Publications by Pablo Gainza Cirauqui

Targeting protein-ligand neosurfaces with a generalizable deep learning tool

Sebastian Maerkl, Bruno Emanuel Ferreira De Sousa Correia, Luc Reymond, Sandrine Madeleine Suzanne Georgeon, Philippe Schwaller, Anthony Marchand, Leo Scheller, Arne Schneuing, Stephen Michael Buckley, Martin Pacesa

Molecular recognition events between proteins drive biological processes in living systems1. However, higher levels of mechanistic regulation have emerged, in which protein-protein interactions are conditioned to small molecules2, 3, 4-5. Despite recent ad ...

NATURE PORTFOLIO2025

Chemically disruptable molecule switch and use thereof

Bruno Emanuel Ferreira De Sousa Correia, Pablo Gainza Cirauqui

The invention relates to chemically disruptable molecule (CDM) switch, their use in controlling cell signaling components, and their use for treatments and therapies. Further disclosed are methods of treating and/or preventing a disease, such as e.g. a can ...

2024

A Synthetic Multivalent Lipopeptide Derived from Pam3CSK4 with Irreversible Influenza Inhibition and Immuno-Stimulating Effects

Francesco Stellacci, Li Tang, Bruno Emanuel Ferreira De Sousa Correia, Quy Ong Khac, Francesca Olgiati, Pablo Gainza Cirauqui, Lixia Wei, Armand Kurum, Yong Zhu

The activation of the host adaptive immune system is crucial for eliminating viruses. However, influenza infection often suppresses the innate immune response that precedes adaptive immunity, and the adaptive immune responses are typically delayed. Dendrit ...

Wiley-V C H Verlag Gmbh2024

Virucidal compounds and use thereof

Francesco Stellacci, Bruno Emanuel Ferreira De Sousa Correia, Pablo Gainza Cirauqui, Francesca Olgiati, Corey Alfred Stevens, Lukasz Richter, Chiara Medaglia

Disclosed herein are peptide-grafted compounds that irreversibly deactivate bacteriophages or influenza virus depending on the peptide and remain safe for bacteria and mammalian cells. The active compounds comprise a core (cyclodextrin or gold nanoparticle ...

2024

Rules and mechanisms governing G protein coupling selectivity of GPCRs

Bruno Emanuel Ferreira De Sousa Correia, Pablo Gainza Cirauqui

G protein-coupled receptors (GPCRs) convert extracellular stimuli into intracellular signaling by coupling to heterotrimeric G proteins of four classes: Gi/o, Gq, Gs, and G12/13. However, our understanding of the G protein selectivity of GPCRs is incomplet ...

Cell Press2023

Machine Learning in Protein Science De Novo Design of Site-Specific Protein Binders Using Surface Fingerprints

Didier Trono, Henning Paul-Julius Stahlberg, Priscilla Turelli, Bruno Emanuel Ferreira De Sousa Correia, Dongchun Ni, Andreas Scheck, Anthony Marchand, Casper Alexander Goverde, Pablo Gainza Cirauqui, Zander Harteveld

WILEY2023

Rational Design of Chemically Controlled Antibodies and Protein Therapeutics

Li Tang, Bruno Emanuel Ferreira De Sousa Correia, Sandrine Madeleine Suzanne Georgeon, Anthony Marchand, Leo Scheller, Lucia Bonati, Pablo Gainza Cirauqui, Stéphane Rosset, Sailan Shui

Protein-based therapeutics, such as monoclonal antibodies and cytokines, are important therapies for various pathophysiological conditions such as oncology, autoimmune disorders, and viral infections. However, the wide application of such protein therapeut ...

2023

De novo design of protein interactions with learned surface fingerprints

Didier Trono, Henning Paul-Julius Stahlberg, Beat Fierz, Priscilla Turelli, Bruno Emanuel Ferreira De Sousa Correia, Elisa Oricchio, Sandrine Madeleine Suzanne Georgeon, Dongchun Ni, Andreas Scheck, Michael Bronstein

Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This k ...

2023

Systems and methods for de novo design of protein interactions with learned surface fingerprints

Andreas Scheck, Michael Bronstein, Anthony Marchand, Pablo Gainza Cirauqui, Zander Harteveld, Sarah Wehrle, Freyr Sverrisson, Alexandra Krina Van Hall-Beauvais

The present application relates to a computer-implemented systems and methods for protein interaction design using surface fingerprints. The method comprises predicting at least one target interface site with high binding propensity, wherein, optionally, t ...

2023

A method and system for fast end-to-end learning on protein surfaces

Bruno Emanuel Ferreira De Sousa Correia, Pablo Gainza Cirauqui, Freyr Sverrisson

The present invention concerns a computer-system-implemented method for predicting properties of a protein molecule, comprising the steps of: receiving an input representation of the protein molecule; applying a surface generator to produce a molecular sur ...

2022