Publications de Pablo Gainza Cirauqui

Targeting protein-ligand neosurfaces with a generalizable deep learning tool

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

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

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, Corey Alfred Stevens, Lukasz Richter, Francesca Olgiati, 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

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

WILEY2023

Rational Design of Chemically Controlled Antibodies and Protein Therapeutics

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

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

Henning Paul-Julius Stahlberg, Didier Trono, Priscilla Turelli, Charlène Mireille Raymonde Raclot, Sandrine Madeleine Suzanne Georgeon, Beat Fierz, Aaron Simone Petruzzella, Anthony Marchand, Bruno Emanuel Ferreira De Sousa Correia, Elisa Oricchio, Zander Harteveld, Pablo Gainza Cirauqui, Freyr Sverrisson, Andreas Scheck, Sarah Wehrle, Stéphane Rosset, Alexandra Krina Van Hall-Beauvais, Alexandra Teslenko, Jane Marsden, Michael Bronstein, Casper Alexander Goverde, Stephen Michael Buckley, Dongchun Ni, Martin Pacesa

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

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

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

Novel chemically controlled cellular switches

Bruno Emanuel Ferreira De Sousa Correia, Pablo Gainza Cirauqui, Sailan Shui

The invention relates to activation by inhibitor release (AIR) switches and chemically disruptable heterodimers (CDH), their use in controlling cell signaling components, and their use for treatments and therapies. ...

2022

Computational design of bioactive protein switches with multi-logics for cell-based therapeutics

Bruno Emanuel Ferreira De Sousa Correia, Che Yang, Pablo Gainza Cirauqui, Sailan Shui, Leo Scheller

WILEY2021

De Novo Design of Site-specific Protein Binders Using Surface Fingerprints

Sandrine Madeleine Suzanne Georgeon, Aaron Simone Petruzzella, Elisa Oricchio, Zander Harteveld, Pablo Gainza Cirauqui, Freyr Sverrisson, Andreas Scheck, Sarah Wehrle, Stéphane Rosset, Alexandra Krina Van Hall-Beauvais

WILEY2021

Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning

Bruno Emanuel Ferreira De Sousa Correia, Pablo Gainza Cirauqui

The optimization of therapeutic antibodies is time-intensive and resource-demanding, largely because of the low-throughput screening of full-length antibodies (approximately 1 x 10(3) variants) expressed in mammalian cells, which typically results in few o ...

NATURE RESEARCH2021

A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy

George Coukos, Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez, Pablo Gainza Cirauqui, Sabrina Susan Vollers, Sailan Shui

The activity of CAR-T cells is reversibly halted with a small-molecule drug. Approaches to increase the activity of chimeric antigen receptor (CAR)-T cells against solid tumors may also increase the risk of toxicity and other side effects. To improve the s ...

2020

Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen

Sai Reddy, Patricia Corthésy Henrioud, Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez, Fabian Sesterhenn, Che Yang, Pablo Gainza Cirauqui, Sabrina Susan Vollers, Stéphane Rosset

Throughout the last several decades, vaccination has been key to prevent and eradicate infectious diseases. However, many pathogens (e.g., respiratory syncytial virus [RSV], influenza, dengue, and others) have resisted vaccine development efforts, largely ...

2019

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

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

Predicting interactions between proteins and other biomolecules solely based on structure remains a challenge in biology. A high-level representation of protein structure, the molecular surface, displays patterns of chemical and geometric features that fin ...

2019

Decrypting interaction fingerprints in protein molecular surfaces

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

SPRINGER2019

Heterodimeric inactivatable chimeric antigen receptors

George Coukos, Bruno Emanuel Ferreira De Sousa Correia, Pablo Gainza Cirauqui

The invention relates to heterodimeric inactivatable chimeric antigen receptors (CARs) and their use for treatment. ...

2019

Computational protein design - the next generation tool to expand synthetic biology applications

Bruno Emanuel Ferreira De Sousa Correia, Pablo Gainza Cirauqui

2018