JACS Au最新文献

Actinomycetota bacteria have specialized in the biosynthesis of antibacterial natural products (NPs), and extract and fraction libraries made from those strains remain a promising source of NP drug leads. Herein, we present a high-throughput screen (HTS), based on engineered Escherichia coli strains expressing the human (Trm5) or bacterial (TrmD) m¹G37 tRNA methyltransferase, to discover NPs as novel anti-Gram-negative antibiotic leads. To harness the evolution of NPs with in vivo activity, the cell-based phenotypic HTS was applied to the Actinomycetota extract and fraction library at the Natural Products Discovery Center (NPDC), the Herbert Wertheim UF Scripps Institute for Biomedical Research & Innovation. From a total of 46,031 extracts and 28,739 fractions made from 14,635 strains, extracts from two Actinomycetota species presented reproducible selectivity against the trmD-expressing E. coli strain over the trm5-expressing counterpart. A shared metabolite was identified as 5-chlorotryptophan, which was correlated to the observed selective inhibitory activities. A metabologenomics analysis indicated 5-chlorotryptophan incorporation into two distinct antibiotic nonribosomal peptide families, longicatenamycins and nonopeptins. Notably, the diketopiperazine-containing heptapeptide nonopeptins display rare chemistry, featuring a 5-nitro-tryptophan moiety that has only been described previously as a biosynthetic shunt product. The most active congener of this new family of NPs, nonopeptin D, exhibits a broad-spectrum antibiotic activity, including against selected Gram-negative pathogens.

Halo-borylsilylcarbanion reagents can be added, with complete stereofacial control, to chiral N-tert-butanesulfinyl imines, featuring an asymmetric C-C bond, followed by concomitant intramolecular asymmetric C-N bond formation. There is exclusive access to α,α-B,Si-disubstituted aziridine units containing up to four contiguous stereocenters in a single operation. In addition, complete stereochemical discrimination has been observed in N-tert-butanesulfinyl alkyl aldimines. Post-transformation of B,Si-disubstituted aziridine generates multichiral aziridine scaffolds.

Saponins are a class of natural products composed of an oxidized triterpene core adorned with glycosylations, ultimately giving rise to medicinally important compounds bearing bioactivity that includes, but is not limited to, anti-inflammatory, antimicrobial, antifungal, antiarrhythmic, and immunostimulatory activities. QS-21 is a prominent immunostimulatory saponin and is a critical adjuvant component of several FDA-approved vaccines. One linchpin modification in the biosynthesis and bioactivity of several saponins, including QS-21, is O-d-fucosylation via an ester linkage. In QS-21, the C28-COOH O-d-fucose residue is part of a linear oligosaccharide that is an integral component of the "core pharmacophore" responsible for its immunomodulatory activity. In this work, we performed in-depth in vitro enzymological characterization of two glycosyltransferases involved in C28-COOH O-d-fucosylation during the maturation of two saponin natural products: QsFucT from QS-21 biosynthesis and SvFucT from vaccaroside biosynthesis. QsFucT was previously shown to be a UDP-4-keto-6-deoxy-d-glucosyltransferase; our data reveal that the taxonomically distant SvFucT also functions as a UDP-4-keto-6-deoxy-d-glucosyltransferase and that both glycosyltransferases act on a triterpene acceptor with low-micromolar affinity. Substrate scope studies demonstrate that both enzymes are highly permissive with regard to both the triterpene acceptor and, unexpectedly, the UDP-sugar donor. These data also reveal that the conserved C3-OH branched trisaccharide of QS-21 and other saponins may serve an unusual biosynthetic role in protecting the C23 aldehyde from spurious reduction during biosynthesis. In addition, we crystallized and solved the structures of QsFucT and SvFucT, providing the first structural characterization of 4-keto-6-deoxy-d-glucosyltranferases in the glycosyltransferase family 1 (GT1) class of enzymes and used these structures to explore the importance of conserved residues in the active site. These data suggest that both QsFucT and SvFucT could be leveraged to rapidly explore saponin chemical space and glycodiversify these important medicinal compounds through engineered biosynthesis or in vitro enzymatic synthesis, possibly leading to novel analogs with enhanced physicochemical or pharmacological properties.

The regioselective activation of alkenyl C-H bonds in conjugated dienols presents significant challenges due to the presence of multiple similarly reactive sites. In this study, we developed a palladium-catalyzed alkynylation method that is both regio- and stereoselective for the activation of internal alkenyl C-H bonds. This approach provides an efficient and versatile strategy for synthesizing dienyne derivatives with precise Z and E configurations. Stereocontrol is achieved through the introduction of acetate salts, which effectively modulate the reaction pathway, allowing for selective outcomes via either a C-H activation process or a Heck coupling mechanism. This innovative strategy not only enhances the specificity of the synthesis but also broadens the potential applications of the resulting dienyne derivatives in various fields.

