科研成果

Abstract: As a key N6-methyladenosine (m6A) reader, YTH domain-containing family protein 1 (YTHDF1) promotes protein synthesis by recognizing m6A-modified mRNA, and its abnormal expression is closely related to breast cancer (BC) progression. To date, the scarce reported YTHDF1 inhibitors suffer from poor selectivity and limited potency, primarily due to the high homology of the YTH domain within the YTHDF family, which poses significant challenges for the discovery of subtype-selective inhibitors. Here, we report SKLB-Y13, the first small-molecule inhibitor achieving exclusive targeting of the YTHDF1 m6A-binding pocket (IC50 = 0.76 µM), via structural optimization of a novel 4,5,6,7-tetrahydrothieno[2,3-c]pyridine scaffold. Uniquely, SKLB-Y13 interacts with YTHDF1-specific residues Tyr397 and Trp470, as confirmed by site-directed mutagenesis, and demonstrates improved selectivity for YTHDF1 over YTH family proteins. Cellular and in vivo studies reveal that SKLB-Y13 disrupts YTHDF1-PRPF6 mRNA interaction in an m6A-dependent manner, thereby impairing the translation of PRPF6 and inhibiting BC proliferation while promoting apoptosis. Chemical proteomics profiling confirms its good target specificity, while pharmacokinetic analysis shows favorable in vivo properties. This study introduces the first selective YTHDF1 inhibitor, serving as a novel chemical probe to elucidate m6A-dependent oncogenesis and a promising starting point for developing precision therapies against YTHDF1-overexpressing BC.

Abstract: Unspecific peroxygenases (UPOs) are promising biocatalysts for selective oxyfunctionalization. Compared to cytochrome P450 enzymes (P450s), the catalytic potential of UPOs has been less investigated, largely due to their limited natural diversity and the challenges associated with their optimization through enzyme engineering. In this study, we engineered an UPO from Aspergillus niger (AniUPO) to catalyze the enantioselective α-hydroxylation of β-ketoesters, a valuable transformation yet to be realized in biocatalysis. Through enzyme engineering, two AniUPO variants, AniUPO-M3 and AniUPO-M6, were developed to produce a wide range of enantioenriched α-hydroxy-β-ketoesters, achieving up to 97% yield, 4140 total turnover number (TTN), and >99:1 enantiomeric ratio (er). The biocatalytic process operates under mild conditions and is scalable for preparative applications. This study broadens the catalytic repertoire of UPOs and enhances their potential for industrial applications.

Abstract: Organofluorines, particularly those containing trifluoromethyl (CF3) groups, play a critical role in medicinal chemistry. While trifluoromethylation of alkenes provides a powerful synthetic route to construct CF3-containing compounds with broad structural and functional diversity, achieving enantioselective control in these reactions remains a formidable challenge. In this study, we engineered a nonheme iron enzyme, quercetin 2,3-dioxygenase from Bacillus subtilis (BsQueD), for the enantioselective trifluoromethylazidation of alkenes. Through directed evolution, the final variant BsQueD-CF3 exhibited excellent enantioselectivity, with an enantiomeric ratio (e.r.) of up to 98 : 2. Preliminary mechanistic studies suggest the involvement of radical intermediates. This work expands biocatalytic organofluorine chemistry by reprogramming metalloenzymes for innovative trifluoromethylation reactions.

Abstract: Molecular generation is a cutting-edge technology with the potential to revolutionize intelligent drug discovery. However, currently reported ligand-based or structure-based molecular generation methods remain unpractical for real-world drug discovery. Here we propose an explicit pharmacophore-oriented 3D molecular generation method, termed PhoreGen. PhoreGen employs asynchronous perturbations and updates on both atomic and bond information, coupled with a message-passing mechanism that incorporates prior knowledge of ligand-pharmacophore mapping during the diffusion-denoising process. Evaluations revealed that PhoreGen efficiently generates 3D molecules well aligned with pharmacophores, maintaining good chemical reasonability, diversity, drug-likeness and binding affinity and, importantly, produces feature-customized molecules at high frequency. By using PhoreGen, we successfully identified new bicyclic boronate inhibitors of evolved metallo-β-lactamase and serine-β-lactamases, which potentiate meropenem against clinically isolated superbugs. Moreover, we identified inhibitors of metallo-nicotinamidases, emerging targets for insecticides. This work explores an explicitly constrained mode for molecular generation and demonstrates its potential in feature-customized drug discovery.

