Small molecules articles within Nature Chemistry

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  • Article
    | Open Access

    Polymethine dyes are bright and red-shifted fluorophores that lack an intrinsic turn-on mechanism, which leads to non-specific staining when applied to biological samples. Now the fluorescence of polymethine dyes was masked through an intracellular cyclization strategy that gets reversed upon binding an intended macromolecular target, providing specificity for live-cell imaging.

    • Annabell Martin
    •  & Pablo Rivera-Fuentes

  • Article |

    Most chemoproteomic screening approaches are indirect. Now, a chemoproteomic platform based on chiral sulfonyl fluoride probes has been developed for the direct identification of probe-modified tyrosines and lysines in live cells. Stereoselective modification by structurally diverse probes was observed for 634 tyrosines and lysines across functionally diverse protein sites.

    • Ying Chen
    • , Gregory B. Craven
    •  & Jack Taunton

  • Article |

    Developing stimuli-responsive bioorthogonal tetrazine ligations remains highly challenging, but a versatile approach that uses photocaged dihydrotetrazines has now been developed. Photouncaging results in the spontaneous formation of reactive tetrazines that rapidly react with dienophiles such as trans-cyclooctenes. As a demonstration, the method was used for live-cell labelling with single-cell precision and light-triggered drug delivery.

    • Luping Liu
    • , Dongyang Zhang
    •  & Neal K. Devaraj

  • Article |

    A deep chemical proteomic investigation of diverse aminophilic electrophiles has identified ligandable lysines across a wide range of human proteins. The proteins cover different functional and structural classes, and the aminophilic electrophiles include compounds that disrupt protein–protein and protein–RNA interactions. This dataset provides a proteome-wide atlas of lysine-reactive chemistry.

    • Mikail E. Abbasov
    • , Madeline E. Kavanagh
    •  & Benjamin F. Cravatt

  • Article |

    A set of enantioprobes—photoreactive, clickable fragment pairs differing only in absolute stereochemistry—have been used to provide a robust and streamlined chemical proteomic map of small-molecule/protein interactions in human cells. More than 170 stereoselective fragment–protein interactions were discovered and shown to occur at functional sites on proteins from diverse classes.

    • Yujia Wang
    • , Melissa M. Dix
    •  & Benjamin F. Cravatt

  • Review Article |

    ortho-Aminomethylphenylboronic acids are routinely used in sensors for carbohydrates, but the function of the o-aminomethyl group in enhancing binding affinity and modulating the emission of appended fluorophores has been the matter of some debate. This Review presents a unified picture of the structural features, mechanisms of sugar complexation and photophysics of these kinds of sensors.

    • Xiaolong Sun
    • , Brette M. Chapin
    •  & Eric V. Anslyn

  • Article |

    Biosynthesis of peptidoglycan requires carefully orchestrated transpeptidation reactions to maintain the structural integrity of this essential component of the bacterial cell wall. Now, rotor-fluorescent d-amino acids have been shown to enable real-time tracking of these transpeptidation reactions in live bacterial cells. These powerful tools allow visualization of peptidoglycan biosynthesis with high spatiotemporal resolution.

    • Yen-Pang Hsu
    • , Edward Hall
    •  & Michael S. VanNieuwenhze

  • Article |

    An effective antiviral against the common cold could prevent exacerbations in asthma and chronic obstructive pulmonary disease, but the diversity and adaptability of the virus makes it a highly challenging target. Now, picomolar inhibitors of a human lipid transferase have been developed. Targeting this human lipid transferase could provide an effective and broad-spectrum approach to block viral replication in the host.

    • Aurélie Mousnier
    • , Andrew S. Bell
    •  & Edward W. Tate

  • Article |

    A chemical proteomic strategy has now been reported for the global profiling of lysine reactivity and ligandability. Using this approach, >9000 lysines in the human proteome were evaluated, leading to the discovery of hyper-reactive lysines, and lysines that can be targeted by electrophilic small molecules to perturb enzyme function and protein–protein interactions.

    • Stephan M. Hacker
    • , Keriann M. Backus
    •  & Benjamin F. Cravatt

  • Article |

    Structure-based drug design has generally focused on calculating binding free energies of protein–ligand complexes. It has now been shown that structural, rather than thermodynamic, stability — specifically, the work necessary to reach a quasi-bound state in which the ligand has just broken the most important contact with the receptor — can be calculated and used as a tool in virtual screening.

    • Sergio Ruiz-Carmona
    • , Peter Schmidtke
    •  & Xavier Barril

  • Article |

    A structure-specific antibody generated and employed to visualize DNA G-quadruplex structures in human cells shows that these structures are modulated during the cell cycle and can be stabilized by a small-molecule ligand. This provides substantive evidence for endogenous DNA G-quadruplex formation in mammalian cells.

    • Giulia Biffi
    • , David Tannahill
    •  & Shankar Balasubramanian

  • Review Article |

    The complexity of living systems makes attempts to gain a molecular-level understanding of them a unique and inspiring challenge. This Review summarizes progress in the development of bioorthogonal reaction-based fluorescent probes used to follow the spatial and temporal dynamics of biologically important analytes within living systems.

    • Jefferson Chan
    • , Sheel C. Dodani
    •  & Christopher J. Chang

  • Article |

    Site-selective functionalizations of complex small molecules can generate targeted derivatives with exceptional step-efficiency, but general strategies for maximizing selectivity in this context are rare. Investigations with the ion-channel-forming natural product amphotericin B have revealed that site-selectivity can be tuned by simply modifying the electronic nature of the reagents.

    • Brandon C. Wilcock
    • , Brice E. Uno
    •  & Martin D. Burke

  • News & Views |

    Nucleic acid aptamers have been employed to shield small molecules so that one among many similar reactive functional groups can be modified. This provides access to new chemical entities with potentially interesting properties while avoiding the use of covalent protecting groups.

    • Scott K. Silverman

  • Editorial |

    Structure by structure, more information is steadily being gathered on how small molecules bind to DNA. A better understanding of the interactions involved in such processes will be crucial for the successful design of compounds for specific diagnostic and therapeutic purposes.

  • Article |

    The natural product thiostrepton is known to have anticancer properties but its mechanism of action is not known. Here, it is shown that thiostrepton binds to the protein FOXM1, preventing its interaction with several gene promoters and inhibits their expression. This illustrates the druggability of transcription factors, and provides a molecular basis for targeting FOXM1.

    • Nagaratna S. Hegde
    • , Deborah A. Sanders
    •  & Shankar Balasubramanian

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