Publications associées à Biologie chimique

Augmenting large language models with chemistry tools

Philippe Schwaller, Oliver Tobias Schilter, Andres Camilo Marulanda Bran, Carlo Baldassari

Large language models (LLMs) have shown strong performance in tasks across domains but struggle with chemistry-related problems. These models also lack access to external knowledge sources, limiting their usefulness in scientific applications. We introduce ...

Nature Portfolio2024

Novel Alkynylation Methods through the Combination of Hypervalent Iodine Reagents and Alkynyl-trifluoroborate Salts

Julien Aymeric Borrel

The alkyne motif is a versatile functional group often encountered in organic chemistry. It can be involved in various transformations such as the alkyne-azide cycloaddition and has found widespread application in medicinal chemistry, chemical biology and ...

EPFL2024

Targeting TDP-43 Proteinopathies in Neurodegeneration by its Native-State Stabilization

Lixin Yang

Preventing the misfolding or aggregation of TDP-43 is the most actively pursued disease-modifying strategy to treat amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases. In our work, we provide proof of concept that native state stabili ...

EPFL2024

Structure-function analysis of the cyclic β-1,2-glucan synthase from Agrobacterium tumefaciens

Henning Paul-Julius Stahlberg, Dongchun Ni

The synthesis of complex sugars is a key aspect of microbial biology. Cyclic beta-1,2-glucan (C beta G) is a circular polysaccharide critical for host interactions of many bacteria, including major pathogens of humans (Brucella) and plants (Agrobacterium). ...

Nature Portfolio2024

Hypervalent Iodine: New Reagents and Functionalization of Peptides

Eliott Hugo Joran Le Du

Alkynes are found in a multitude of natural or synthetic bioactive compounds. In addition to the capacity of these chemical motifs to impact the physicochemical properties of a molecule of interest, the well-established reactivity of alkynes makes them ide ...

EPFL2023

Finding a vocation for validation: taking proteomics beyond association and location

Yimon Aye, Jinmin Liu

First established in the seventies, proteomics, chemoproteomics, and most recently, spatial/proximity-proteomics technologies have empowered researchers with new capabilities to illuminate cellular communication networks that govern sophisticated decision- ...

ROYAL SOC CHEMISTRY2022

Hiding in Plain Sight: The Issue of Hidden Variables

Yimon Aye, Mahdi Assari

Here we discuss "hidden variables", which are typically introduced during an experiment as a consequence of the application of two independent variables together to create a stimulus. With increased sophistication in modern chemical biology tools and relat ...

AMER CHEMICAL SOC2022

Optical microscopy gets down to angstroms

Suliana Manley, Giorgio Tortarolo

Super-resolution microscopy at angstrom precision could pave the way to optical structural biology in cells. ...

NATURE PORTFOLIO2022

Ring-Opening Reactions of Aminocyclopropanes and Aminocyclobutanes

Mingming Wang

Nitrogen-containing compounds are an important class of molecules in medicinal chemistry, chemical biology, biochemistry, material sciences or environmental sciences. Organic nitrogen occurs in many forms, ranging from small building blocks such as urea, a ...

EPFL2022

Alkynyl triazenes enable divergent syntheses of 2-pyrones

Kay Severin, Nicolai Cramer, Carl Thomas Bormann, Jin Fay Tan

The 2-pyrone motif occurs frequently in bioactive natural products and is appreciated as synthetic intermediates. However, only few methods allow for diversifying functional group modifications on this relevant heterocycle. The distinct properties of 1-alk ...

2021

Image- and Fluorescence-Based Test Shows Oxidant-Dependent Damages in Red Blood Cells and Enables Screening of Potential Protective Molecules

Gerardo Turcatti, Benjamin Rappaz, David Crettaz, Michel Prudent, Manon Sandra Bardyn

An increase of oxygen saturation within blood bags and metabolic dysregulation occur during storage of red blood cells (RBCs). It leads to the gradual exhaustion of RBC antioxidant protective system and, consequently, to a deleterious state of oxidative st ...

2021

Genetically Encoded Activators of Small Molecules for Imaging and Drug Delivery

Pablo Rivera Fuentes, Zacharias Thiel, Jade Noémie Nam Nguyen

Chemical biologists have developed many tools based on genetically encoded macromolecules and small, synthetic compounds. The two different approaches are extremely useful, but they have inherent limitations. In this Minireview, we highlight examples of st ...

Wiley-VCH Verlag GmbH2020

Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities

Yimon Aye, Yi Zhao

Transient associations between numerous organelles-e.g., the endoplasmic reticulum and the mitochondria-forge highly-coordinated, particular environments essential for cross-compartment information flow. Our perspective summarizes chemical-biology tools th ...

ROYAL SOC CHEMISTRY2020

Development of chemical biology tools to reveal the function and organization of the silenced chromatin state

Nora Guidotti

Effector proteins are recruited to chromatin via transient interactions between their reader domains and histone post-translational modification (PTM) patterns. These interactions form signaling pathways that control gene expression or repression and which ...

EPFL2020

Development of Photocatalysts towards the Visible-Light driven C-Terminal Bioconjugation of Peptides and Proteins

Marion Marie-Agnès Garreau

If small molecules have led to tremendous progress in curing diseases, new therapeutic agents such as peptides or antibody-drugs conjugates have emerged as a highly promising next generation of pharmaceuticals. As for small molecules, their derivatization ...

EPFL2020

Stabilization strategies in biomass depolymerization using chemical functionalization

Jeremy Luterbacher, Ydna Marie Questell-Santiago

A central feature of most lignocellulosic-biomass-valorization strategies is the depolymerization of all its three major constituents: cellulose and hemicellulose to simple sugars, and lignin to phenolic monomers. However, reactive intermediates, generally ...

2020

Design and validation of bioorthogonal probes for cellular disease models

Pier Luca D'Alessandro

Well-validated chemical probes enable testing of biological hypotheses, investigation of target tractability and translatability to the clinical phase. Consequently, these important tool compounds play a key role in the drug discovery process. Moreover, th ...

EPFL2019

Aerolysin, a Powerful Protein Sensor for Fundamental Studies and Development of Upcoming Applications

Françoise Gisou van der Goot Grunberg

The nanopore electrical approach is a breakthrough in single molecular level detection of particles as small as ions, and complex as biomolecules. This technique can be used for molecule analysis and characterization as well as for the understanding of con ...

AMER CHEMICAL SOC2019

Cyclic Hypervalent Iodine Reagents for Azidation: Safer Reagents and Photoredox-Catalyzed Ring Expansion

Thierry Meyer, Jérôme Waser, Stefano Nicolai, Annik Nanchen, Raphaël Michel Henri Simonet-Davin, Sébastien Pierre Louis Alazet, Johannes Preindl

Azides are building blocks of increasing importance in synthetic chemistry, chemical biology, and materials science. Azidobenziodoxolone (ABX, Zhdankin reagent) is a valuable azide source, but its safety profile has not been thoroughly established. Herein, ...

2018

Can Biomimetic Zinc Compounds Assist a (3 + 2) Cycloaddition Reaction? A Theoretical Perspective

Ursula Röthlisberger, Esra Bozkurt

Compounds bearing tetrazole rings are valuable facets in numerous branches of chemistry including metabolic imaging and the production of drugs and high-energy materials. Synthesis of tetrazoles with the help of organocatalysts has intensively been explore ...

2017