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Related publications (28)

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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

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

Augmented Memory: Sample-Efficient Generative Molecular Design with Reinforcement Learning

Philippe Schwaller, Jeff Guo

Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal calls to oracles (computational property predictors). This problem becomes more apparen ...

Amer Chemical Soc2024

Optimised three-dimensional in vitro retinoblastoma models tailored for drug discovery and clinical translatability

Irina Sinenko

Retinoblastoma, while relatively rare, stands as the most prevalent intraocular cancer. In Switzerland, the survival rate approaches 100%, but it drops to less than 50% in low-income countries. The current treatment options for retinoblastoma rely on a lim ...

EPFL2023

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

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

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

Macrocycle synthesis strategy based on step-wise “adding and reacting” three components enables screening of large combinatorial libraries

Christian Heinis, Gerardo Turcatti, Alessandro Angelini, Alessandro Zorzi, Jonathan Patrice Vesin, Kaycie Marie Butler, Julien Bortoli Chapalay, Sangram Shivdas Kale, Ganesh Kumar Mothukuri, Carl Leonard Stenbratt

Macrocycles provide an attractive modality for drug development, but generating ligands for new targets is hampered by the limited availability of large macrocycle libraries. We have established a solution-phase macrocycle synthesis strategy in which three ...

2020

Enantioselective C(sp(3))-C(sp(3)) cross-coupling of non-activated alkyl electrophiles via nickel hydride catalysis

Xile Hu, Runze Mao, Srikrishna Bera

Cross-coupling of two alkyl fragments is an efficient method to produce organic molecules rich in sp(3)-hybridized carbon centres, which are attractive candidate compounds in drug discovery. Enantioselective C(sp(3))-C(sp(3)) coupling is challenging, espec ...

2020

Algorithms and flowchart for the design of synthetic biochemical networks

Homa Mohammadi Peyhani

New drugs are needed to assure effective therapies for previously untreated diseases, emerging diseases, and personalized medicine, but the process of drug development is complex, costly, and time-consuming. This is especially problematic considering that ...

EPFL2020

Advancing Drug Discovery via Artificial Intelligence

Horst Arthur Vogel, Shuguang Yuan, Thamani Dahoun

Drug discovery and development are among the most important translational science activities that contribute to human health and wellbeing. However, the development of a new drug is a very complex, expensive, and long process which typically costs 2.6 bill ...

ELSEVIER SCIENCE LONDON2019

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

The virtuous cycle of human genetics and mouse models in drug discovery

Johan Auwerx

Ongoing studies in many species seek to understand the origins, architecture and consequences of phenotypic variation under normal and dysfunctional conditions, with the aim of identifying targets for intervention that can prevent, stabilize or reverse dis ...

NATURE PUBLISHING GROUP2019

Innovative Tools and in vivo Methods for Tuberculosis Drug Discovery and Development

Raphael Christopher Sommer

Worldwide, tuberculosis (TB) is the leading cause of death due to a single infectious agent, claiming 1.6 million human lives and causing >10 million new cases in 2017 alone, mostly in low-income regions. The intracellular pathogen Mycobacterium tuberculos ...

EPFL2019

Structure-Based Drug Design and Characterization of Sulfonyl-Piperazine Benzothiazinone Inhibitors of DprE1 from Mycobacterium tuberculosis

Stewart Cole, Anthony Vocat, Jérémie Piton, Shi-Yan Caroline Foo, Andréanne Lupien

Macozinone (MCZ) is a tuberculosis (TB) drug candidate that specifically targets the essential flavoenzyme DprE1, thereby blocking synthesis of the cell wall precursor decaprenyl phosphoarabinose (DPA) and provoking lysis of Mycobacterium tuberculosis. As ...

AMER SOC MICROBIOLOGY2018

More Medicines for Tuberculosis: Fuelling Drug Discovery against Mycobacterium tuberculosis

Shi-Yan Caroline Foo

Tuberculosis (TB), whose etiological agent is Mycobacterium tuberculosis (M. tuberculosis), has plagued humanity since antiquity. Even with chemotherapy available today, TB is the leading cause of death due to an infectious disease. Modern day factors, suc ...

EPFL2018

Microfluidic platforms for high-throughput mammalian cell printing, transfection, and dosage-dependent studies

Kristina Pan Woodruff

With the advent of high-throughput and genome-wide screening initiatives, there is a need for improved methods for cell-based assays. Current approaches require expensive equipment, rely on large-scale culturing formats not suited for small or rare sample ...

EPFL2017

On the role of water density fluctuations in the inhibition of a proton channel

Lucie Monique Françoise Delemotte

Hv1 is a transmembrane four-helix bundle that transports protons in a voltage-controlled manner. Its crucial role in many pathological conditions, including cancer and ischemic brain damage, makes Hv1 a promising drug target. Starting from the recently sol ...

National Academy of Sciences2016

Next-generation antimicrobials: from chemical biology to first-in-class drugs

Paul Murima

The global emergence of multi-drug resistant bacteria invokes an urgent and imperative necessity for the identification of novel antimicrobials. The general lack of success in progressing novel chemical entities from target-based drug screens have prompted ...

Pharmaceutical Soc Korea2015

Antihypertensive drugs metabolism: an update to pharmacokinetic profiles and computational approaches

Vassily Hatzimanikatis, Ljubisa Miskovic, Aikaterini Zisaki

Drug discovery and development is a high-risk enterprise that requires significant investments in capital, time and scientific expertise. The studies of xenobiotic metabolism remain as one of the main topics in the research and development of drugs, cosmet ...

Bentham Science Publishers2015