Zhiwei Yang

Chronic ultraviolet (UV) irradiation-induced skin photoaging is driven by oxidative stress, extracellular matrix degradation, and cellular senescence. To overcome the poor skin permeability and rapid clearance of neferine (Nef), PEGylated liposomes were prepared via thin-film hydration. The Nef-loaded liposomes (Lipo) were spherical, with a mean diameter of 137.90 ± 0.56 nm, a PDI of 0.117 ± 0.016, an encapsulation efficiency of 68.79% ± 1.01%, and a drug loading of 13.38% ± 0.22%. Ex vivo Franz diffusion cell assays demonstrated significantly higher cumulative transdermal permeation over 24 h for Lipo compared with free Nef, along with sustained-release behavior. In a chronic UVA-induced mouse photoaging model, epidermal thickness, dermal collagen networks, and fibroblast mitochondrial ultrastructure were restored by topical Lipo application, with superior effects over free Nef. In UVA-irradiated human dermal fibroblasts, senescence-associated β-galactosidase activity was reduced, intracellular ROS accumulation was eliminated, and SOD activity was restored by the treatment of Lipo. These redox modulations were associated with downregulation of the p53/p21 senescence signaling pathway. Collectively, the antioxidant and anti-senescence efficacy of Nef was enhanced by this liposomal nanoencapsulation strategy through improved transdermal kinetics and cellular responses, providing a functionalized nanoplatform for localized anti-photoaging therapy.

Carnitine palmitoyltransferase 1A (CPT1A) catalyzes a rate-limiting step in fatty acid β-oxidation and is a target for studies of metabolic disease and cancer. However, the structural dynamics of CPT1A remain poorly understood due to the lack of full-length structure. In this study, we employed an integrated computational approach combining molecular dynamics (MD) simulations, Markov state models (MSMs), and binding free energy calculations to elucidate the conformational landscape of human CPT1A. We performed an all-atom MD simulation of CPT1A embedded in a realistic outer mitochondrial membrane, and root-mean-square fluctuation (RMSF)-guided local region analysis coupled with MSM transition-path analysis and GROMOS clustering convergently identified a representative conformation. The pathway probabilities reported here describe dominant local transitions within specific mobile segments rather than the global equilibrium population of the full-length protein. Using this representative conformation, we performed a virtual screening of over 1.23 million compounds from the ChemDiv library, followed by Lipinski filtering, yielding five candidates with docking scores below −10 kcal/mol. Subsequent MD simulations and binding free energy calculations confirmed stable binding, with Compound 2 exhibiting the most favorable free energy of −25.99 kcal/mol. Principal component analysis (PCA) and secondary-structure analyses revealed ligand-specific modulation of CPT1A dynamics. A preliminary in vitro CPT1 activity assay revealed candidate-specific responses, and the free-energy and activity data were partially consistent. These results provide a dynamically informed structural basis for CPT1A ligand recognition, identify candidates with distinct energetic and functional profiles, and establish an integrated strategy for ligand discovery in structurally uncharacterized proteins.

Native transcription factor (TF)-promoter modules generally function as fixed regulatory units, limiting the quantitative programming of transcriptional outputs required for synthetic biology applications. Here, we present a structure-guided promoter engineering strategy that converts the D-allulose-responsive PsiR-pPsiTacI module into a quantitatively tunable promoter library without modifying the transcription factor itself. Candidate promoter variants were rationally designed through AlphaFold3-based protein–DNA docking and molecular dynamics simulations to modulate PsiR–DNA binding affinity. Experimental characterization using both Pepper RNA and sfGFP reporters demonstrated that the engineered promoters generated graded transcriptional outputs while preserving the native regulatory mechanism. Quantitative dose-response modeling further revealed distinct promoter response functions, spanning different maximal outputs, induction thresholds, dynamic ranges, and activation kinetics. These experimentally calibrated response profiles were consistent with computational predictions of protein-DNA binding energetics, establishing an interpretable sequence-to-structure-to-function relationship. Collectively, this work transforms a native TF-promoter module into a reusable library of programmable regulatory elements with quantitatively defined response functions. The proposed structure-guided strategy provides a general framework for engineering inducible promoters with predictable regulatory behaviors and expands the toolkit for dynamic gene expression control, pathway optimization, and synthetic regulatory circuit design.

Breast cancer (BC), one of the most aggressive female cancers, has limited treatment options due to the absence of viable therapeutic targets. Here, we identified that FK506-binding protein 10 (FKBP10), a peptidyl-proline isomerases, was strikingly elevated in BC tissues and enhanced the malignant behaviors of BC cells in vitro and in vivo . Besides, we discovered that FKBP10 was positively correlated with enhanced homologous recombination (HR)-mediated DNA repair and drove resistance to multiple DNA-damaging therapies, including cisplatin, ionizing radiation and PARP inhibitor. Mechanistically, FKBP10 interacted with DNA repair protein RAD51, a core member of HR, and isomerized its X-Pro conformation to block the recognition of RAD51 by heat shock protein family A (Hsp70) member 8 (HSC70), thereby preventing its degradation via chaperone-mediated autophagy (CMA) pathway. Furthermore, FKBP10 attenuated excessive CMA flux to prevent RAD51 degradation in manner of ATF6-mediated endoplasmic reticulum stress (ERS). Importantly, we identified a repurposable therapeutic strategy using selumetinib to downregulate FKBP10, which effectively sensitized to chemoradiotherapy and PARP inhibitor in preclinical BC models. Collectively, our findings uncover a previously unappreciated function of FKBP10 in BC progression and resistance to DNA-damaging therapies, underscoring its promise as an actionable therapeutic target for treatment-refractory BCs.

