ChemBioChem最新文献

The severe acute respiratory syndrome virus 2 (SARS-CoV-2) seriously impacted public health. The evolutionarily conserved viral chymotrypsin-like main protease (M^pro) is an important target for anti-SARS-CoV-2 drug development. Previous studies have shown that the eight N-terminal amino acids (N8) of SARS-CoV M^pro are essential for its dimerization, and are used to design inhibitors against SARS-CoV M^pro dimerization. Here, we established a simple readout assay using SDS-PAGE and Coomassie blue staining to measure inhibitory activity of N8 peptide derived from SARS-CoV-2 M^pro. To optimize its inhibitory effect, we then modified the side-chain length, charge, and hydrophilicity of the N8 peptide, and introduced a mutated M^pro recognition sequence. As a result, we obtained a series of potent peptide inhibitors against SARS-CoV-2 M^pro, with N8-A24 being the most efficient with an IC₅₀ value of 1.44 mM. We observed that N8-A24 reduced M^pro dimerization with an IC₅₀ value of 0.86 mM. Molecular docking revealed that N8-A24 formed hydrogen bond interactions with critical dimeric interface residues, thus inhibiting its dimerization and activity. In conclusion, our study not only discovers a series of peptide inhibitors targeting the SARS-CoV-2 M^pro dimerization, but also provides a promising strategy for the rational design of new inhibitors against COVID-19.

The Psilocybe cubensis SAM-dependent methyltransferase, PsiM, catalyzes the last step in the biosynthesis of psilocybin. Likely evolved from monomethylating RNA methyltransferases, PsiM acquired a key amino acid exchange in the secondary sphere of the active site, M247 N, which is responsible for its capacity to dimethylate. Two variants, PsiM^N247M and PsiM^N247A, were generated to further examine the role of Asn247 for mono- and dimethylation in PsiM. Herein, we present the kinetic profiles of both variants and crystal structures at resolutions between 0.9 and 1.0 Å. Each variant was crystallized as a ternary complex with the non-methylated acceptor substrate, norbaeocystin and S-adenosyl-l-homocysteine, and in a second complex with the cofactor analog, sinefungin, and the monomethylated substrate, baeocystin. Consistent with the inability of the variants to catalyze a second methyl transfer, these structures reveal catalytically non-productive conformations and a high level of disorder of the methylamine group of baeocystin. Additionally, both variants exhibit destabilization in the β5-β7 sheets and a conserved β-turn of the core Rossmann fold, causing 20-fold reduced substrate binding and 2-fold lower catalytic efficiency even with norbaeocystin. Our structural and kinetic analyses of the variants suggest that Asn247 is essential to allow enough space in the active site for multiple methylations while also participating in a network of hydrogen bonds that stabilizes secondary structure elements in the immediate vicinity of the active site for optimal methylation of norbaeocystin.

Phenazine natural products play various roles such as signal molecules, antibiotics, or electron carriers in their producer strains. Among these products, phenazinomycin and lavanducyanin, which are produced by Streptomyces species, are characterized by an N-alkyl modification. Herein, we established the biosynthetic pathways for these two phenazine natural products. Gene-disruption experiments and in vitro reconstitution of the phenazine-tailoring pathway revealed the late steps of the biosynthetic pathway of the phenazines. The class II terpene cyclase homolog Pzm1 catalyzes the cyclization reaction of farnesyl diphosphate to form monocyclic farnesyl diphosphate. Additionally, the prenyltransferase homolog PzmP functions as the N-prenyltransferase of 5,10-dihydrophenazine-1-carboxylic acid. The flavin monooxygenase homolog PzmS catalyzes the oxidative decarboxylation of prenylated 5,10-dihydrophenazine-1-carboxylic acid to yield phenazinomycin. This study highlights unprecedented modification enzymes for phenazine natural products.

The cover image depicts a novel “acid-washable” acyl donor, namely vinyl 3-(dimethylamino)propanoate, dedicated to a chromatography-free lipase-catalyzed kinetic resolution (KR) of racemic sec-alcohols. The employed vinyl ester allows the synthesis of both enantiomers of a range of structurally diverse benzylic alcohols with high conversions and excellent enantioselectivity, and, most importantly, significantly simplifies enzymatic KR by eliminating a silica gel chromatographic separation, leading to a more sustainable and ecologically friendly bioprocess. More details can be found in article 10.1002/cbic.202400394 by Beata Zdun and Paweł Borowiecki. Cover image designed by Paweł Borowiecki and created by Paulina Marek-Urban.

The article 10.1002/cbic.202400484 by Samya Banerjee, Tukki Sarkar, Akhtar Hussain, and co-workers highlights the synthesis, characterization, and evaluation of six new mixed-ligand cobalt(III) complexes for photodynamic therapy (PDT) in cancer treatment. Notably, complexes Co5 and Co6, featuring dipyridophenazine and the naturally occurring flavonoids chrysin and silibinin, exhibit significant toxicity against cervical and lung cancer cells under visible light with low micromolar IC₅₀ values, while showing minimal toxicity in the absence of light. These complexes induce apoptosis via singlet oxygen generation following a type-II PDT pathway, displaying remarkable selectivity and biocompatibility for potential cancer PDT applications.

