A chemical probe based on the PreQ1 metabolite enables transcriptome-wide mapping of binding sites

The role of metabolite-responsive riboswitches in regulating gene expression in bacteria is well known and makes them useful systems for the study of RNA-small molecule interactions. Here, we study the PreQ1 riboswitch system, assessing sixteen diverse PreQ1-derived probes for their ability to selectively modify the class-I PreQ1 riboswitch aptamer covalently. For the most active probe (11), a diazirine-based photocrosslinking analog of PreQ1, X-ray crystallography and gel-based competition assays demonstrated the mode of binding of the ligand to the aptamer, and functional assays demonstrated that the probe retains activity against the full riboswitch. Transcriptome-wide mapping using Chem-CLIP revealed a highly selective interaction between the bacterial aptamer and the probe. In addition, a small number of RNA targets in endogenous human transcripts were found to bind specifically to 11, providing evidence for candidate PreQ1 aptamers in human RNA. This work demonstrates a stark influence of linker chemistry and structure on the ability of molecules to crosslink RNA, reveals that the PreQ1 aptamer/ligand pair are broadly useful for chemical biology applications, and provides insights into how PreQ1, which is similar in structure to guanine, interacts with human RNAs

DIRECTED sp3 C–C AND C–H BOND CLEAVAGE FOR RADICAL BASED FUNCTIONALIZATIONS

Fluorine-containing organic molecules have become an indispensable in medicinal chemistry, agrochemistry, materials science, and biology. Despite all these applications in many fields of chemistry, there are limited ways to access most fluorinated molecules, especially organic molecules containing aliphatic fluorides. Ideally, one would like to access aliphatic fluorides through direct functionalization of sp3 C–H bonds (via radical based routes), and this would open limitless possibilities to synthesize a variety of fluorinated molecules. Recently, our laboratory and others accomplished a notable improvement in controlling the reactivity of aliphatic C–H bonds towards radical based fluorinations, but had only demonstrated selective sp3 C–H bond fluorination on highly symmetric substrates or those containing more activated benzylic C–H bonds. As a next step in progress, there was a great need to direct radical fluorination in complex natural products. We envisioned two approaches to accomplish this task through directed sp3 C–C bond cleavage or C–H bond functionalization. Accordingly, herein, directed-fluorination methods, and advances in selectivity in functionalizing peptides, terpenoids, and other complex organic molecules using either guided C–C cleavage or carbonyl groups to target unactivated C–H bonds are discussed. These strategies have helped radical based fluorination reactions become a valuable synthetic approach to functionalize complex natural products through late-stage fluorination. Additionally, we briefly explored the use of cyclopropanol derived radicals to couple with electron deficient heteroaromatic rings

Tandem C-C Bond Cleavage of Cyclopropanols and Oxidative Aromatization by Manganese(IV) Oxide in a Direct C-H to C-C Functionalization of Heteroaromatics

Abstract: We report a direct C-H to C-C bond functionalization of electron-deficient heteroaromatics enabled by mild C-C bond cleavage of cyclopropanols as a new route to β-aryl carbonyl-containing products. Additionally, as an alternative to using a "catalyst" that requires an excess amount of a sacrificial oxidant for regeneration and/or oxidative aromatization, this paper features manganese(IV) oxide as an inexpensive "dual role" reagent -effecting both C-C bond cleavage and ultimate rearomatization. Under the specified conditions, a variety o

Sensitized Aliphatic Fluorination Directed by Terpenoidal Enones: A “Visible Light” Approach

In our continued effort to address the challenges of selective sp³ C–H fluorination on complex molecules, we report a sensitized aliphatic fluorination directed by terpenoidal enones using catalytic benzil and visible light (white LEDs). This sensitized approach is mild, simple to set up, and an economical alternative to our previous protocol based on direct excitation using UV light in a specialized apparatus. Additionally, the amenability of this protocol to photochemical flow conditions and preliminary evidence for electron-transfer processes are highlighted

Multiple Enone-Directed Reactivity Modes Lead to the Selective Photochemical Fluorination of Polycyclic Terpenoid Derivatives

In the realm of aliphatic fluorination, the problem of reactivity has been very successfully addressed in recent years. In contrast, the associated problem of selectivity, that is, directing fluorination to specific sites in complex molecules, remains a great, fundamental challenge. In this report, we show that the enone functional group, upon photoexcitation, provides a solution. Based solely on orientation of the oxygen atom, site-selective photochemical fluorination is achieved on steroids and bioactive polycycles with up to 65 different sp³ CH bonds. We have also found that γ-, β-, homoallylic, and allylic fluorination are all possible and predictable through the theoretical modes reported herein. Lastly, we present a preliminary mechanistic hypothesis characterized by intramolecular hydrogen atom transfer, radical fluorination, and ultimate restoration of the enone. In all, these results provide a leap forward in the design of selective fluorination of complex substrates that should be relevant to drug discovery, where fluorine plays a prominent role

Multiple Enone-Directed Reactivity Modes Lead to the Selective Photochemical Fluorination of Polycyclic Terpenoid Derivatives

In the realm of aliphatic fluorination, the problem of reactivity has been very successfully addressed in recent years. In contrast, the associated problem of selectivity, that is, directing fluorination to specific sites in complex molecules, remains a great, fundamental challenge. In this report, we show that the enone functional group, upon photoexcitation, provides a solution. Based solely on orientation of the oxygen atom, site-selective photochemical fluorination is achieved on steroids and bioactive polycycles with up to 65 different sp³ CH bonds. We have also found that γ-, β-, homoallylic, and allylic fluorination are all possible and predictable through the theoretical modes reported herein. Lastly, we present a preliminary mechanistic hypothesis characterized by intramolecular hydrogen atom transfer, radical fluorination, and ultimate restoration of the enone. In all, these results provide a leap forward in the design of selective fluorination of complex substrates that should be relevant to drug discovery, where fluorine plays a prominent role