ChemBioChem最新文献

The cover shows the direct and site-specific modification of a native antibody and the generation of an antibody-conjugate using click-chemistry. First, the positively-charged peptide (shown in yellow) carrying a functional group (highlighted in orange) is conjugated to the antibody by microbial transglutaminase followed by a click-reaction with a functional payload to generate the antibody-conjugate. More details can be found in article 10.1002/cbic.202400511 by Roger Schibli, Philipp R. Spycher, and co-workers. Illustration created by Bara Krautz.

The cytochromes P450 are a powerful class of heme-containing enzymes capable of a wide range of oxidative transformations in nature. A potent example of their power is their role in the biosynthesis of the biarylitides, a class of ribosomal encoded peptide natural products. This cover image draws an analogy with black holes to highlight the power of these enzymes in their demonstrated ability to catalyse peptide crosslinking even when fluorine is present. More details can be found in article 10.1002/cbic.202400916 by James J. De Voss, Max Crüsemann, Max J. Cryle, and co-workers.. Image created by Dr. Yongwei Zhao.

Benzoboroxole facilitates the delivery of ubiquitin to living cells by utilizing the apo-zinc finger protein domain and thereby converts the apo-zinc finger protein (apo-ZFP) into a cell-penetrating peptide (CPP), despite being inherently a non-CPP. The introduction of point mutations within the skeletal structure, along with the incorporation of benzoboroxole into the lysine side chain, further enhances the efficacy of apo-ZFP. Cellular delivery was monitored using fluorescence microscopy and validated through flow cytometry. More details can be found inarticle 10.1002/cbic.202401040 by Pritam Ghosh and Oliver Seitz. Parts of the image were created with BioRender.com.

Cell-penetrating peptides (CPPs) are favored for protein delivery due to their efficiency, rapidity, and low toxicity. However, conjugation of CPPs to proteins often requires significant amounts of CPPs to ensure yields, which also may result in increased proteins dimer formation. Here, we report that the use of low equivalents 2,2'-dithiodipyridine (DPDS)-activated CPP for conjugation cargo allows for high-conversion-rate CPP-cargo conjugates. Using this strategy, we obtained high-conversion-rate conjugates of cyclic deca-arginine peptide (cR10) with ubiquitin (Ub) and UbcH7 using only low equivalents of cR10. Furthermore, we successfully conjugate three CPPs to cargo via DPDS and confirmed its successful cytosolic delivery through fluorescence imaging.

The indole moiety is a privileged fragment that frequently populates existing bioactive compound collections. We describe the development of an indole-dearomatization sequence and its application for library expansion of a collection of indole-containing pseudo-NPs. The resulting compounds are topologically distinct from the original compound class. Phenotyping by means of the cell painting assay initially indicated that the dearomatized compounds are morphologically different than the original pseudo-NP compound class and guiding NPs. However, analysis by means of a new sub-profile analysis of the same cell painting assay data indicated that similar morphologies persisted throughout the compound classes. Further biological studies supported the findings of the sub-profile analysis and highlights its potential to more effectively characterize novel compounds. The biological findings suggest that a plethora of indole-dearomatization reactions could be applied to existing indole-containing compound collections to rapidly access new biologically relevant scaffolds.

Single α-helical turns (SαHT) are biorelevant peptide structures with potential applications in drug design. We envisioned augmented applications for thermal folding (T-folding) SαHT, wherein, a dynamic SαHT in equilibrium with non-helical conformers can be biased to favor SαHT by increasing the temperature. Short peptides cannot fold into native SαHT due to large conformational entropy. Covalent hydrogen bond surrogates (HBS) for the peptide H-bond have been designed to counter the entropy and enable such SαHT folds. Here, HBS-constrained SαHT are synthesized. NMR, CD spectral and computational analyses reveal their existence in a SαHT conformer which is in equilibrium with non-helical conformers. Temperature-dependent spectral analyses reveal their T-folding behaviour, the extent of which can be controlled by varying the number of Cα-substituents at the i+1st and i+2nd residues and solvent polarities. The conformational transition of the minor non-helical conformers to SαHT with increasing temperature, is at the origin of T-folding. T-folding molecules can uniquely serve as therapeutics with thermally augmentable potencies.

