Almost all drugs exert their effects in a dose-dependent fashion, but a central challenge in drug discovery and pharmacology is to bridge the gap between observed phenotypic and the often complex underlying molecular mechanisms. Important questions to answer are: which proteins are physically bound by the compound, which pathways are engaged in the cell and how is the cell molecularly and physiologically reprogrammed en route to its eventual, drug-determined fate? In light of the advances in quantitative mass spectrometry speed and sensitivity over the past decade, it has become feasible to perform systematic full dose-response experiments at the level of: (1) target deconvolution; (2) pathway engagement; (3) proteome reprogramming; and (4) cellular consequences. Each enables the extraction of potency and effect size information for thousands of proteins and post-translational modification sites in parallel. In this mini-review, the conceptual framework of system-level dose-response measurements is outlined and key published studies are used to illustrate how such data inform successive layers of drug mechanisms of action.

Target discovery is pivotal in cutting-edge drug development and impacts translational outcomes and efficacy, the current state of research depends heavily on empirical approaches that can be costly, while there is no publicly available database of drug-target for polypharmacological correlates incorporating relevant clinical data. In the present perspective, 3 Therapeutic Target Database (TTD) exports are utilized: (1) counts of unique target classes having at least one approved drug, (2) approved-drug counts per target class, and (3) the top 20 de-duplicated drug-driven target co-occurrence pairs. These data enabled development of a data-driven map of the targetome. Through comparison of class richness versus translational yield, rating of frequency of drug driven co-occurrence target pairs, we identified emerging, high-yield and biologically plausible but understudied target families, and guide rational combination therapies. The next generation of research should update drug-target databases with more clinical information, quantitative polypharmacology, and provenance metadata to advance combination therapy.

A new study published inNature Neurosciencedemonstrated that Fc effector function is essential for amyloid aggregate clearance during lecanemab treatment, a recently FDA-approved therapy for Alzheimer's disease. These findings underscore the requirement for intact Fc-mediated activity to achieve therapeutic efficacy. In addition, single-cell RNA sequencing identified microglia transcriptomic changes that are unique to lecanemab treatment and extend beyond previously characterized microglial activation signatures. Together with a retrospective review of anti-amyloid antibody development and related mechanisms, this commentary provides important insights into new directions for the design of next-generation therapies for Alzheimer's disease.

Acute lung injury (ALI) is a diffuse alveolar injury caused by infections and other predisposing factors, with associated alveolar dysfunction, pulmonary oedema, and acute respiratory failure. Currently, no specific therapeutic agents are clinically available for ALI. Xuebijing injection (XBJ) is a widely used clinical traditional Chinese medicine formulation, primarily used for respiratory infections. However, the effects and mechanisms of XBJ in ALI are not fully understood. This study demonstrated that XBJ treatment ameliorated ALI progression by heightening alveolar barrier integrity and reducing histopathological lung damage. Mechanistically, XBJ inhibited the activation of the mitogen-activated protein kinase (MAPK), nuclear factor-κB (NF-κB), and NOD-like receptor thermal protein domain associated protein 3 (NLRP3) inflammasome pathways, resulting in reduced production of key pro-inflammatory cytokines (e.g., IL-6, IL-1β, and TNF-α). It also restored immune balance by regulating Treg/Th17 cells and inhibited ferroptosis. Using integrated chemical biology approaches, pyruvate kinase M2 (PKM2), enolase 1 (ENO1), PDZ binding kinase (PBK), eukaryotic translation initiation factor 3i (EIF3I), and kelch-like ECH-associated protein 1 (Keap1) were identified as direct intracellular targets of XBJ, which was further confirmed through various chemical and biological methods. Moreover, compounds from XBJ, which is entered into the blood and lungs, such as palmitic acid, ethyl 4-hydroxy-3-methoxycinnamate, sugiol, oleic acid, and 10,12-octadecadiynoic acid, could bind to these targets, respectively. In summary, XBJ protected against lipopolysaccharide (LPS)-induced ALI by multi-targets, thereby modulasting inflammatory and immune responses, while inhibiting the MAPK/NF-κB/NLRP3 pathways and ferroptosis. These findings offered mechanistic evidence of the application value of XBJ in the treatment of ALI.

Identifying host programs that connect micronutrient biology to COVID-19 immunopathology may enable more precise host-directed strategies. Zinc deficiency is linked to worse outcomes, yet the intracellular mediators that couple metal/redox stress to disease severity remain unclear. In this study, a PRISMA-guided meta-analysis of zinc supplementation was performed in hospitalized COVID-19 (seven studies; 1,972 participants), and observed reduced mortality (OR 0.48, 95% CI 0.36-0.64). Statistical heterogeneity was low, although regimens varied substantially in formulation, elemental dose, route, and duration. The study then integrated single-cell and bulk transcriptomes across blood and respiratory compartments, to map zinc-homeostasis pattern across disease states. In a large single-cell atlas (GSE158055; 1,462,702 cells from 196 individuals) spanning PBMC, bronchoalveolar lavage fluid, sputum, in bulk RNA-seq from postmortem lung tissue (GSE183533), and longitudinal peripheral blood (GSE198449), MT2A showed the most reproducible association with disease severity among metallothioneins, and was enriched in myeloid lineages. Its associations were compartment- and state-dependent, and SARS-CoV-2-relevant entry/processing and innate-sensing are involved, including TMPRSS2, CTSB/CTSL, and RNA-sensing pathways. In a longitudinal subset with complete timepoints (n = 9; days 0, 1, 8, and 12), MT2A peaked early after infection and declined thereafter, consistent with an inducible acute-phase response. Together, these results prioritize MT2A as a cross-compartment marker of metal/redox immune stress and a testable host node for biomarker-guided stratification and intervention timing, pending perturbation-based causal validation.

Iron homeostasis is tightly regulated by systemic and intracellular pathways, yet how transcriptional programs and chromatin states contribute to the maintenance of iron availability remains poorly understood. A recent study developed an elegant tool by leveraging iron regulatory protein 2 (IRP2) as a metabolic sensor, in combination with CRISPR-based functional screening to map the regulatory landscape of cellular iron metabolism. Using this strategy, the histone methyltransferase SETD2 is identified as a chromatin-based regulator of IRP2 levels, ferritinophagy, and ferroptosis sensitivity. These findings reveal a new epigenetic layer of iron regulation, and provide a broader model for the metabolite-responsive sensors, through functional screening, to identify upstream networks and potential targetome.

The mechanistic connection between intramuscular invasion and distant metastasis in muscle-invasive bladder cancer (MIBC) remains unclear. In this study, a TGFβ3 signaling pathway that drives metastatic progression by altering succinate metabolism was identified. Mechanistically, a SMAD3/4-independent TGFβ3 signaling cascade that promotes the formation of a SMAD2/ETV4/CARM1 transcriptional complex was discovered. This complex epigenetically activates sulfide quinone oxidoreductase (SQOR), leading to mitochondrial metabolic reprogramming and succinate accumulation. The accumulated succinate then acts as a powerful paracrine signal, activating succinate receptor (SUCNR1) on smooth muscle cells (SMCs) to coordinate stromal remodeling and vascular niche formation that supports metastasis. Additionally, structure-based virtual screening reveals L-chicoric acid as a specific inhibitor that disrupts the critical SMAD2-ETV4 interaction, thereby blocking the metabolic loop and inhibiting metastasis. These findings establish TGFβ3 as an essential mediator of metabolic flexibility, and highlight the TGFβ3/SMAD2/ETV4/succinate axis as a promising therapeutic target.