Chemical biology articles within Nature Communications

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  • Article
    | Open Access

    Antimicrobial resistance is a global health threat and the development of alternative strategies to overcome it is of high interest. Here, the authors report proteolysis targeting chimeras active in bacteria (BacPROTACs) that bind to ClpC1, a component of the mycobacterial protein degradation machinery, and apply them for targeting a range of mycobacterial strains, including antibiotic-resistant ones.

    • Lukas Junk
    • , Volker M. Schmiedel
    •  & Guido Boehmelt

  • Article
    | Open Access

    I-Motifs (iM) are non-canonical DNA structures potentially forming in the accessible, single stranded, cytosine-rich genomic region, but the specific contributions of several factors involved in their formation are unknown. Using in-cell NMR, the authors examined DNA i-motif formation in human cells at body temperature, suggesting i-M occur in a small portion (<1%) of genomic sites predisposed to its formation.

    • Pavlína Víšková
    • , Eva Ištvánková
    •  & Lukáš Trantírek

  • Article
    | Open Access

    Here, the authors identify a conformational switch in the amino-terminal transactivation domain of c-MYC, termed coreMYC, which cycles between a closed, inactive state and an open, active conformation. Polyphenol epigallocatechin gallate (EGCG) is used to modulate the conformational landscape of coreMYC, stabilizing the closed and inactive conformation.

    • Dilraj Lama
    • , Thibault Vosselman
    •  & Marie Arsenian Henriksson

  • Article
    | Open Access

    Mirror-image phage display has the potential for high-throughput generation of biologically stable macrocyclic D-peptide binders but is hindered by the optimization required for D-protein chemical synthesis. Here, the authors report a general mirror-image phage display pipeline based on automated flow peptide synthesis and use it to prepare and characterize 12 L/D-protein pairs.

    • Alex J. Callahan
    • , Satish Gandhesiri
    •  & Bradley L. Pentelute

  • Article
    | Open Access

    Sleep-disordered breathing (SDB) is a prevalent disorder linked to higher cardiovascular disease risk. Here, the authors show that summary scores reflecting SDB metabolite signatures are associated with increased risks for incident hypertension and diabetes, potentially useful in guiding risk stratification.

    • Ying Zhang
    • , Bing Yu
    •  & Tamar Sofer

  • Article
    | Open Access

    The delivery of CRISPR RNPs has potential advantages over other genome editing approaches, including reduced off-target editing and reduced immunogenicity. Here the authors report self-deliverable Cas9 RNPs capable of robustly editing cultured cells in vitro and the mouse brain upon direct injections.

    • Kai Chen
    • , Elizabeth C. Stahl
    •  & Jennifer A. Doudna

  • Article
    | Open Access

    Kinetic modeling of in vitro enzymatic reaction networks (ERNs) is severely hampered by the lack of training data. Here, authors introduce a methodology that combines an active learning-like approach and flow chemistry to create optimized datasets for an intricate ERN.

    • Bob van Sluijs
    • , Tao Zhou
    •  & Wilhelm T. S. Huck

  • Article
    | Open Access

    InsP3 3-kinase phosphorylates 1,4,5-trisphosphate (InsP3) specifically at its secondary 3-hydroxyl group to generate a tetrakisphosphate. Here, the authors used a combination of methods to survey InsP3 3-kinase ligand specificity and determined that IP3K specificity surpasses that of its natural substrate, allowing it to bind diverse ligands with a primary hydroxyl in the reactive position and based on a carbohydrate moiety.

    • María Ángeles Márquez-Moñino
    • , Raquel Ortega-García
    •  & Beatriz González

  • Article
    | Open Access

    Paclitaxel is an important anticancer drug whose biosynthetic pathway reconstruction is hindered by the propensity of heterologously expressed pathway cytochromes P450, including taxadiene 5α-hydroxylase (T5αH), to form multiple products. Here, the authors tune the promoter strength for T5αH expression in Nicotiana plants to increase the levels of paclitaxel precursor taxadien-5α-ol by three-fold and reconstitute the six step early biosynthetic pathway of paclitaxel.

    • Jack Chun-Ting Liu
    • , Ricardo De La Peña
    •  & Elizabeth S. Sattely

  • Article
    | Open Access

    The antitumor drug trabectedin is more toxic to DNA-repair-proficient cells. Here the authors show that this is caused by persistent DNA breaks induced from an abortive repair reaction and develop “TRABI-Seq” to map the breaks to transcribed regions of the genome. Trabectedin may thus be used as a diagnostic and therapeutic in precision oncology.

    • Kook Son
    • , Vakil Takhaveev
    •  & Orlando D. Schärer

  • Article
    | Open Access

    The molecular characterisation of soft tissue sarcomas (STSs) across diverse populations remains crucial. Here, the authors perform a proteomics and phosphoproteomics analysis of 272 Chinese STS patients across 12 subtypes, and obtain insights related to progression, metastasis, and immune signatures.

    • Shaoshuai Tang
    • , Yunzhi Wang
    •  & Chen Ding

  • Article
    | Open Access

    Previous genetically encoded H2O2 probes are based on reversible thiol oxidation. Here, a heme peroxidase is introduced as a thiol-independent H2O2 probe. APEX2 converts H2O2 into fluorescent or luminescent signals, allowing its quantification.

    • Mohammad Eid
    • , Uladzimir Barayeu
    •  & Tobias P. Dick

  • Article
    | Open Access

    Hemiacetal compounds are valuable building blocks in synthetic chemistry, but difficult to obtain by enzymatic synthesis. Here, the authors use reaction engineering of an immobilized unspecific peroxygenase from Agrocybe aegerita for selective C-H bond oxyfunctionalisation of environmentally significant cyclic ethers to chiral cyclic hemiacetals.