Carbohydrate-active enzymes (CAZymes) are critical for sustainable biomass utilization due to their ability to degrade complex polysaccharides. Frequently, a multimodularity can be observed combining several CAZyme domains and activities in close proximity which can benefit this degradation process. In this study, three multimodular xylanolytic carbohydrate esterases (CEs), named Fl6, Fll1, and Fll4, originating from Flavimarina sp. Hel_I_48 that represent a novel arrangement of catalytic and/or binding domains, are investigated. While Fl6 acts as a glucuronyl esterase, it also contains a carbohydrate binding module which is normally associated with xylanase activity. Fll1 combines xylosidase with acetylxylan esterase (AXE) activity mediated by a CE3 domain. The third enzyme, Fll4, is the first enzyme that comprises three distinct CE domains and shows bifunctional activity as an AXE and a feruloyl esterase (FAE). Investigation of the single domains reveals that the CE6 domain of Fll4 mediates its AXE activity while one of the putative CE1 domains, CE1a, mediates the FAE activity. This investigation of multimodularity of marine CAZymes not only enhances our understanding of these enzymes but may provide a promising route toward more efficient algal biomass utilization for biotechnological applications.

Modification of proteins and other biomolecules with ubiquitin regulates virtually all aspects of eukaryotic cell biology. Ubiquitin can be attached to substrates as a monomer or as an array of polyubiquitin chains with defined linkages between the ubiquitin moieties. Each ubiquitin linkage type adopts a distinct structure, enabling the individual linkage types to mediate specific functions or outcomes in the cell. The dynamics, heterogeneity, and in some cases low abundance, makes analysis of linkage type-specific ubiquitin signaling a challenging and complex task. Here we review the strategies and molecular tools available for enrichment, detection, and characterization of linkage type-specific ubiquitin signaling. The molecular 'toolbox' consists of a range of molecularly different affinity reagents, including antibodies and antibody-like molecules, affimers, engineered ubiquitin-binding domains, catalytically inactive deubiquitinases, and macrocyclic peptides, each with their unique characteristics and binding modes. The molecular engineering of these ubiquitin-binding molecues makes them useful tools and reagents that can be coupled to a range of analytical methods, such as immunoblotting, fluorescence microscopy, mass spectrometry-based proteomics, or enzymatic analyses to aid in deciphering the ever-expanding complexity of ubiquitin modifications.

The scent of the well-known monoterpene limonene is thoroughly investigated. Despite this, the scientific community does not reach consensus. In this Perspective article, a discussion is contributed by giving a simple overview of the olfactory system, as well as presenting the smell of well-known compounds and their odor threshold values in citrus oils, from which (R)-limonene is extracted. In particular, the composition of oils from orange and lemon peel and their association with the (R)- and (S)-enantiomers of limonene, respectively, are considered. Then, the controversy surrounding the odors of (R)- and (S)-limonene and the myth that has been spun from this are reported, particularly in the organic chemistry literature, before an argument for why this myth should be dismantled. Based on the chemical and physiological processes involved in the sense of smell, whether the odor attributed to a certain compound is from that compound and/or from derivatives produced by enzymes associated with the olfactory system is also briefly discussed.

Herein, we describe the synthesis, characterization and anticancer activity of ruthenium(II) p-cymene complexes comprising naphthoyl thiourea-based ligands. The synthesized  ruthenium(II) complexes(1-3) were fully characterized by elemental analysis and spectral methods. The structure of complex 2 has been elucidated by employing single crystal X-ray diffraction (SC-XRD), which verifies the two bidentate N^O and N^S coordination of the thiourea ligand to two Ru(II) centres. Further, the complexes have been subjected to stability studies to illustrate their aquation behavior in an aqueous medium. All the complexes have been screened for their anticancer efficacy in Breast (MCF-7), Colon (HT-29), Liver (HepG2) cancerous cells and non-cancerous kidney (Hek-293) cells. Among them, complex 2 with an IC50 concentration of 3.59 ± 0.72 µM exhibits the most potent activity in HT-29 cells, surpassing the positive control, cisplatin.  In addition, AO-EB and Hoechst labelling of all the complexes(1-3) on HT-29 cells reveals morphological alterations such as nuclear fragmentation and chromatin condensation resulting from the death of cancerous cells via apoptosis. Biochemical assays such as reactive oxygen species (ROS), mitochondrial membrane potential (MMP), and flow cytometry strongly confirm the cell death via mitochondrial dysfunction-mediated apoptosis.