Publications by Bruno Emanuel Ferreira De Sousa Correia

Custom CRISPR—Cas9 PAM variants via scalable engineering and machine learning

Bruno Emanuel Ferreira De Sousa Correia, Martin Pacesa

Engineering and characterizing proteins can be time-consuming and cumbersome, motivating the development of generalist CRISPR-Cas enzymes1–4 to enable diverse genome editing applications. However, such enzymes have caveats such as an increased risk of off- ...

Springer Science and Business Media LLC2025

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

Boosting Protein Graph Representations through Static-Dynamic Fusion

Pierre Vandergheynst, Bruno Emanuel Ferreira De Sousa Correia, Daniel Probst

Machine learning for protein modeling faces significant challenges due to proteins' inherently dynamic nature, yet most graph-based machine learning methods rely solely on static structural information. Recently, the growing availability of molecular dynam ...

2025

Equivariant 3D-conditional diffusion model for molecular linker design

Pascal Frossard, Bruno Emanuel Ferreira De Sousa Correia, Clément Arthur Yvon Vignac, Ilia Igashov, Arne Schneuing

Fragment-based drug discovery has been an effective paradigm in early-stage drug development. An open challenge in this area is designing linkers between disconnected molecular fragments of interest to obtain chemically relevant candidate drug molecules. I ...

2024

An atlas of protein homo-oligomerization across domains of life

Sandrine Madeleine Suzanne Georgeon, Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde, Martin Pacesa, Yoan Désiré Duhoo

Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a scalabl ...

2024

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

Isoperimetry in Finitely Generated Groups

Marc Troyanov, Bruno Emanuel Ferreira De Sousa Correia

We revisit the isoperimetric inequalities for finitely generated groups introduced and studied by N. Varopoulos, T. Coulhon and L. Saloff-Coste. Namely we show that a lower bound on the isoperimetric quotient of finite subsets in a finitely generated group ...

Springer2024

Antibody-peptide conjugates deliver covalent inhibitors blocking oncogenic cathepsins

Luc Reymond, Florence Pojer, Albert Santamaria Martinez, Sandrine Madeleine Suzanne Georgeon, Aaron Simone Petruzzella, Bruno Emanuel Ferreira De Sousa Correia, Elisa Oricchio, Natalya Katanayeva, Sarah Wehrle, Kelvin Ka Ching Lau

Cysteine cathepsins are a family of proteases that are relevant therapeutic targets for the treatment of different cancers and other diseases. However, no clinically approved drugs for these proteins exist, as their systemic inhibition can induce deleterio ...

Nature Portfolio2024

Exploring “dark-matter” protein folds using deep learning

Pierre Vandergheynst, Sandrine Madeleine Suzanne Georgeon, Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Andreas Loukas, Stéphane Rosset, Alexandra Krina Van Hall-Beauvais, Casper Alexander Goverde

De novo protein design explores uncharted sequence and structure space to generate novel proteins not sampled by evolution. A main challenge in de novo design involves crafting “designable” structural templates to guide the sequence searches toward adoptin ...

2024

A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins

Bruno Emanuel Ferreira De Sousa Correia, Stéphane Rosset

Deep mutational scanning is a powerful method for exploring the mutational fitness landscape of proteins. Its adaptation to anti-CRISPR proteins, which are natural CRISPR-Cas inhibitors and key players in the co-evolution of microbes and phages, facilitate ...

2024

Dual ON/OFF-switch chimeric antigen receptor controlled by two clinically approved drugs

Sandrine Madeleine Suzanne Georgeon, Bruno Emanuel Ferreira De Sousa Correia, Sailan Shui, Leo Scheller

The ability to remotely control the activity of chimeric antigen receptors (CARs) with small molecules can improve the safety and efficacy of gene-modified T cells. Split ON- or OFF-switch CARs involve the dissociation of tumor–antigen binding from T cell ...

National Academy of Sciences2024

Epitope-focused immunogens targeting the hepatitis C virus glycoproteins induce broadly neutralizing antibodies

Bruno Emanuel Ferreira De Sousa Correia, Sabrina Susan Vollers, Andreas Scheck, Stéphane Rosset

Hepatitis C virus (HCV) infection causes similar to 290,000 annual human deaths despite the highly effective antiviral treatment available. Several viral immune evasion mechanisms have hampered the development of an effective vaccine against HCV, among the ...

AMER ASSOC ADVANCEMENT SCIENCE2024

The physiological landscape and specificity of antibody repertoires are consolidated by multiple immunizations

Bruno Emanuel Ferreira De Sousa Correia, Fabian Sesterhenn

Diverse antibody repertoires spanning multiple lymphoid organs (i.e., bone marrow, spleen, lymph nodes) form the foundation of protective humoral immunity. Changes in their composition across lymphoid organs are a consequence of B-cell selection and migrat ...

2024

Computational design of soluble and functional membrane protein analogues

Sandrine Madeleine Suzanne Georgeon, Bruno Emanuel Ferreira De Sousa Correia, Stéphane Rosset, Casper Alexander Goverde, Martin Pacesa

De novo design of complex protein folds using solely computational means remains a substantial challenge1. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, ...

2024

Structure-based drug design with equivariant diffusion models

Bruno Emanuel Ferreira De Sousa Correia, Ilia Igashov, Arne Schneuing

Structure-based drug design (SBDD) aims to design small-molecule ligands that bind with high affinity and specificity to pre-determined protein targets. Generative SBDD methods leverage structural data of drugs with their protein targets to propose new dru ...

SPRINGERNATURE2024

FSscore: A Personalized Machine Learning-Based Synthetic Feasibility Score

Philippe Schwaller, Bruno Emanuel Ferreira De Sousa Correia

Determining whether a molecule can be synthesized is crucial in chemistry and drug discovery, as it guides experimental prioritization and molecule ranking in de novo design tasks. Existing scoring approaches to assess synthetic feasibility struggle to ext ...

2024

Structures of the Foamy virus fusion protein reveal an unexpected link with the F protein of paramyxo- and pneumoviruses

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

Foamy viruses (FVs) constitute a subfamily of retroviruses. Their envelope (Env) glycoprotein drives the merger of viral and cellular membranes during entry into cells. The only available structures of retroviral Envs are those from human and simian immuno ...

2024

An evolved artificial radical cyclase enables the construction of bicyclic terpenoid scaffolds via an H-atom transfer pathway

Bruno Emanuel Ferreira De Sousa Correia

While natural terpenoid cyclases generate complex terpenoid structures via cationic mechanisms, alternative radical cyclization pathways are underexplored. The metal-catalysed H-atom transfer reaction (M-HAT) offers an attractive means for hydrofunctionali ...

2024

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

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