Abstract: Naïve T cells are maintained in a homeostatic state to preserve a stable T cell pool with diverse T cell receptor (TCR) repertoires, ensuring preparedness for priming. However, the underlying mechanisms controlling naïve T cell homeostasis and priming remain unclear. Leveraging a machine learning-based functional genetic screen, we identified DEAD-box helicase 55 (Ddx55) as the top factor responsible for naïve T cell homeostasis. DDX55 was highly expressed in naïve T cells and suppressed enhancer- and promoter-like transposable elements (TEs) near T cell activation-associated genes. Ddx55 loss led to derepression of these TEs, resulting in TE-derived R loops and genomic instability, ultimately disrupting naïve T cell homeostasis and abolishing T cell proliferation. Mechanistically, DDX55-targeted TEs harbored myelocytomatosis oncogene (MYC)-binding motifs. DDX55 directly bound MYC and restricted its access to these TE loci, thereby preventing inappropriate TE activation in naïve T cells. Thus, naïve T cells exploit DDX55 as a vital regulator of T cell activation, ensuring their genomic stability and homeostatic maintenance.

Abstract: Cardiovascular diseases (CVDs) are experiencing a rapid surge and are widely recognized as the leading cause of mortality in the current aging society. Given the multifactorial etiology of CVDs, understanding the intricate molecular and cellular mechanisms is imperative. Over the past 2 decades, many scientists have focused on Sirtuins, a family of nicotinamide adenine dinucleotide-dependent deacylases. Sirtuins are highly conserved across species, from yeasts to primates, and play a crucial role in linking aging and diseases. Sirtuins participate in nearly all key physiological and pathological processes, ranging from embryogenic development to stress response and aging. Abnormal expression and activity of Sirtuins exist in many aging-related diseases, while their activation has shown efficacy in mitigating these diseases (eg, CVDs). In terms of research, this field has maintained fast, sustained growth in recent years, from fundamental studies to clinical trials. In this review, we present a comprehensive, up-to-date discussion on the biological functions of Sirtuins and their roles in regulating cardiovascular biology and CVDs. Furthermore, we highlight the latest advancements in utilizing Sirtuin-activating compounds and nicotinamide adenine dinucleotide boosters as potential pharmacological targets for preventing and treating CVDs. The key unresolved issues in the field-from the chemicobiological regulation of Sirtuins to Sirtuin-targeted CVD investigations-are also discussed. This timely review could be critical in understanding the updated knowledge of Sirtuin biology in CVDs and facilitating the clinical accessibility of Sirtuin-targeting interventions.

Abstract: Atherosclerosis remains the leading type of cardiovascular disease, yet its pathogenesis is not completely understood, hindering the development of effective early diagnostics and therapeutics. Recent work by Mastrangelo et al. in Nature has identified a novel driver of atherosclerosis, the gut microbiota-derived metabolite imidazole propionate, which triggers atherosclerosis via the imidazoline-1 receptor in myeloid cells.

Abstract: Pubertal timing is highly variable and is associated with long-term health outcomes. Phenotypes associated with pubertal timing include age at menarche, age at voice break, age at first facial hair and growth spurt, and pubertal timing seems to have a shared genetic architecture between the sexes. However, puberty phenotypes have primarily been assessed separately, failing to account for shared genetics, which limits the reliability of the purported health implications. Here, we model the common genetic architecture for puberty timing using a multivariate GWAS, with an effective population of 514,750 European participants. We find 266 independent variants in 197 loci, including 18 novel variants. Transcriptomic, proteome imputation and fine-mapping analyses reveal genes causal for pubertal timing, including KDM4C, LEPR, CCNC, ACP1, and PCSK1. Linkage disequilibrium score regression and Mendelian randomisation analysis establish causal associations between earlier puberty and both accelerated ageing and the risk of developing cardiovascular disease and osteoporosis. We find that alanine aminotransferase, glycated haemoglobin, high-density lipoprotein cholesterol and Parabacteroides levels are mediators of these relationships, and establish that controlling oily fish and retinol intake may be beneficial for promoting healthy pubertal development.