue Volume 30; Issue 30, 2024, Page(s) e202400660, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.202400660

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

Author(s): Nanina Reininghaus, Sarah Paisdzior, Friederike Höpfner, Sabine Jyrch, Cigdem Cetindag, Patrick Scheerer, Peter Kühnen, Heike Biebermann
Published in: Biomolecules, Issue Volume 12; Issue 8, 2022, Page(s) 1119, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12081119

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

Author(s): 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
Published in: ACS Chemical Biology, Issue Volume 17; Issue 10, 2022, Page(s) 2728–2733, ISSN 1554-8929
Publisher: American Chemical Society
DOI: 10.1021/acschembio.2c00626

The orchestrated signaling by PI3Kα and PTEN at the membrane interface

Author(s): Danai Maria Kotzampasi, Kyriaki Premeti, Alexandra Papafotika, Vasiliki Syropoulou, Savvas Christoforidis, Zoe Cournia, George Leondaritis
Published in: Computational and Structural Biotechnology Journal, Issue Volume 20, 2022, Page(s) 5607-5621, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2022.10.007

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

Author(s): Diego E. Barreto Gomes, Katia Galentino, Marion Sisquellas, Luca Monari, Cédric Bouysset, Marco Cecchini
Published in: Journal of Chemical Information and Modeling, Issue Volume 63; Issue 2, 2023, Page(s) 407–411, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.2c00919

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

Author(s): David Speck, Gunnar Kleinau, Michal Szczepek, Dennis Kwiatkowski, Rusan Catar, Aurélie Philippe, Patrick Scheerer
Published in: Frontiers in Endocrinology, Issue Volume 13, 2022, Page(s) 880002, ISSN 1664-2392
Publisher: 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

Author(s): Léxane Fournier, Paul Arras, Lukas Pekar, Harald Kolmar, Stefan Zielonka, Lars Toleikis, Stefan Becker
Published in: Molecular Therapy: Oncology, Issue 33, 2024, Page(s) 200917, ISSN 2950-3299
Publisher: Elsevier Inc.
DOI: 10.1016/j.omton.2024.200917