Browse Articles

Filter By:

  • Microbial α-L-fucosidases pertain to the glycoside hydrolases (GHs) family and catalyse the hydrolysis of terminal α-L-fucosidic linkages and transglycosylation reactions, however, prediction of their function directly from protein sequences remains challenging. Here, the authors combine a protein sequence similarity network and protein language model to explore the sequence-function space of GH29 fucosidases and substrate specificity of uncharacterised GH29 sequences.

    • Ana Martínez Gascueña
    • Haiyang Wu
    • Nathalie Juge
    ArticleOpen Access
  • Nucleic acids are key elements in numerous applications such as therapeutics and nanotechnology. However, the synthesis of long and modified oligonucleotides remains challenging and alternative, biocatalytic approaches are needed. Here, the authors discuss recent progress in the controlled enzymatic synthesis of oligonucleotides.

    • Maëva Pichon
    • Marcel Hollenstein
    PerspectiveOpen Access
  • Deep learning models have gained popularity for chemical reaction outcome prediction due to their ability to learn representations directly from the molecular structure, whereas Gaussian processes provide reliable uncertainty estimates but are unable to learn representations from the data. Here, the authors combine the feature learning ability of neural networks with uncertainty quantification of Gaussian processes in a deep kernel learning framework to predict reaction outcomes.

    • Sukriti Singh
    • José Miguel Hernández-Lobato
    ArticleOpen Access
  • For atomically precise nanoparticle synthesis, it is crucial to understand hierarchical interactions during nanostructure formation. Here, the authors observe the crystal seed formation and simultaneous nanocrystal aggregation of ceria from aqueous solution in real time to understand hierarchically different intra- and interparticle interactions governing the particle shapes.

    • Noboru Aoyagi
    • Ryuhei Motokawa
    • Atsushi Ikeda-Ohno
    ArticleOpen Access
  • Voltage-gated sodium channel subtype Nav1.7 is a promising drug target associated with neuropathic pain disorder, however, the current Nav1.7 inhibitors show limited efficacy in clinical trials. More new molecular entities need to be discovered. Here, the authors report a selective Nav1.7 inhibitor by using carbenoid-involved reactions to construct an oxindole-based library, applying it to the scaffold-oriented virtual screening, and validating the hit compound in a clinically relevant model.

    • Jirong Shu
    • Yuwei Wang
    • Wenhao Hu
    ArticleOpen Access
  • Machine learning (ML) is a powerful tool in the field of drug discovery, with the continuous development of new models, however, rational selection of the most appropriate model based on the task remains challenging. Here, the authors explore the capabilities of classical ML algorithms and newer models over a range of dataset tasks and show an optimal zone for each model type, developing a predictive model to aid in the selection of a modeling method based on dataset size and diversity.

    • Scott H. Snyder
    • Patricia A. Vignaux
    • Sean Ekins
    ArticleOpen Access
  • In machine learning of molecular properties, adequate molecular representation is crucial, as minor structural changes result in significant differences in the activity of interest. Here, the authors use a lower-dimensional representation of a molecular manifold to embed electronic attributes and retain the chemical intuition of molecular interactions, invariant to translational and rational degrees of freedom of the molecular surface, to ease model complexities and facilitate generalization even with relatively small datasets.

    • Tonglei Li
    • Nicholas J. Huls
    • Peng Hou
    ArticleOpen Access
  • The electrochemical Leaf (e-Leaf) is an emerging technology that addresses complex enzyme cascades nanoconfined within a porous conducting material—exploiting efficient electron tunneling and local NADP(H) recycling to transduce catalysis and electricity. Here, the authors describe how the e-Leaf was discovered, the steps in its development so far, and the outlook for future research and applications.

    • Bhavin Siritanaratkul
    • Clare F. Megarity
    • Fraser A. Armstrong
    PerspectiveOpen Access
  • CRISPR-Cas proteins appear not only as a genome editing tool but also as a promising diagnostic tool to detect nucleic acid targets, however, most of the CRISPR-based biosensors rely on labelled reporters for signal acquisition. Here, the authors develop a label-free CRISPR-Cas12a-based sensing platform by using supercoiled plasmid DNA as ratiometric reporters, detecting ssDNA targets with a limit of detection of around 100 fM, and applying it to detect various virus samples.

    • Noor Mohammad
    • Logan Talton
    • Qingshan Wei
    ArticleOpen Access
  • Metal-based nanoparticles are promising agents used for photothermal and photodynamic therapy, and as an efficient strategy against multi-drug resistant bacteria. Here, the authors report a one-pot synthesis of SeTe-CuO nanoparticles for such dual-mode therapy, achieving near-infrared activated eradication of bacteria and inhibition of biofilm formation in vitro, as well as promoting wound healing in vivo.

