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Related publications (27)

Development of cysteine cathepsin inhibitors combined with cell type-specific delivery for the treatment of B-cell lymphoma and solid tumors

Aaron Simone Petruzzella

Cysteine cathepsins proteases are enzymes that play essential physiological roles, but their activity is also associated to different aspects of cancer progression and to the development of other diseases. Therefore, cysteine cathepsins are relevant and pr ...

EPFL2024

Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7

Alexander Lund Nielsen

The sirtuins are NAD+-dependent lysine deacylases, comprising seven isoforms (SIRT1-7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic m ...

Wiley-VCH Verlag GmbH2023

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Generating macrocyclic inhibitors of protein-protein interactions

Gontran Sangouard

Protein-protein interactions (PPIs) play important roles in many diseases and their modulation is an attractive strategy for developing new therapeutics. However, the relatively large and often flat binding surfaces of PPIs makes the development of inhibit ...

EPFL2022

Synthesis and direct assay of large macrocycle diversities by combinatorial late-stage modification at picomole scale

Gerardo Turcatti, Christian Heinis, Julien Bortoli Chapalay, Jonathan Patrice Vesin, Alessandro Angelini, Manuel Leonardo Merz, Sevan Mleh Habeshian, Mischa Schüttel, Ganesh Kumar Mothukuri, Gontran Sangouard, Cristina Diaz Perlas, Zsolt Bognár

Macrocycles have excellent potential as therapeutics due to their ability to bind challenging targets. However, generating macrocycles against new targets is hindered by a lack of large macrocycle libraries for high-throughput screening. To overcome this, ...

Nature Research2022

A fluorescent multi-domain protein reveals the unfolding mechanism of Hsp70

Paolo De Los Rios, Satyam Tiwari, Pierre Goloubinoff, Bruno Claude Daniel Fauvet, Salvatore Assenza

Detailed understanding of the mechanism by which Hsp70 chaperones protect cells against protein aggregation is hampered by the lack of a comprehensive characterization of the aggregates, which are typically heterogeneous. Here we designed a reporter chaper ...

NATURE PORTFOLIO2022

New Methods for the Integrative Dynamic Modeling of Biomolecular Structures

Sylvain Träger

The true understanding of most cellular functions is only really achievable through the structural determination of their underlying macromolecular assemblies. However, their size, large number of individual components and metastable states make their eluc ...

EPFL2021

A general strategy to develop cell permeable and fluorogenic probes for multicolour nanoscopy

Kai Johnsson, Lu Wang, Lin Xue

It is difficult to develop suitable fluorescent probes for live-cell nanoscopy, but a general strategy is now reported that can transform regular fluorophores into fluorogenic probes with excellent cell permeability and low unspecific background signals. U ...

NATURE PUBLISHING GROUP2020

Establishing a Ternary System for Optical Monitoring of DNA-Protein Interactions with Single-Walled Carbon Nanotubes

Shang-Jung Wu

DNA-protein interactions lie at the crux of life's essential processes. As such, various technologies have been developed to characterize these interactions. The distinct advantages of these technologies can be leveraged to study different facets of these ...

EPFL2020

Hybrid Transcriptional Regulators for the Screening of Target DNA Motifs in Organohalide-Respiring Bacteria

Christof Holliger, Julien Maillard, Mathilde Stéphanie Willemin, Marie Vingerhoets

The bioremediation of persistent organohalide molecules under anoxic conditions mostly relies on the bacterial process called organohalide respiration (OHR). Organohalide-respiring bacteria (OHRB) are phylogenetically diverse anaerobic bacteria that share ...

Frontiers Media SA2020

Accurate optical spectra through time-dependent density functional theory based on screening-dependent hybrid functionals

Alfredo Pasquarello, Aleksei Tal

We investigate optical absorption spectra obtained through time-dependent density functional theory (TD-DFT) based on nonempirical hybrid functionals that are designed to correctly reproduce the dielectric function. The comparison with state-of-the-art GW ...