Heterogenous catalysis involves complex reactions with dynamic changes in catalyst morphology, challenging the capabilities of traditional density functional theory (DFT) methods. To address this, we introduce the catalytic large atomic model (CLAM), a comprehensive data set and pretrained model for machine learning interatomic potential, specifically designed for heterogeneous catalysis. CLAM is trained on a diverse data set that includes metal and alloy slabs with adsorbates, oxides, clusters, two-dimensional materials, and small molecules, ensuring high accuracy across a wide range of catalytic systems. Additionally, we introduce a "local fine-tuning" algorithm, which substantially improves the accuracy of machine learning interatomic potentials for structural optimizations and transition state searches. This approach achieves 94% prediction accuracy within chemical accuracy thresholds (<1 kcal/mol) for adsorption energies of small adsorbates on transition metal surfaces, while demonstrating 3.4× computational acceleration relative to conventional DFT calculations. Furthermore, the method maintains comparable performance in transition state searches, delivering 81% identification accuracy (<1 kcal/mol) with a 10.1× speed-up compared to standard DFT-based CI-NEB approaches. Furthermore, the pretrained CLAM model can accurately reproduce reported dynamic catalysis phenomena via molecular dynamics simulations without additional fine-tuning.

Amides and ketones are essential carbonyl compounds with widespread applications in pharmaceuticals, materials science, and synthetic chemistry. Herein, we present a Ni/photoredox dual-catalyzed strategy for the divergent synthesis of amides and ketones from isocyanates and alcohols. This transformation is facilitated by N-heterocyclic carbene (NHC)-mediated activation of alcohols and is selectively controlled by the choice of additive: NaOAc promotes amide formation, whereas nBu₄NPO₄H₂ directs the reaction toward ketone synthesis. This approach offers a versatile and practical route to access amides and ketones from readily available alcohol feedstocks.

Decarbonizing nitrogen fixation is essential for sustainable fertilizer production, as the conventional Haber-Bosch process remains highly energy-intensive and a significant contributor to global greenhouse gas emissions. Plasma electrification offers a fossil-free, electricity-driven, and decentralized modular alternative that can operate flexibly with intermittent renewable energy sources. In this Perspective, we critically examine the current progress in plasma-based NO _x synthesis, with particular emphasis on reactor engineering, plasma-catalyst synergy, and plasma-liquid systems. We discuss how key operating parameters and plasma-induced reaction pathways govern efficiency and selectivity, and highlight recent advances that enhance NO _x yield while reducing energy consumption. Furthermore, we outline forward-looking strategies to improve plasma-gas interactions, suppress backward reactions, develop robust catalysts stable under nonequilibrium conditions, advance in situ diagnostics, and perform comprehensive techno-economic and life-cycle analyses to enable scalable and practical implementations. By highlighting these opportunities, this Perspective positions plasma-enabled nitrogen fixation as a transformative complement to the Haber-Bosch process, offering a sustainable route to fertilizer production that reduces fossil fuel dependence and mitigates environmental impact.

Water structure is crucially important to protein function and catalysis and can be conserved throughout related proteins despite differences in sequence. The complex hydrogen-bonding networks formed by water molecules and protein residues have been studied extensively, and graph-theory-based methods have frequently been used to describe these networks. Although there exist a number of tools which can be used to track water positions and networks, corresponding methods for easily analyzing complex water network structure across related proteins are limited. To address this challenge, we present here a new tool, WatCon, an open-source Python package which can be used to analyze water positions and water network structure across protein families using both dynamic and static structural information. Importantly, WatCon can be used to classify conservation of water networks, characterize water networks across structures, and project subsequent results for easy visual interpretation. To illustrate WatCon usage, we provide five example applications illustrating WatCon analyses of static structures, dynamic trajectories, and cross-family analysis. This in turn showcases the utility of WatCon for enhancing our understanding of biochemical systems, predicting water hotspots of potential relevance to protein engineering and predicting pathogenic mutations. WatCon can be downloaded at https://github.com/kamerlinlab/WatCon and is available under the GNU General Public License v3.0.

Despite significant progress in extracellular targeted protein degradation (eTPD), existing approaches rarely achieved tissue-specific drug accumulation while maintaining efficient systemic clearance, a critical challenge in treating bone disorders. In this study, we introduced GalNAc-Apc001, a novel aptamer-based lysosome-targeting chimera (LYTAC) that uniquely combined bone-specific retention with hepatocyte-mediated clearance through a spatiotemporally controlled mechanism. By conjugating a tri-N-acetylgalactosamine (GalNAc) moiety to a bone-homing sclerostin aptamer (Apc001), we engineered a bifunctional molecule capable of accumulating in bone via hydroxyapatite binding, capturing circulating sclerostin with high affinity and directing it to hepatocytes for ASGPR-mediated lysosomal degradation. In the absence of ASGPR-positive cells, GalNAc-Apc001 functioned via the conventional aptamer mechanism of binding inhibition, demonstrating efficacy comparable to that of Apc001 but notably lower than that of a sclerostin antibody. However, in ASGPR-positive cell coculture systems, GalNAc-Apc001 achieved a 40% greater activation of the Wnt signaling pathway compared to the sclerostin antibody, effectively reversing sclerostin-mediated inhibition (96 vs 60% recovery). Pharmacologically, GalNAc-Apc001 exhibited superior therapeutic efficacy by mitigating the suppressive effects of sclerostin on Wnt signaling, upregulating bone formation markers, and enhancing bone mass in a Col1a2 ^+/G610C osteogenesis imperfecta mouse model. These findings provided compelling mechanistic evidence that the spatiotemporal control of protein degradation could resolve the inherent trade-off between tissue targeting and systemic clearance, supporting the clinical potential of GalNAc-Apc001 in bone disorders.