In this study, we have successfully synthesized bis (cholesterol-dibenzo-18-crown-6-ether)-pillar[5]arene compound 1 through a click reaction, which could spontaneously insert into lipid bilayers to form ion channel due to the membrane anchor cholesterol group and show significant transport activity of K⁺ superior to Na⁺, with a permeability ratio of K⁺/Na⁺ equal to 4.58. Compound 1 two crown ether modules act as selective filters similar to natural K⁺ channel, which are determined to 1 : 2 binding stoichiometry to K⁺ by Job's plot and NMR titration. This structurally unambiguously unimolecule artificial channel provides ideas for constructing highly K⁺/Na⁺ selective molecular filters.

Fluorogenic substrates are essential tools for studying the activity of many enzymes including the protein tyrosine phosphatases (PTPs). Here, we have taken the first step toward the development of genetically encodable sensors for PTP activity using fluorescent and fluorogen-activating proteins. The Fluorescence-Activating and absorption Shifting Tag (FAST) is a small protein that becomes fluorescent upon binding to a small molecule dye. We demonstrate that FAST protein can be used as a sensor for PTP-mediated dephosphorylation of phosphorylated dye molecules. Phosphorylated 4-hydroxybenzylidene rhodanine (pHBR) is not able to bind to the FAST protein and induce fluorescence, but provides a sensitive assay for PTP activity, readily detecting 100 pM concentrations of PTP1B in the presence of FAST with a k_cat value of 19±1 s^-1 and a K_M value of 93±3 μM. In addition, while phosphorylation of the C-terminal peptide of split GFP does not result in appreciable change in fluorescence of the reconstituted protein, phosphorylation of the C-terminal peptide of the split FAST protein abrogates fluorescence. Upon PTP-mediated dephosphorylation of the C-terminal peptide, the ability of the N- and C-terminal components to form a fluorescent complex with the small molecule dye is restored, leading to fluorescence.

We report the synthesis, characterisation, and anti-breast cancer stem cell (CSC) properties of two copper(II)-terpyridine complexes with bidentate salicylaldehyde moieties (2-hydroxybenzaldehyde for 1 and 2-hydroxy-1-naphthaldehyde for 2). The copper(II)-terpyridine complexes 1 and 2 are stable in biologically relevant aqueous solutions and display micromolar potency towards breast CSCs. The most effective complex 1 is 5-fold and 6.6-fold more potent towards breast CSCs than salinomycin and cisplatin, respectively. The copper(II)-terpyridine complexes 1 and 2 also decrease the formation and viability of three-dimensionally cultured mammospheres within the micromolar range. Notably complex 1 is up to 7-fold more potent towards mammospheres than salinomycin or cisplatin. Mechanistic studies suggest that the copper(II)-terpyridine complexes 1 and 2 are able to readily enter breast CSCs, elevate intracellular reactive oxygen species levels, induce DNA damage (presumably by oxidative DNA cleavage), and evoke apoptosis that is independent of caspases. This study shows that the copper(II)-terpyridine motif is a useful building block for the design of anti-breast CSC agents and reinforces the therapeutic potential of copper coordination complexes.

Rubrobacter radiotolerans nerolidol synthase (NerS) and trans-α-bergamotene synthase (BerS) are among the first terpene synthases (TPSs) discovered from thermotolerant bacteria, and, despite sharing the same substrate, make terpenoid products with different carbon scaffolds. Here, the potential thermostability of NerS and BerS was investigated, and NerS was found to retain activity up to 55 °C. A library of 22 NerS and BerS variants was designed to probe the differing reaction mechanisms of NerS and BerS, including residues putatively involved in substrate sequestration, cation-π stabilisation of reactive intermediates, and shaping of the active site contour. Two BerS variants showed improved in vivo titres vs the WT enzyme, and also yielded different ratios of the related sesquiterpenoids (E)-β-farnesene and trans-α-bergamotene. BerS-L86F was proposed to encourage substrate isomerisation by cation-π stabilisation of the first cationic intermediate, resulting in a greater proportion of trans-α-bergamotene. By contrast, BerS-S82L significantly preferred (E)-β-farnesene formation, attributed to steric blocking of the isomerisation step, consistent with what has been observed in several plant TPSs. Our work highlights the importance of isomerisation as a key determinant of product outcome in TPSs, and shows how a combined computational and experimental approach can characterise TPSs and variants with improved and altered functionality.

8-Oxoguanine glycosylase 1 (OGG1) repairs the major oxidative DNA damage, 8-oxo-2'-deoxyguanosine. It has been reported that OGG1 incises the most frequently formed DNA lesion, apurinic/apyrimidinic (AP) site, and in the process a stable DNA-OGG1 cross-link is formed. However, the chemical structure of the adduct is not characterized. Here, we report that DNA-OGG1 cross-links result from cysteine and histidine addition to incised AP sites at 3'-DNA termini.