2020

Rapid Screen for Tyrosine Kinase Inhibitor Resistance Mutations and Substrate Specificity

Sandrine Madeleine Suzanne Georgeon, Oliver Hantschel, Sina Maren Reckel

We present a rapid and high-throughput yeast and flow cytometry based method for predicting kinase inhibitor resistance mutations and determining kinase peptide substrate specificity. Despite the widespread success of targeted kinase inhibitors as cancer t ...

AMER CHEMICAL SOC2019

Detecting topological variations of DNA at single-molecule level

Aleksandra Radenovic, Georg Fantner, Adrian Pascal Nievergelt, Ke Liu

In addition to their use in DNA sequencing, ultrathin nanopore membranes have potential applications in detecting topological variations in deoxyribonucleic acid (DNA). This is due to the fact that when topologically edited DNA molecules, driven by electro ...

Nature Research2019

An optimized and validated 384-well plate assay to test platelet function in a high-throughput screening format

Nikolaos Stergiopoulos, Olivier Burri, Marc Chambon, Rodrigo Araujo Fraga Da Silva, Fabiana Pereira Da Costa Fraga, Julien Bortoli Chapalay, Augusto Martins Lima, Maiia Bragina

Despite significant advances in the treatment of cardiovascular diseases, antiplatelet therapies are still associated with a high risk of hemorrhage. In order to develop new drugs, methods to measure platelet function must be adapted for the high-throughpu ...

TAYLOR & FRANCIS INC2019

Microfluidic device performing on flow study of serial cell–cell interactions of two cell populations

Philippe Renaud, Margaux Catherine Marie Duchamp, George Coukos, Thamani Dahoun, Alexandre Harari, Marion Arnaud

In this study we present a novel microfluidic hydrodynamic trapping device to probe the cell–cell interaction between all cell samples of two distinct populations. We have exploited an hydrodynamic trapping method using microfluidics to immobilize a batch ...

2019

Toward a unified scoring function for native state discrimination and drug-binding pocket recognition

Stefano Zamuner

Protein folding and receptor–ligand recognition are fundamental processes for any living organism. Although folding and ligand recognition are based on the same chemistry, the existing empirical scoring functions target just one problem: predicting the cor ...

2018

Hippo, TGF-beta, and Src-MAPK pathways regulate transcription of the upd3 cytokine in Drosophila enterocytes upon bacterial infection

Bart Deplancke, Yu-Chen Tsai

Cytokine signaling is responsible for coordinating conserved epithelial regeneration and immune responses in the digestive tract. In the Drosophila midgut, Upd3 is a major cytokine, which is induced in enterocytes (EC) and enteroblasts (EB) upon oral infec ...

Public Library of Science2017

Potential Direct Regulators of the Drosophila yellow Gene Identified by Yeast One-Hybrid and RNAi Screens

Bart Deplancke

The regulation of gene expression controls development, and changes in this regulation often contribute to phenotypic evolution. Drosophila pigmentation is a model system for studying evolutionary changes in gene regulation, with differences in expression ...

Genetics Society of America2016

Structural Features of the Box C/D snoRNP Pre-assembly Process Are Conserved through Species

Benjamin Marcel Daniel Rothé

Box C/D small nucleolar ribonucleoparticles (snoRNPs) support 2'-O-methylation of several target RNAs. They share a common set of four core proteins (SNU13, NOP58, NOP56, and FBL) that are assembled on different guide small nucleolar RNAs. Assembly of thes ...

Cell Press2016

GreA and GreB Enhance Expression of Escherichia coil RNA Polymerase Promoters in a Reconstituted Transcription-Translation System

Sebastian Maerkl, Zoe Newell Swank, Henrike Marie Niederholtmeyer

Cell-free environments are becoming viable alternatives for implementing biological networks in synthetic biology. The reconstituted cell-free expression system (PURE) allows characterization of genetic networks under defined conditions but its applicabili ...

Amer Chemical Soc2016

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