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ConspectusSkeletal editing, as a synthetic tool, offers the unique potential to selectively and efficiently modify the core skeleton of a target molecule at a late-stage. The main benefit of such transformations is the rapid exploration of the chemical space around lead compounds without necessitating a synthesis for each new molecule. However, many skeletal editing transformations are inherently restricted to generating a single product from a single starting compound, limiting the potential for diversification, a concept central to expediting structure-activity relationship (SAR) investigations. In this Account, we describe our efforts to develop novel skeletal editing transformations in which a modification to the central motif of a molecule is performed simultaneously with the incorporation of additional functionality that can be easily varied through a judicious choice of the reagents. Specifically, we successfully developed an α-iodonium diazo-based carbynyl radical equivalent reagent that, under photoredox conditions, could facilitate the ring-expansion of indene scaffolds while enabling the insertion of over ten different functionalized carbon atoms into the corresponding naphthalene products. This concept was later extended to the design of an atomic carbon equivalent reagent that could promote mild and selective Ciamician-Dennstedt-type indole ring-expansion reactions, while simultaneously installing an oxime ester handle that could undergo further functionalization. Furthermore, we highlight recent work from our group on multiple-atom insertion reactions, namely, the development of a photocatalyzed De Mayo reaction for the ring-expansion of cyclic ketones and a photocatalyzed dearomative ring-expansion of thiophenes via small-ring insertion. In both of these cases, multiple products can be potentially accessed from a single starting material upon variation of the insertion reagent. The diversity-generating skeletal editing strategy could also be applied to single-atom transmutation, as demonstrated by the development of a nitrogen-to-functionalized carbon atom transmutation reaction to convert pyridine to benzene rings. Here, the desired transformation was achieved via a sequence of pyridine ring-opening, Horner-Wadsworth-Emmons (HWE) olefination, and ring-closure, with a judicious choice of the HWE reagent allowing the installation of a wide variety of versatile functional groups. Finally, an energy transfer-mediated quinoline ring-contraction is discussed, specifically with reference to the ways in which it does and does not fit the criteria of a skeletal editing reaction. Although formal atom deletion transformations are typically restricted to single products from each discrete substrate, this [2 + 2] cycloaddition/rearrangement cascade also involves the incorporation of an alkene into the molecule and introduces a point of variation that can be exploited for diversity generation. We hope to not only highlight the transformations reported herein but also inspire further research into this synthetic strategy to access new classes of skeletal editing transformations that, through rapid diversity generation, provide the potential to expedite SAR investigations.
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http://dx.doi.org/10.1021/acs.accounts.4c00820 | DOI Listing |
J Am Soc Nephrol
September 2025
Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
Background: Genetic modifiers are believed to play an important role in the onset and severity of polycystic kidney disease (PKD), but identifying these modifiers has been challenging due to the lack of effective methodologies.
Methods: We generated zebrafish mutants of IFT140, a skeletal ciliopathy gene and newly identified autosomal dominant PKD (ADPKD) gene, to examine skeletal development and kidney cyst formation in larval and juvenile mutants. Additionally, we utilized ift140 crispants, generated through efficient microhomology-mediated end joining (MMEJ)-based genome editing, to compare phenotypes with mutants and conduct a pilot genetic modifier screen.
Recent advances in computer vision have enabled the development of automated animal behavior observation tools. Several software packages currently exist for concurrently tracking pose in multiple animals; however, existing tools still face challenges in maintaining animal identities across frames and can demand extensive human oversight and editing. Here we report on DIPLOMAT, a D eep learning-based, I dentity- P reserving, L abeled- O bject M ulti- A nimal T racker, which implements automated algorithms to improve identity continuity, supplemented by an efficient human interface to help eliminate remaining errors.
View Article and Find Full Text PDFPharmaceuticals (Basel)
July 2025
Department of Anatomy and Genetics, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.
Bone metastasis remains a significant cause of morbidity and diminished quality of life in patients with advanced breast, prostate, and lung cancers. Emerging research highlights the pivotal role of reversible epigenetic alterations, including DNA methylation, histone modifications, chromatin remodeling complex dysregulation, and non-coding RNA networks, in orchestrating each phase of skeletal colonization. Site-specific promoter hypermethylation of tumor suppressor genes such as and , alongside global DNA hypomethylation that activates metastasis-associated genes, contributes to cancer cell plasticity and facilitates epithelial-to-mesenchymal transition (EMT).
View Article and Find Full Text PDFProc Natl Acad Sci U S A
September 2025
Gavin Herbert Eye Institute-Robert M. Brunson Center for Translational Vision Research, Department of Ophthalmology and Visual Sciences, University of California Irvine, Irvine, CA 92697.
In vivo genome editing has the potential to address many inherited and environmental disorders. However, a major hurdle for the clinical translation of genome editing is safe, efficient delivery to disease-relevant tissues. A modality-agnostic reporter animal model that facilitates rapid, precise, and quantifiable assessment of functional delivery and editing could greatly enhance the evaluation and translation of delivery technologies.
View Article and Find Full Text PDFJ Am Chem Soc
August 2025
Department of Chemistry, University of Manchester, Manchester M13 9PL, U.K.
We report the deletion of nitrogen atoms from multiple template sites in rotaxanes, catenanes, and a molecular knot. Nitrogen extrusion from secondary amines in the backbone of the interlocked structures is achieved using -diphenylphosphinylhydroxylamine (DPPH), forming carbon-carbon bonds while largely maintaining the integrity of the original mechanical bonding. We find that DPPH gives improved yields (up to 51%) for nitrogen atom deletions from template sites in rotaxanes compared to an anomeric amide nitrogen-deletion reagent and overcomes a major substrate limitation in that, using DPPH, only one of the substituents of the secondary amine in the rotaxane axle needs to be radical-stabilizing.
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