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Advancing Drug Discovery via Artificial Intelligence

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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

Advancing EGFR mutation subtypes prediction in NSCLC by combining 3D pretrained ConvNeXt, radiomics, and clinical features

Jiancheng Yang

Purpose The aim of this study was to develop a novel approach for predicting the expression status of Epidermal Growth Factor Receptor (EGFR) and its subtypes in patients with Non-Small Cell Lung Cancer (NSCLC) using a Three-Dimensional Convolutional Neura ...

FRONTIERS MEDIA SA2024

Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets

Christoph Merten, Ngoc Hien Du

Anti-cancer therapies often exhibit only short-term effects. Tumors typically develop drug resistance causing relapses that might be tackled with drug combinations. Identification of the right combination is challenging and would benefit from high-content, ...

Nature Research2022

Enhancing Dexterity in Confined Spaces: Real-Time Motion Planning for Multifingered In-Hand Manipulation

Aude Billard, Kunpeng Yao, Farshad Khadivar, Xiao Gao

Dexterous in-hand manipulation in robotics, particularly with multi-fingered robotic hands, poses significant challenges due to the intricate avoidance of collisions among fingers and the object being manipulated. Collision-free paths for all fingers must ...

2024

NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism

Vassily Hatzimanikatis, Noushin Hadadi, Jasmin Maria Hafner, Anush Chiappino-Pepe, Homa Mohammadi Peyhani

The discovery of a drug requires over a decade of intensive research and financial investments – and still has a high risk of failure. To reduce this burden, we developed the NICEdrug.ch resource, which incorporates 250,000 bioactive molecules, and studied ...

2021

Exploring “dark-matter” protein folds using deep learning

Irina Morozova, Pierre Vandergheynst, Bruno Emanuel Ferreira De Sousa Correia, Andreas Loukas, Sandrine Madeleine Suzanne Georgeon, Stéphane Rosset, Zander Harteveld, 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

High-content, targeted RNA-seq screening in organoids for drug discovery in colorectal cancer

Jörg Hülsken, Maxim Norkin

Organoids allow the recapitulation of intestinal homeostasis and cancerogenesis in vitro; however, RNA sequencing (RNA-seq)-based methods for drug screens are missing. We develop targeted organoid sequencing (TORNADO-seq), a high-throughput, high-content d ...

2021

Quantitative convergence rates for scaling limit of SPDEs with transport noise

Lucio Galeati

We consider on the torus the scaling limit of stochastic 2D (inviscid) fluid dynamics equations with transport noise to deterministic viscous equations. Quantitative estimates on the convergence rates are provided by combining analytic and probabilistic ar ...

Academic Press Inc Elsevier Science2024

Alpha-Synuclein oligomerization and aggregation: All models are useful but only if we know what they model This is the reply to a comment "Alpha-synuclein oligomerization and aggregation: A model will always be a model" on the original article "Monitoring alpha-synuclein oligomerization and aggregation using bimolecular fluorescence complementation assays: What you see is not always what you get". The articles are accompanied by a Preface "How good are cellular models?"

Hilal Lashuel

Alpha-synuclein oligomerization is one of the early events on the pathway to Lewy body formation. Therefore, interfering with this process holds tremendous potential for developing therapies that block alpha-Syn pathology formation and toxicity. The develo ...

Wiley-Blackwell2021

Sequential CNN-based Enhancement of Ultrafast Ultrasound Imaging for Sparse Arrays

Jean-Philippe Thiran, Roser Vinals Terres

With the emergence of ultra-portable ultrasound systems, the need to reduce cost and complexity of ultrasound systems has intensified. Sparse arrays, employing fewer transducer elements to acquire images, offer a viable solution by effectively minimizing d ...

European Signal Processing Conference, EUSIPCO2024

Drug-to-Antibody Ratio Estimation via Proteoform Peak Integration in the Analysis of Antibody-Oligonucleotide Conjugates with Orbitrap Fourier Transform Mass Spectrometry

Yury Tsybin, Natalia Gasilova, Laure Menin, Anton Kozhinov, Konstantin Nagornov

The therapeutic efficacy and pharmacokinetics of antibody-drug conjugates (ADCs) in general, and antibody-oligonucleotide conjugates (AOCs) in particular, depend on the drug-to-antibody ratio (DAR) distribution and average value. The DAR is considered a cr ...

AMER CHEMICAL SOC2021

RAPNet: Resolution-Adaptive and Predictive Early Exit Network for Efficient Image Recognition

Yung-Cheng Chiang

Deploying compute-intensive deep neural networks (DNNs) on resource-constrained end devices has become a prominent trend, enabling localized intelligence. However, efficiently deploying these DNNs at scale poses challenges. To address this, extensive resea ...

2024

Towards the Development of Orally Available Peptide Therapeutics

Christian Heinis, Xudong Kong

Peptides have a number of attractive properties that make them an interesting modality for drug development, including their ability to bind challenging targets, their high target specificity, and their non-toxic metabolic products. However, a major limita ...

2021

Therapeutic approaches against coronaviruses acute respiratory syndrome

Francesco Stellacci

Coronaviruses represent global health threat. In this century, they have already caused two epidemics and one serious pandemic. Although, at present, there are no approved drugs and therapies for the treatment and prevention of human coronaviruses, several ...

JOHN WILEY & SONS LTD2021

Cyclic Peptides for Drug Development

Christian Heinis, Alexander Lund Nielsen, Xinjian Ji

Cyclic peptides are fascinating molecules abundantly found in nature and exploited as molecular format for drug development as well as other applications, ranging from research tools to food additives. Advances in peptide technologies made over many years ...

Wiley-VCH Verlag GmbH2024

No Representation, No Trust: Connecting Representation, Collapse, and Trust Issues in PPO

Andréa Serge Alfredo Miele, Daniil Pyatko, Caglar Gulcehre, Skander Moalla

Reinforcement learning (RL) is inherently rife with non-stationarity since the states and rewards the agent observes during training depend on its changing policy. Therefore, networks in deep RL must be capable of adapting to new observations and fitting n ...

2024

Novel irreversible covalent BTK inhibitors discovered using DNA-encoded chemistry

Sevan Mleh Habeshian

Libraries of DNA-Encoded small molecules created using combinatorial chemistry and synthetic oligonucleotides are being applied to drug discovery projects across the pharmaceutical industry. The majority of reported projects describe the discovery of rever ...

PERGAMON-ELSEVIER SCIENCE LTD2021

Deconvolution of ex-vivo drug screening data and bulk tissue expression predicts the abundance and viability of cancer cell subpopulations

Alexandre Coudray

Ex-vivo drug sensitivity screening (DSS) allows the prediction of cancer treatment effectiveness in a personalized fashion. However, it only provides a readout on mixtures of cells, potentially occulting important information on clinically relevant cell su ...

EPFL2023

Miniaturized technologies for high-throughput drug screening enzymatic assays and diagnostics - A review

Paul Joseph Dyson

Drug discovery is a complex, multistep process, in which many challenges need to be overcome at each stage, from the discovery of a biomolecular target to the ensuring of the efficacy and safety of a compound in humans. Today's analytical methods allow ten ...

ELSEVIER SCI LTD2020

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