Next-Generation Organic Chemistry for Labeling and Imaging

Abstract

This article is part of the Next-Generation Organic Chemistry for Labeling and Imaging special issue. In efforts to expand the portfolio of bioluminescence imaging probes, M. J. Schnermann, J. A. Prescher, J. Mills, and co-workers recently developed a new synthetic strategy that gives access to π-extended luciferins in only two steps. This new synthetic route bypasses previous multistep heterocycle assembly strategies. In this work, they also established the potential of these molecules through enzymatic optimization and mutagenesis, biological assays, and time-dependent density functional theory (TDDFT) calculations (10.1021/acs.joc.3c01920). This approach can be applied to generate a series of π-extended AkaLumine, naphthalene, and coumarin-luciferin analogues, providing new scaffolds with the potential to expand the bioluminescence imaging toolbox. Rhodamine dyes are fluorescent reporters used in a variety of biological imaging applications and possess a high quantum yield. N. W. Pino and co-workers introduce improved diazoketorhodamines for single-molecule tracking microscopy by enhancing the performance of the dyes as well as reducing the need for extensive washing steps (doi:10.1021/acs.joc.4c00718). This synthetic approach involves the use of Ghosez’s reagent that enables the synthesis of [1.1.3]-bridged bicyclic azetidines and expanding access to rhodamines with amides and sulfonamides on the southern arene. The synthesized photoactivated dyes are amenable to high-throughput single-molecule tracking screening and can be used in various biological settings. J. Yuan and co-workers (10.1021/acs.joc.3c01227) describe the synthesis of substituted benzo[4,5]imidazo[1,2-a]pyrimidines by a [3+2+1]-type intermolecular cyclization starting from 2-aminobenzimidazole, acetophenone, and N,N-dimethylformamide. This one-pot, three-component reaction allows for the facile and cost-efficient introduction of this class of important nitrogen-containing heterocycles that exhibit fluorescent properties. P. G. Harran and co-workers (10.1021/acs.joc.4c01203) report a high-yield, scalable synthesis of indolizine and directly elaborated the molecule into three optically active indolizinylalanine regioisomers. When incorporated into peptides, the indolizine demonstrates a larger quantum yield in aqueous environments than indole and ample fluorescence intensity for detection at low micromolar concentrations. These data suggest that indolizinylalanines could be broadly useful probes of protein structure and dynamics, functioning as true tryptophan isosteres. Bioorthogonal reactions are important tools for the construction of positron emission tomography (PET) agents due to the short half-life of the frequently used radionuclides. Particularly desirable is the use of ¹⁸F-labeled tetrazines for PET tracer construction, which leverages the exceptionally fast reaction rates of the inverse electron demand Diels–Alder (IEDDA) reaction between tetrazines and trans-cyclooctenes as a valuable technique for PET imaging. H. Wu, W. Chen, and co-workers have developed a rapid entry to ¹⁸F-triazolyl-tetrazines through copper-catalyzed alkyne–azide cycloaddition (CuAAC) (10.1021/acs.joc.4c00574). In this work, ¹⁸F-labeled azides were obtained from simple cartridge isolation and then used to synthesize ¹⁸F-triazolyl-tetrazines via an indirect labeling approach that allows for the better stability of the tetrazines and very high radiochemical yield (>99% RCC), exhibiting considerable potential for the development of PET agents. Inspired by extensive advances on the bioorthogonal coupling of tetrazines, M. Vrabel and co-workers introduce triazinium ligation as a novel bioorthogonal conjugation method (10.1021/acs.joc.3c02454). They synthesized several triazinium derivatives that were investigated for their ligation kinetics and stability and discovered that triazinium-coumarin conjugates exhibit fluorogenic properties under biological conditions. These properties enable no-wash fluorescent labeling in live cells and introduce the future potential application of these molecules in a variety of biological processes. X. Lei and co-workers investigated the mechanism of peptide labeling with o-phthalaldehyde (OPA) and 2-acylbenzaldehyde using isotope labeling mass spectrometry-based experiments (10.1021/acs.joc.3c01397). While OPA has been known to react with amine groups and form phthalimidine products, the only interactions reported to date were two-group reactions of OPA and lysine or three-group reactions involving another cysteine amino acid. In this work, the Lei group identified three-group reactions among OPA, lysine, and nucleophilic amino acids that have not been reported previously and highlighted the potential of OPA as a probe for proximal amino acids. S. Yang, B. Xing, and co-workers introduce a series of molecular probes for imaging gut bacterial strains that express myrosinase, an enzyme that can produce bioactive agents from natural and gut bacterial metabolite glucosinolates (10.1021/acs.joc.3c02848). The design of the imaging probes involves the conjugation of various fluorophores to an artificial glucosinolate backbone via click chemistry. The synthetic approach of these Myr-responsive fluorescent probes is an efficient strategy to enzyme-responsive fluorescent labeling of gut bacteria in vivo that can lead further metabolic mechanistic studies. Carboxylesterases (CESs) make up important class of serine hydrolases that play a vital role in metabolizing esters, amides, and thioesters, and their upregulation is linked to liver cancer and neuroblastomas. Y. Bai, Z. Chen, L. Zhang, and co-workers have recently designed and synthesized three new BODIPY-based fluorescent probes to detect CESs (10.1021/acs.joc.4c00699). Among these three probes, BDPN2-CES showed high selectivity and excellent performance in detecting CES, with 182-fold fluorescence enhancement within 10 min and a low detection limit of ≤3.37 × 10^–5 unit/mL. This work also discloses the application of BDPN2-CES in monitoring cellular CES activities in a high-throughput screening toward the discovery of a novel inhibitor for CES. Neal Devaraj is a Professor of Chemistry and Biochemistry and the Murray Goodman Endowed Chair in Chemistry and Biochemistry at the University of California, San Diego. He received Ph.D. in chemistry at Stanford University in the laboratories of Professors James Collman and Christopher Chidsey. After a postdoctoral fellowship at Harvard Medical School in the lab of Prof. Ralph Weissleder, he joined University of California, San Diego, in 2011. Since 2021, he has been the Murray Goodman Endowed Chair in Chemistry and Biochemistry. His research interests are artificial cells, lipid membranes, and bioconjugation. Joseph M. Fox is Professor of Chemistry in the Department of Chemistry and Biochemistry at the University of Delaware, where he also is the Director of the NIH-funded Center of Biomedical Research Excellence on the Discovery of Chemical Probes and Therapeutic Leads. He received his Ph.D. at Columbia University with Professor Thomas Katz and then as an NIH postdoctoral fellow studied organometallic chemistry with Professor Stephen Buchwald at Massachusetts Institute of Technology. In 2001, he joined the faculty at the University of Delaware. In 2023, he was named a Francis Alison Professor, the highest faculty honor at University of Delaware. His research centers on the development of new types of chemical reactions, the application of these new reactions to the synthesis of natural occurring and designed molecules with biological function, and the use of design concepts in organic synthesis for applications in materials science. Xiaoguang Lei is the Professor of Chemical Biology in the College of Chemistry and Molecular Engineering at Peking University and a senior Principal Investigator of the Peking-Tsinghua Center for Life Sciences. He obtained his Ph.D. in organic synthesis from Boston University with Professor John A. Porco and then conducted his postdoctoral work with Professor Samuel J. Danishefsky at Columbia University. In 2009, he started his independent career as a Principal Investigator and Director of Chemistry Center at the National Institute of Biological Sciences (NIBS) in Beijing. In 2014, he moved to Peking University as a Full Professor. His major research areas are chemical biology, organic synthesis, and medicinal chemistry. This article has not yet been cited by other publications.