    • Irfan Ullah
    • Shahin Shah Khan
    • Yushu Wang
    ArticleOpen Access
  • Fungi constitute the Earth’s second most diverse kingdom, however, only a small percentage of these have been thoroughly examined and categorized for their secondary metabolites, which still limits our understanding of the ecological, chemical, and pharmacological potential of fungi. Here, the authors explore members of the co-evolved termite-associated fungal genus Xylaria and identify a family of highly oxygenated polyketide-terpene hybrid natural products using an MS/MS molecular networking-based dereplication approach.

    • Seoung Rak Lee
    • Marie Dayras
    • Ki Hyun Kim
    ArticleOpen Access
  • The ability to precisely engineer nanostructures is crucial for a wide range of applications in areas such as electronics, optics, and biomedical sciences. Here, the authors present an approach for templated growth of gold nanoparticle assemblies leveraging the weak van der Waals forces between metal atoms and small molecular templates in superfluid helium.

    • Gokhan Topcu
    • Aula M. A. Al Hindawi
    • Shengfu Yang
    ArticleOpen Access
  • Large classes of metal clusters are expected to have dipole-allowed electronic transitions in the near-infrared, but precise experimental characterization of such low-lying states is lacking. Here, the authors probe cationic cobalt clusters of 4 to 15 atoms using IR photofragmentation spectroscopy with krypton as a messenger atom to show that low-lying electronic excited states are responsible for the size-dependent radiative decay of these highly excited clusters.

    • Kevin A. Kaw
    • Rick J. Louwerse
    • Piero Ferrari
    ArticleOpen Access
  • Photolysis can induce the homolytic cleavage of chemical bonds through the excited state under specific irradiation wavelengths, producing free radical species. Here, the authors report the photoinduced homolysis of electronegative interelement bonds (N–Cl, N–F, and O–Cl bonds) using light with wavelengths longer than that predicted for the S0–Sn or S0–Tn transitions, initiating diverse radical reactions.

    • Antônio Junio Araujo Dias
    • Atsuya Muranaka
    • Yuki Nagashima
    ArticleOpen Access
  • Data-driven computational methods have demonstrated promising potential in predicting compound activities from chemical structures, however, unbiased practical applications remain challenging due to the lack of proper benchmarking methods. Here, the authors develop a benchmark termed CARA to eliminate the biases in current compound activity data by using new train-test splitting schemes and evaluation metrics, revealing accurate and informative model performances.

    • Tingzhong Tian
    • Shuya Li
    • Jianyang Zeng
    ArticleOpen Access
  • Membranization of coacervate microdroplets can stabilize coacervates and enable the construction of hierarchical protocells by using various interfacial layers. Here, the authors demonstrate the modulation of interfacial membrane fluidity and thickness of dextran-bound coacervate protocells by adjusting the molecular weight of dextran or through enzymatic hydrolysis, achieving control over colloidal stability, interfacial molecular transport and cell-protocell interactions.

    • Yanglimin Ji
    • Yan Qiao
    ArticleOpen Access
  • Enzymes play an important role in organic synthesis thanks to their high selectivity, however, such selectivity limits their substrate scope and hampers their wide application. Here, the authors report an approach to rationally select enzymes with proposed functionalities based on sequence analysis, exploring the substrate scope of 4-phenol oxidases by in silico sequence-function correlation analysis.

    • Daniel Eggerichs
    • Nils Weindorf
    • Dirk Tischler
    ArticleOpen Access
  • Ion channels are known to be important actors in cellular signaling, and their functions correlate to their conformational states, however, detailed function–conformation relationships remain underexplored. Here, the authors use a molecular modeling-based approach to assess water and ion conductivity along with pore hydrophobicity and residue packing to characterize the ion channel structural intermediates, revealing three major states of vanilloid-subfamily transient receptor potential channels.

    • Yury A. Trofimov
    • Nikolay A. Krylov
    • Roman G. Efremov
    ArticleOpen Access
  • Droplet interface bilayers can be used as a model of artificial membranes for synthetic biology and drug delivery applications, however, their accessibility using non-invasive techniques remains challenging. Here, the authors develop an in-situ bilayer manipulation of encapsulated droplet interface bilayers in hydrogel capsules, generated by high-order emulsification in monolithic 3D-printed microfluidic devices.

    • Pantelitsa Dimitriou
    • Jin Li
    • David Anthony Barrow
    ArticleOpen Access