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Advancing Ligand-based Virtual Screening and Molecular Generation with Pretrained Molecular Embedding Distance

arXiv:2604.24474v2 Announce Type: replace Abstract: Molecular similarity plays a central role in ligand-based drug discovery, such as virtual screening, analog searching, and goal-directed molecular generation. However, traditional similarity measures, ranging from fingerprint-based Tanimoto coefficients to 3D shape overlays, are often computationally expensive at scale or rely on hand-crafted molecular descriptors. Meanwhile, many deep learning approaches to similarity-aware design still...

arXiv CS 1d ago

In situ nanocrystal confinement for efficient blue perovskite LEDs

Abstract Metal halide perovskites have emerged as promising semiconductors for light-emitting diodes (LEDs) owing to their excellent luminescence properties1. However, their performance remains limited, primarily owing to the inherent contradiction between ‘high crystallinity’ and ‘small size’ in the in situ synthesis of perovskite nanocrystals on substrates. Here we report efficient blue perovskite LEDs (PeLEDs) achieved via in situ polymerization-driven nanocrystal confinement to...

Nature 1d ago

From Holo Pockets to Electron Density: GPT-style Drug Design with Density

arXiv:2605.08767v2 Announce Type: replace Abstract: Recent advances in generative modeling have enabled significant progress in structure-based drug design (SBDD). Existing methods typically condition molecule generation on empty binding pockets from holo complexes, overlooking informative components such as the filler (ligands and solvent). Here, we leverage low-resolution electron density (ED) derived from the filler as a physically grounded condition for \textit{de novo} drug design.

arXiv CS 7d ago

Synthesized peptides can slip into cells to block hard-to-target protein interactions

Synthesized peptides can slip into cells to block hard-to-target protein interactions Sadie Harley Scientific Editor Robert Egan Associate Editor Many diseases are driven by proteins interacting with each other inside cells. But blocking these interactions with drugs is difficult because typical "small-molecule" drugs often prove to be too small to grip the broad, flat surfaces involved in protein-protein interactions. On the other hand, peptides—short chains of amino acids—can cover larger...

Phys.org 9d ago

HDAC3 inhibition stabilizes the IL-37 receptor module to enhance anti-inflammatory signaling in cystic fibrosis airway epithelium

Airway inflammation in cystic fibrosis (CF) persists despite advances in CFTR modulator therapy. IL-37b suppresses innate immune signaling through a receptor complex containing IL-18R and wild-type SIGIRR (WT-SIGIRR; IL-1R8), but this pathway is compromised in CF airway epithelial cells by the dominant-negative exon 8-skipped SIGIRR isoform ({Delta}8-SIGIRR). Here, a natural-product screen identified short-chain fatty acids as preferential enhancers of WT-SIGIRR.

bioRxiv 6d ago

A first-in-class pulsatile FXR agonist for bile-acid-related liver diseases

Abstract Nuclear receptors are central regulators of metabolism1, yet therapeutic strategies that enforce continuous receptor activation frequently lead to reduced efficacy and unacceptable toxicity. Here we report a first-principles drug design strategy that aligns pharmacokinetics with physiological signalling cycles. We developed linafexor, a potent non-bile-acid agonist of the farnesoid X receptor (FXR)2; it is engineered for rapid systemic clearance, which enables pulsatile receptor...

Nature 1d ago

Light-induced quantum friction of carbon nanotubes in water

Abstract Friction slows down moving objects at both macroscopic and microscopic scales1. At the electronic level, quantum friction describes direct transfer of momentum between a liquid and the electrons of a solid2. Owing to its microscopic nature, this phenomenon remains experimentally challenging to capture3.

Nature 1d ago

Structural basis for chaperone-guided assembly of RNA-induced silencing complex

Abstract The RNA-induced silencing complex (RISC), comprising an Argonaute (AGO) protein and a small RNA, is the central effector in RNA silencing. Small RNAs are loaded onto AGO as bulky duplexes in an HSP70- and HSP90-dependent process1,2,3, but the molecular mechanism remains poorly understood. Here we identify the human AGO–HSP90–p23 complex, which captures AGO in an RNA-free state, termed the AGO maturation complex (AMC).

Nature 1d ago

Mutation-dependent responses to sleep and exercise in clonal haematopoiesis

Abstract Clonal haematopoiesis (CH) activates inflammation and increases the risk of atherosclerosis1,2. Whether lifestyle alters CH clone expansion or the phenotypic programming of CH mutant cells, thereby affecting atherosclerosis, is unknown. Here, in humans and mice and across mutations in Jak2, Tet2, Trp53 and Dnmt3a, we demonstrate mutation-dependent responses to sleep and exercise in CH and show that mutant cells are uniquely sensitive to lifestyle.

Nature 1d ago