RSC Chemical Biology最新文献

Polyamines are essential metabolites that play a crucial role in regulating key cellular processes. While previous studies have shown that polyamines modulate protein function through non-covalent interactions, the lack of robust analytical methods has limited the systematic identification of these interactions in living cells. To address this challenge, we synthesized a series of novel photoaffinity probes and applied them to a model cell line, identifying over 400 putative protein interactors with remarkable polyamine analog structure-dependent specificity. Analysis of probe-modified peptides revealed photocrosslinking sites for dozens of protein binders and demonstrated that all but one of the probes, the spermine analog, were intracellularly stable. The interaction profiles of these probes were visualized through in-gel fluorescence scanning, and their subcellular localization was examined using fluorescence microscopy. Spermidine analogs interacted with proteins in the nucleoplasm, colocalizing with nucleolar and nuclear-speckle proteins, as well as in the cytoplasm. By contrast, diamine analogs localized to vesicle-like structures near the Golgi apparatus, implying that different polyamine types exhibit a proclivity for specific cellular compartments. Notably, spermidine analogs bound preferentially to proteins containing acidic stretches, often located within intrinsically disordered regions. Focusing on one such case, we provide in-cellulo evidence of direct interactions between G3BP1/2 and spermidine analogs and advance the hypothesis that such interactions influence stress-granule dynamics. Overall, this study provides a comprehensive profile of polyamine analogs–protein interactions in live cells, offering valuable insights into their roles in cellular physiology.

Enzymes are powerful catalysts that perform chemical reactions with remarkable speed and specificity. Their intrinsic dynamics often play a crucial role in determining their catalytic properties. To achieve a comprehensive understanding of enzymes, a diverse and sophisticated experimental toolbox capable of studying enzyme dynamics at the single-molecule level is necessary. In this review, we discuss nanopore technology as an emerging and powerful platform in single-molecule enzymology. We demonstrate how nanopores can be employed to probe enzyme dynamics in real-time, and we highlight how these studies have contributed to fundamentally and quantitatively elucidating enzymological concepts, such as allostery and hysteresis. Finally, we explore the potentials and limitations of nanopores in advancing single-molecule enzymology. By presenting the unique possibilities offered by nanopores, we aim to inspire the integration of this technology into future enzymology research.

Chemokines such as CCL5 (RANTES) mediate immune responses via interaction with G-protein-coupled receptors like CCR5, which also serves as a co-receptor for HIV-1 entry into host cells. Modified CCL5 analogues have shown promise as CCR5 antagonists for anti-HIV strategies, but current approaches involve hydrolytically unstable linkages or laborious synthesis. Here, we demonstrate the use of an organocatalyst-mediated protein aldol ligation (OPAL) to construct N-terminally modified CCL5 analogues bearing hydrolytically stable carbon–carbon linkages. Using a recombinant CCL5 P2G mutant and selective oxidation to introduce an α-oxo aldehyde at the N-terminus, we achieved efficient OPAL bioconjugation with various aldehyde donors, including alkyl and aryl acetaldehydes. Notably, a 4-azido aryl acetaldehyde CCL5 OPAL product was utilised as a CCR5 photoaffinity probe. This modified chemokine successfully captured CCR5 from mammalian cells via photo-crosslinking, enabling receptor pull-down for biochemical analysis. Our work showcases cross-aldol bioconjugations as a versatile and convergent strategy for stable chemokine functionalisation, with potential applications in therapeutic development and mechanistic studies of chemokine–receptor interactions. This method offers a promising chemical biology platform for modulating or probing the CCL5–CCR5 axis with enhanced precision and synthetic accessibility.