Necroptosis, driven by RIP3, is critical for intestinal homeostasis but requires stringent regulation to prevent inflammatory pathology. While inhibitory checkpoints of RIP3 are known, mechanisms enabling its physiological activation remain unclear. We identify PRMT5-mediated symmetric di-methylation of RIP3 at arginine 479 (R479) serves as a gatekeeper specifically suppresses RIP1- but not ZBP1- driven necroptosis in intestinal epithelial cells (IECs). Notably, even though STORM super-resolution imaging and molecular dynamics simulations revealed that R479 methylation adjacent to the RHIM domain sterically blocks RIP3 oligomerization both with RIP1 and ZBP1. Mice harboring IEC-specific Rip3^R479K knockin mutation developed spontaneous necroptosis-driven colitis in vivo, directly linking this PTM to pathogenesis. Leveraging these insights, we engineered an SDMA-mimetic peptide that competitively inhibit necroptosis, rescuing Prmt5-deficient mice from lethal colitis without disrupting global signaling homeostasis. Unlike conventional kinase inhibitors, this "methylation mimicry" strategy selectively targets pathogenic cell death, offering a therapeutically actionable advance for IBD and related disorders.

Acyl-CoA dehydrogenase-9 (ACAD9) is classically known for its role in mitochondrial fatty acid β-oxidation and complex I assembly. Here, we identify ACAD9 deficiency as a clinically relevant risk factor for fragility fractures and reveal a previously unrecognized cytosolic function of ACAD9 in suppressing osteoclast differentiation, thereby protecting against osteoporosis. Mechanistically, while preserving its canonical mitochondrial role in complex I assembly, we find that ACAD9 also facilitates the formation of respiratory chain supercomplexes. Notably, in the cytosol, ACAD9 competitively binds to TRAF6, preventing its interaction with the E2 ubiquitin-conjugating complex UBC13/UEV1A, and thereby blocking K63-linked polyubiquitination and downstream activation of the RANK/TRAF6/TAK1/NFATc1 signaling cascade. Additionally, ACAD9 promotes K48-linked polyubiquitination of TRAF6, leading to its proteasomal degradation. Osteoclast-specific Acad9 knockout mice exhibit increased osteoclast numbers and decreased bone mass. These findings uncover a novel extramitochondrial function of ACAD9 in regulating osteoclast differentiation and maturation, and offer potential therapeutic insights for targeting osteoclast hyperactivity in osteoporosis.

The high mortality caused by severe COVID-19 poses great challenges to the public health. However, the underlying pathogenesis of severe cases remains unclear. Here, we find that SARS-CoV-2 infection boosts CD147 inducible up-regulation in the lung tissues of virus-infected rhesus macaques coupled with down-regulated membrane-bound ACE2, which conduces to extended virus infection and severe pathological lesions. Specifically, SARS-CoV-2 infection enhances the expression of transcriptional factor aryl hydrocarbon receptor and facilitates its nucleus translocation, which causes CD147 gene transcription and its up-regulation in protein level, thereby leading to virus susceptibility of the hosts and extended virus infection. Meanwhile, SARS-CoV-2 infection triggers immune imbalance of lung tissues by promoting cell death of CD4 + T cells and B cells and mediating abnormal cell-cell communications, especially for M2 macrophages. Meplazumab, a humanized anti-CD147 antibody, effectively inhibits virus entry and cytokine level, and restores immune balance in the lung tissues of virus-infected rhesus macaque model. Importantly, we further present the cryo-EM structure of CD147-spike complex, and identify five pairs of functional residues for their interaction, which could be interrupted by Meplazumab via steric hindrance effect. Our findings provide direct evidence for CD147-SARS-CoV-2 spike interaction and uncover the pathogenesis of severe COVID-19 caused by CD147-mediated extended virus infection.

Peroxisome proliferator-activated receptor γ (PPAR_γ) is a nuclear receptor whose functional versatility plays a central role in metabolic regulation due to its ligand-dependent conformational dynamics. However, the molecular mechanism through which different ligand classes selectively modulate the conformational landscape of PPAR_γ remains poorly understood. In this study, we applied an integrative computational approach combining extensive molecular dynamics (MD) simulations, Markov state modeling (MSM), and binding free energy calculations to dissect the dynamic allostery underlying PPAR_γ activation and inhibition. Our simulations revealed that ligand binding reshapes the conformational landscape of PPAR_γ by selectively altering dynamic hubs within the R2 (Gly284-Gln294) and R3 (Ile341-Gln345) regions. Energetic analysis revealed a thermodynamic hierarchy of ligand efficacy, with antagonists exhibiting the highest binding affinity (-76.19 kcal·mol^-1), driven predominantly by hydrophobic interactions that sterically restrict Helix 12 (H12) mobility. Key residues, particularly Arg288 and Ile341, were identified as critical nodes within the allosteric network. To prospectively validate this mechanistic model, we conducted an MSM-guided virtual screening of the ZINC20 database. This yielded two natural compounds, ZINC000000834437 and ZINC000008952648, predicted by our model to stabilize distinct receptor conformations associated with antagonist-like and partial agonist-like states, respectively. Overall, this work provides atomistic insights into the conformational selection mechanism of PPAR_γ, and presents a transferable computational framework for probing allosteric regulation in nuclear receptors, with direct implications for the design of selective modulators.