    • Xiaofeng Han
    • , Fuqiang Chen
    •  & Wuyuan Zhang

  • Article
    | Open Access

    In this work, the authors report NMR lipids Databank to promote decentralised sharing of biomolecular molecular dynamics (MD) simulation data with an overlay design. Programmatic access enables analyses of rare phenomena and advances the training of machine learning models.

    • Anne M. Kiirikki
    • , Hanne S. Antila
    •  & O. H. Samuli Ollila

  • Article
    | Open Access

    Specialized pro-resolving mediators (SPM) are involved in the reprogramming of immune responses. Here the authors show that resolvin (RvT) 4 limits the progression of vascular disease in mouse models of arthritis exacerbated atherosclerotic inflammation.

    • Mary E. Walker
    • , Roberta De Matteis
    •  & Jesmond Dalli

  • Article
    | Open Access

    Conventional CRISPR-based approaches to monitor genomic loci can be hampered by high background and nonspecific nucleolar signal. Here, the authors propose a fluorogenic CRISPR (fCRISPR) tool that allows for high-contrast and sensitive imaging of genomic DNA.

    • Zhongxuan Zhang
    • , Xiaoxiao Rong
    •  & Xing Li

  • Article
    | Open Access

    Proteins labelled site-specifically with small molecules are valuable assets for chemical biology and drug development. Here, the authors report Baylis Hillman orchestrated protein aminothiol labelling (BHoPAL), a bioconjugation strategy for specific labelling of the 1,2-aminothiol moiety and combine it with a lipoic acid ligase-based technology to achieve labelling at any desired site within proteins.

    • Mudassir H. Mir
    • , Sangeeta Parmar
    •  & Dimpy Kalia

  • Article
    | Open Access

    Succinate dehydrogenase converts malate to enoloxaloacetate, a metabolically inactive and inhibitory side product of the TCA cycle. Here, Zmuda et al. describe a conserved metabolite damage repair enzyme that can remove enol-oxaloacetate and is critical for efficient aerobic respiration.

    • Anthony J. Zmuda
    • , Xiaojun Kang
    •  & Thomas D. Niehaus

  • Article
    | Open Access

    In vivo detection of cell senescence remains a challenge in aging research. This work introduces a novel fluorogenic probe for β-Gal activity that is excreted in urine, providing a simple diagnosis method to estimate the systemic load of senescent cells during aging and senolytic interventions.

    • Sara Rojas-Vázquez
    • , Beatriz Lozano-Torres
    •  & Ramón Martínez-Máñez

  • Article
    | Open Access

    No consensus exists on the computationally tractable use of dynamic models for strain design. To tackle this, the authors report a framework, nonlinear-dynamic-model-assisted rational metabolic engineering design, for efficiently designing robust, artificially engineered cellular organisms.

    • Bharath Narayanan
    • , Daniel Weilandt
    •  & Vassily Hatzimanikatis

  • Article
    | Open Access

    The mechanical dysregulation of cells is associated with several diseases and strategies to deliver drugs based on the “mechanical phenotype” of a cell are desirable. Here, the authors design and characterize DNA mechanocapsules comprised of DNA tetrahedrons that are force responsive, and showed they can encapsulate macromolecular cargo and release it upon application of force.

    • Arventh Velusamy
    • , Radhika Sharma
    •  & Khalid Salaita

  • Article
    | Open Access

    Stapled α-helical peptides are promising for targeting challenging targets such as transcription factors, but achieving sufficient cell permeability while avoiding off-target cleavage is difficult. Here, the authors present workflows for identifying stapled peptides against Mdm2(X) with in vivo activity and no off-target effects based on comprehensive investigations of their properties.

    • Arun Chandramohan
    • , Hubert Josien
    •  & Anthony W. Partridge

  • Article
    | Open Access

    Ajmaline is an antiarrhythmic monoterpenoid indole alkaloid produced by the root of Rauwolfia serpentina. Here, the authors complete the ajmaline biosynthetic pathway by identifying two reductases and two esterases, and achieve the de novo ajmaline biosynthesis by engineering Baker’s yeast.

    • Jun Guo
    • , Di Gao
    •  & Yang Qu

  • Article
    | Open Access

    IgG molecules are glycosylated at a conserved asparagine residue of their constant region, and this modification is essential for the effector functions of their soluble form, such as complement activation and binding to Fcɣ receptors. Here authors show that in a model B-cell line, neither the expression nor the function of the membrane-bound form of IgG depend on glycosylation.

    • Theresa Kissel
    • , Veerle F. A. M. Derksen
    •  & René E. M. Toes

  • Article
    | Open Access

    Much is still unknown of the evolution of animal metabolic enzymes. This study describes a new enzyme family bridging the production of polyketides and membrane lipids. This expands the known biochemical repertoire of animals for making ecologically and biomedically important natural products.

    • Zhenjian Lin
    • , Feng Li
    •  & Eric W. Schmidt

  • Article
    | Open Access

    Avapritinib, a potent inhibitor, offers hope for D842V-mutant GIST patients with high response rates; however, resistance and side effects remain challenges. Here, crystal structures shed light on this and reveal a Gα-pocket for drug development.

    • A. Teuber
    • , T. Schulz
    •  & D. Rauh

  • Article
    | Open Access

    Coacervate droplets have potential as components for cell-like materials, but are limited by complex molecular structure and control of the internal microenvironment. Here, the authors report stable dipeptide-based coacervates with a microenvironment for the encapsulation of hydrophobic species.

    • Shoupeng Cao
    • , Tsvetomir Ivanov
    •  & Lucas Caire da Silva

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