Interactions between cell surface glycans and lectins mediate vital biological processes, yet their characterization is hindered by the low affinity of these binding events. While photoaffinity labeling can capture these interactions, traditional custom probes often demand tedious synthesis, are limited to simple glycans, and lack versatility. To overcome these limitations, we report a trifunctional scaffold enabling modular assembly of glycan probes. This scaffold integrates orthogonal sites for: (i) efficient late-stage ligation of native oligosaccharides via an N-alkoxy-amine, preserving glycan structure; (ii) flexible amide coupling of various photocrosslinkers, including a recently developed fluorogenic azidocoumarin for traceable labeling; and (iii) conjugation to reporter tags (e.g., biotin) or multivalent carriers through a carboxylic acid motif. We demonstrate the scaffold's utility by synthesizing probes bearing various fucosylated glycans. Probes incorporating the fluorogenic photocrosslinker achieved specific, light-induced labeling of the model lectin BambL. The platform's adaptability was further confirmed by generating monovalent biotinylated probes displaying the photoactive glycan. This modular strategy offers a practical solution to rapidly construct advanced chemical probes, facilitating the investigation of complex glycan recognition events in diverse biological systems.

Novel time-resolved terbium luminescence assays were developed for CDK5 and CDK2 by designing synthetic substrates which incorporate phospho-inducible terbium sensitizing motifs with kinase substrate consensus sequences. A substrate designed for CDK5 showed no phosphorylation by CDK2, opening the possibility for CDK5-specific assay development for selective drug discovery.

RNA-cleaving oligonucleotide catalysts composed of DNA and/or nucleic acid analogues (DNAzymes, modified DNAzymes and XNAzymes) are promising agents for specific knockdown of disease-associated RNAs. However, we and others have identified discrepancies between their apparent activity in vitro versus when transfected into cells. Here, using examples of catalysts targeting the codon 12 region of KRAS RNA – an unmodified DNAzyme based on the classic “10–23” motif, a modified DNAzyme (“10–23_v46”) or an XNAzyme (“FR6_1_KRas12B”) – we examine confounding effects including unintended activity during standard RNA work-up steps, leading to mismeasurement of knockdown. We find that catalysts are not irreversibly denatured by typical cell lysis reagents, nor fully degraded by typical DNase treatments, exacerbated by nuclease resistant modification chemistries. In standard RT-qPCR workflows, DNAzymes and XNAzymes were found to be capable of cleaving their target RNAs during (1) DNase treatment and (2) reverse transcription (RT) reactions, in both instances with enhanced rates compared with under quasi-physiological conditions, producing cleavage-dependent false positives. Furthermore, catalysts were found to site-specifically inhibit cDNA synthesis (i.e. producing cleavage-independent false positives) and in the case of DNAzymes also had the capacity to act as primers during RT, leading to an enhancement of target site cDNA as judged by digital PCR, producing (cleavage-independent) false negatives. These effects could be broadly mitigated by purification to remove catalysts at the point of RNA extraction, under denaturing conditions. We recommend that studies of oligo catalysts in cells must include a 0 h timepoint after catalyst delivery or transfection to assess the collective impact of these mismeasurements on a case by case basis.

Oncoprotein c-Myc (Myc) plays a critical role in regulating cellular gene expression. Although Myc dysregulation is found in more than 70% of cancers and can facilitate tumor initiation and progression, it is still considered to be an “undruggable” oncotarget years after its first discovery. Recent advances in the field of targeted protein degradation provide alternative Myc-targeting strategies. Here, we develop the first Myc-NanoLuc fusion plasmid transfected cell-based high-throughput screening assay to identify Myc-downregulating small molecules. We verified the effectiveness of our assay by demonstrating that previously known Myc-downregulating compounds (G9 and SY-1365) were successfully identified from a library of bioactive compounds with established biological function. Next, we screened another 108 800 compounds from the diverse ChemDiv library collection, and 14 novel Myc-downregulating compounds were identified after cherry-pick triplicate confirmation, counter-screening, dose–response and western blotting experiments. A cellular thermal shift assay further demonstrated that five out of the 14 Myc-downregulating compounds bound to endogenous Myc protein in crude 293T whole-cell lysate. Subsequently, compound C1 was shown to selectively degrade Myc protein at a DC₅₀ value of around 5 μM. Further characterization showed that C1 killed cancer cells with high Myc expression at a lower dose than it killed cancer cells with low Myc expression. Moreover, C1 selectively reduced the expression of various Myc-target genes. Intriguingly, co-immunoprecipitation showed that C1 functionally acted like a molecular glue to aggregate Myc proteins and block Myc/Max interaction. The self-aggregation of Myc and the dissociation of the Myc/Max dimer by C1 promoted Myc degradation. Using a target–NanoLuc fusion strategy in our novel cell-based high-throughput screening system, we identified a molecular glue-like small molecule degrader of Myc.

