Publications associées à Directed Evolution of Bicyclic Peptides for Therapeutic Application

Variational quantum time evolution without the quantum geometric tensor

Giuseppe Carleo, Riccardo Rossi, Julien Sebastian Gacon, Stefan Woerner, Jannes Willy E. Nys

Realand imaginary -time quantum state evolutions are crucial in physics and chemistry for exploring quantum dynamics, preparing ground states, and computing thermodynamic observables. On near -term devices, variational quantum time evolution is a promising ...

Amer Physical Soc2024

Homogeneous vs. heterogeneous photo-Fenton elimination of antibiotic-resistant bacteria bearing intracellular or extracellular resistance: Do resistance mechanisms interfere with disinfection pathways?

César Pulgarin, Stefanos Giannakis, Truong-Thien Melvin Le, Jérémie Decker

The present study aimed to fill the knowledge gap between the implications of intracellular and extracellular antibiotic resistance mechanisms may inflict on the inactivation pathways of the photo-Fenton process under mild conditions. It was thus designed ...

Elsevier Sci Ltd2024

Stability of a liquid layer draining around a horizontal cylinder: Interplay of capillary and gravity forces

François Gallaire, Shahab Eghbali, Simeon Vladimirov Djambov

We study the drainage of a viscous liquid film coating the outside of a solid horizontal cylinder, where gravity acts vertically. We focus on the limit of large Ohnesorge numbers Oh, where inertia is negligible compared to viscous effects. We first study t ...

Amer Physical Soc2024

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

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins

Ghérici Hassaïne

Scaffold-based protein libraries are designed to be both diverse and rich in functional/folded proteins. However, introducing an extended diversity while preserving stability of the initial scaffold remains a challenge. Here we developed an original approa ...

Nature Portfolio2023

De novo designed proteins: a study in engineering novel folds and functions

Alexandra Krina Van Hall-Beauvais

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

EPFL2023

Simple optical nanomotion method for single-bacterium viability and antibiotic response testing

Sandor Kasas, María Inés Villalba, Allan Bonvallat, Eugenia Rossetti

Antibiotic resistance is nowadays a major public health issue. Rapid antimicrobial susceptibility tests (AST) are one of the options to fight this deadly threat. Performing AST with single-cell sensitivity that is rapid, cheap, and widely accessible, is ch ...

National Academy of Sciences2023

Computer-implemented design of peptide:receptor signaling complexes for enhanced chemotaxis

Patrick Daniel Barth, Robert Everett Jefferson

The present invention relates to a computer-implemented method for engineering the interaction between a protein and a cognate peptide that are capable of forming a molecular complex, wherein the method comprises (a) preparing in silico a library of test p ...

2023

Synthesis and application of bifunctional hypervalent iodine reagents for peptide modification

Elija Grinhagena

Protein-protein interactions (PPIs) are responsible for regulating many biological processes in human bodies. PPIs often have a large binding site and often interact through an alpha helical segment. Therefore, the inhibition of PPIs can be difficult using ...

EPFL2023

Molecular analysis and therapeutic applications of human serum albumin-fatty acid interactions

Alessandro Angelini, Alessandro Zorzi, Sara Linciano

Human serum albumin (hSA) is the major carrier protein for fatty acids (FAs) in plasma. Its ability to bind multiple FA moieties with moderate to high affinity has inspired the use of FA conjugation as a safe and natural platform to generate long-lasting t ...

ELSEVIER2022

De novo developed small cyclic peptides that are orally available

Manuel Leonardo Merz

Cyclic peptides are ring-shaped molecules that emerged as a promising class of therapeutics. While it is often difficult to find small molecule binders for challenging disease targets, cyclic peptides can bind to featureless surfaces or inhibit protein-pro ...

EPFL2022

Protein Engineering for Personalized therapy and diagnosis

Lixia Wei

Protein Engineering, especially protein post-translational modification (PTM), ex-tends proteomes in a more complex way than one can expect from analysis of their encod-ing genomes. It can activate or deactivate certain catalytic functions, add new desired ...

EPFL2022

Exploiting Marginal Stability in Slow-Fast Quasilinear Dynamical Systems

Alessia Ferraro

The accurate investigation of many geophysical phenomena via direct numerical simulations is computationally not possible nowadays due to the huge range of spatial and temporal scales to be resolved. Therefore advances in this field rely on the development ...

EPFL2022

Targeting molecular surfaces to engineer novel protein-based immunogens and inhibitors

Sarah Wehrle

Proteins are the basic building blocks necessary for the operation and regulation of virtually all functions in living organisms. Over millions of years, evolution has created a vast repertoire of proteins finely tuned to execute their biological functions ...

EPFL2022

Directed evolution of DNA-wrapped single-walled carbon nanotube complexes for optical sensing

Benjamin Paul Johanès Gabriel Lambert

Single-walled carbon nanotubes (SWCNTs) have garnered significant interest for their applications in optical biosensing. SWCNTs exhibit a sensitive and photostable fluorescence in the near-infrared (NIR) range, allowing for the continuous monitoring of tar ...

EPFL2021

An efficient quantum algorithm for the time evolution of parameterized circuits

Giuseppe Carleo, Filippo Vicentini, Stefano Barison

We introduce a novel hybrid algorithm to simulate the real-time evolution of quantum systems using parameterized quantum circuits. The method, named "projected - Variational Quantum Dynamics" (p-VQD) realizes an iterative, global projection of the exact ti ...

VEREIN FORDERUNG OPEN ACCESS PUBLIZIERENS QUANTENWISSENSCHAF2021

A minimalistic cyclic ice-binding peptide from phage display

Harm-Anton Klok, Matthew Gibson, Luciano Andres Abriata, Xudong Kong, Corey Alfred Stevens

Developing molecules that emulate the properties of naturally occurring ice-binding proteins (IBPs) is a daunting challenge. Rather than relying on the (limited) existing structure–property relationships that have been established for IBPs, here we report ...

Nature Research2021

Methods for the generation of large combinatorial macrocycle libraries

Sevan Mleh Habeshian

Macrocycles are an attractive class of molecules due to their good binding properties and yet rather small size that allows, in many cases, crossing membranes to reach intracellular targets. In comparison to classical small molecule drugs, macrocycles are ...

EPFL2021

On the exploration of novel methodological approaches for immunogen design: case studies in influenza and hepatitis C

Andreas Scheck

Proteins are fundamental components in biological systems and crucial for a variety of biological functions. Over the last decades, significant progress in structural biology has facilitated the study of proteins and their interactions with molecular partn ...

EPFL2021