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One aspirational goal of computational chemistry is to predict potent and drug-like binders for any protein, such that only those that bind are synthesized. In this Roadmap, we describe the launch of Critical Assessment of Computational Hit-finding Experiments (CACHE), a public benchmarking project to compare and improve small molecule hit-finding algorithms through cycles of prediction and experimental testing. Participants will predict small molecule binders for new and biologically relevant protein targets representing different prediction scenarios. Predicted compounds will be tested rigorously in an experimental hub, and all predicted binders as well as all experimental screening data, including the chemical structures of experimentally tested compounds, will be made publicly available, and not subject to any intellectual property restrictions. The ability of a range of computational approaches to find novel binders will be evaluated, compared, and openly published. CACHE will launch 3 new benchmarking exercises every year. The outcomes will be better prediction methods, new small molecule binders for target proteins of importance for fundamental biology or drug discovery, and a major technological step towards achieving the goal of Target 2035, a global initiative to identify pharmacological probes for all human proteins.
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http://dx.doi.org/10.1038/s41570-022-00363-z | DOI Listing |
Plant Dis
September 2025
Shenyang Agricultural University, College of Plant Protection, Nematology Institute of Northern China, Shenyang, China;
Root-knot nematodes (Meloidogyne spp.) cause catastrophic yield losses in global agriculture. This study identified itaconic acid (IA), through comparative metabolomic analysis (the study of small molecules in biological systems), as a key virulence-related metabolite produced by the fungus Trichoderma citrinoviride Snef1910.
View Article and Find Full Text PDFMagn Reson Chem
September 2025
Department of Chemistry, Clemson University, Clemson, South Carolina, USA.
Saturation transfer difference (STD) NMR is a robust, versatile technique for detecting small molecules binding to large receptors. In addition to identifying binding molecules in the presence of nonbinding molecules, the STD-NMR technique can be used to determine epitope maps and binding constants. In recent years, this technique has been applied to small molecules interacting with nanoparticles.
View Article and Find Full Text PDFJ Cancer Res Clin Oncol
September 2025
Inner Mongolia Medical University Affiliated Hospital, Hohhot, 010030, Inner Mongolia, China.
Purpose: Lung cancer is currently the most common malignant tumor worldwide and one of the leading causes of cancer-related deaths, posing a serious threat to human health. MicroRNAs (miRNAs) are a class of endogenous non-coding small RNA molecules that regulate gene expression and are involved in various biological processes associated with lung cancer. Understanding the mechanisms of lung carcinogenesis and detecting disease biomarkers may enable early diagnosis of lung cancer.
View Article and Find Full Text PDFNat Genet
September 2025
Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
Aberrant DNA methylation has been described in nearly all human cancers, yet its interplay with genomic alterations during tumor evolution is poorly understood. To explore this, we performed reduced representation bisulfite sequencing on 217 tumor and matched normal regions from 59 patients with non-small cell lung cancer from the TRACERx study to deconvolve tumor methylation. We developed two metrics for integrative evolutionary analysis with DNA and RNA sequencing data.
View Article and Find Full Text PDFNat Biotechnol
September 2025
Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
Targeted protein degraders hold potential as therapeutic agents to target conventionally 'undruggable' proteins. Here, we develop a high-throughput screen, DEath FUSion Escaper (DEFUSE), to identify small-molecule protein degraders. By conjugating the protein of interest to a fast-acting triggerable death protein, this approach translates target protein degradation into a cell survival phenotype to illustrate the presence of degraders.
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