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    1. Computational and Systems Biology
    2. Medicine

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

    Homa MohammadiPeyhani, Anush Chiappino-Pepe ... Vassily Hatzimanikatis
    NICEdrug.ch is a resource allowing systematic and large-scale computational analysis of drug biochemistry, enzymatic targets, and toxicity in the context of cellular metabolism.
    1. Microbiology and Infectious Disease

    Genetic validation of PfFKBP35 as an antimalarial drug target

    Basil T Thommen, Jerzy M Dziekan ... Nicolas MB Brancucci
    Knocking out the FK506-binding protein in Plasmodium falciparum (PfFKBP35) affects ribosome homeostasis and results in a delayed death-like phenotype that is independent of the mode of action of FK506.
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Discovery of a heparan sulfate binding domain in monkeypox virus H3 as an anti-poxviral drug target combining AI and MD simulations

    Bin Zheng, Meimei Duan ... Peng Zheng
    The identification of a conserved α-helical domain in monkeypox virus H3 protein as critical for heparan sulfate binding unveils a novel therapeutic target, validated through AI and molecular dynamics simulations, offering potential for broad-spectrum antiviral development.
    1. Cancer Biology

    BRAF inhibitors suppress apoptosis through off-target inhibition of JNK signaling

    Harina Vin, Sandra S Ojeda ... Kenneth Y Tsai
    The cancer drug vemurafenib has potent off-target effects on JNK signaling that contribute to the development of squamous cell carcinomas in humans and in mice.
    1. Cell Biology
    2. Cancer Biology

    Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer

    Keren Yizhak, Edoardo Gaude ... Eytan Ruppin
    Genome-scale metabolic modeling of individual cancer cells and healthy human cells identifies specific and selective metabolic vulnerabilities.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Transmission genetics of drug-resistant hepatitis C virus

    Nicholas van Buuren, Timothy L Tellinghuisen ... Karla Kirkegaard
    Interactions between viral genomes within the same cells can impact the selection of drug-resistant variants and this has been finessed by hepatitis C virus.
    1. Cancer Biology

    CRISPR/Cas9 mutagenesis invalidates a putative cancer dependency targeted in on-going clinical trials

    Ann Lin, Christopher J Giuliano ... Jason M Sheltzer
    A putative therapeutic target undergoing clinical trials in breast cancer is non-essential and the drug used in those trials blocks cell division through an off-target effect.
    1. Cancer Biology
    2. Developmental Biology

    Targeting mutant RAS in patient-derived colorectal cancer organoids by combinatorial drug screening

    Carla S Verissimo, René M Overmeer ... Hugo J Snippert
    Libraries of patient-derived tumor organoids are a reliable and scalable model system that can help identify and optimize targeted therapies in a pre-clinical setting.
    1. Developmental Biology
    2. Neuroscience

    Large-scale phenotypic drug screen identifies neuroprotectants in zebrafish and mouse models of retinitis pigmentosa

    Liyun Zhang, Conan Chen ... Jeff S Mumm
    Using a cross-species phenotypic drug discovery pipeline, compounds promoting rod photoreceptor survival in zebrafish and mouse models of retinitis pigmentosa were identified, evidence of additive effects of paired compounds and inhibition of PARP-dependent cell death suggest novel therapeutic strategies.
    1. Cancer Biology
    2. Computational and Systems Biology

    shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data

    Kenichi Shimada, John A Bachman ... Timothy J Mitchison
    shinyDepMap helps users explore the essentiality, selectivity, and function of the genes across hundreds of cancer cell lines and identify cancer drug targets.