Protein long-chain S-acylation, the reversible attachment of fatty acids such as palmitate to cysteine residues via thioester bonds, is a widespread post-translational modification that plays a crucial role in regulating protein localization, trafficking, and stability. Despite its prevalence and biological relevance, the study of long-chain S-acylation has long lagged behind that of other dynamic PTMs due to the hydrophobic nature and lability of the lipid modification, which complicate conventional proteomic workflows. Recent advances in mass spectrometry-based strategies have significantly expanded the toolbox for studying long-chain S-acylation, with improved workflows enabling more sensitive, site-specific, and quantitative analysis. This review summarizes key developments from the past decade across both direct and indirect mass spectrometry-based strategies, including acyl-biotin exchange, lipid metabolic labeling, and novel enrichment and fragmentation methods. We also highlight emerging challenges in distinguishing lipid-specific modifications, achieving robust quantification, and mitigating artifacts from in vitro systems, while outlining future directions to advance functional and therapeutic exploration of the S-acyl-(prote)ome.

Light serves as an exceptional stimulus for the precise spatiotemporal regulation of protein activity and protein–protein interactions. Here, we introduce a light-responsive supramolecular ligand system designed to modulate Taspase 1, a protease critical for embryogenesis and implicated in tumor progression. Our approach utilizes photoswitchable divalent molecular tweezers engineered to target lysine-rich regions within the Taspase 1 loop. By incorporating arylazopyrazole (AAP) photoswitches, we achieve dynamic and reversible control of ligand binding. These photoswitches exhibit high photostationary states, excellent reversibility, and prolonged thermal stability of the Z isomer, ensuring reliable switching without photodegradation. The tweezer distance varies between E and Z isomers, enabling tunable binding interactions. Through a combination of surface plasmon resonance, enzymatic cleavage assays, and molecular dynamics simulations, we demonstrate that these ligands bind Taspase 1 with low micromolar affinity and effectively inhibit its proteolytic activity. While isomerization did not significantly affect the inhibition of protein–protein interaction, the E-isomers of larger tweezers exhibited powerful enzyme inhibition, likely due to their ability to bridge lysines flanking the active site. This photoswitchable tweezer system provides a versatile tool for light-controlled modulation of protein function, offering new opportunities for selectively targeting lysine-rich proteins in dynamic biological environments.

Proline cis/trans isomerism plays an important role in protein folding and mediating protein–protein interactions in short linear interacting motifs within intrinsically disordered protein regions. The slow exchange rate between cis and trans prolyl bonds provides distinct signals in ¹⁹F NMR analysis of fluorinated peptides, allowing for simple quantification of each population. However, fluorine is not naturally found in proteins but can be introduced using chemical tags. In this study, we evaluate a range of fluorinated cysteine-reactive ¹⁹F NMR tags to assess their ability to react with short, linear proline-containing peptides and accurately report on the equilibrium cis/trans-Pro populations. Several fluorinated electrophilic tags, including nitrobenzenes, sulfonylpyrimidines, and acrylamides, were found to react chemoselectively and reliably report on the %cis-Pro in the model peptide Ac-LPAAC. Other ¹⁹F NMR tags were found to be poor reporters of local proline conformation. Although pentafluoropyridine was non-chemoselective, it still reliably reported on %cis-Pro when conjugated via cysteine or tyrosine in Ac-LPAAX (X = Cys, Tyr, Lys) peptides. 3,4-Difluoronitrobenzene was found to be compatible with protein tagging, albeit it had modest reactivity and afforded a pair of regioisimeric tagging-products when reacted with a cysteine mutant of α-synuclein. These tools may be valuable for probing cis/trans-Pro populations in proteins.