Structure-selective catalytic alkylation of DNA and RNA

Smartphone-Based Sensing of Cortisol by Functionalized Rhodamine Probes

During a stress condition, the human body synthesizes catecholamine neurotransmitters and specific hormones (called "stress hormones"), the most important of which is cortisol. The monitoring of cortisol levels should be extremely important to control the stress levels, and for this reason, it shows important medical applications. The common analytical methods (HPLC, GC-MS) cannot be used in real life, due to the bulky size of the instruments and the necessity of specialized personnel. Molecular probes solve these problems due to their fast and easy use. The synthesis of new fluorescent rhodamine probes, able to interact by non-covalent interactions with cortisol, the recognition properties in solution as well as in solid state by Strip Test, using a smartphone as detector, are here reported. DFT calculations and FT-IR measurements suggest the formation of supramolecular complexes through hydrogen bonds as main non-covalent interaction. The present study represents one of the first sensor, based on synthetical chemical receptors, able to detect cortisol in a linear range from 1 mM to 1 pM, based on non-covalent molecular recognition and paves the way to the realization of practical point-of-care device for the monitoring of cortisol in real live.

Rhodium(II)-Catalyzed N-H Insertions of Carbenes under Mechanochemical Conditions

Under mechanochemical conditions in a mixer mill, Rh2(OAc)4 catalyzes the reaction between aryldiazoesters and anilines to give α-amino esters. The process proceeds under mild conditions and is insensitive to air. It is solvent-free and scalable. A broad substrate scope, short reaction times, operational simplicity, and good functional group tolerance are additional salient features of this protocol.

Amphiphilic polymeric nanoparticles enable homogenous rhodium-catalysed NH insertion reactions in living cells

Rh-catalysed NH carbene insertion reactions were exported to living cells with help of amphiphilic polymeric nanoparticles. Hereto, hydrophobic dirhodium carboxylate catalysts were efficiently encapsulated in amphiphilic polymeric nanoparticles comprising dodecyl and Jeffamine as side grafts. The developed catalytic nanoparticles promoted NH carbene insertions between α-keto diazocarbenes and 2,3-diaminonaphthalene, followed by intramolecular cyclisation to form fluorescent or biologically active benzoquinoxalines. These reactions were studied in reaction media of varying complexity. The best-performing catalyst was exported to HeLa cells, where fluorescent and cytotoxic benzoquinoxalines were synthesized in situ at low catalyst loading within a short time. Most of the developed bioorthogonal transition metal catalysts reported to date are easily deactivated by the reactive biomolecules in living cells, limiting their applications. The high catalytic efficiency of the Rh-based polymeric nanoparticles reported here opens the door to expanding the repertoire of bioorthogonal reactions and is therefore promising for biomedical applications.

Organometallic catalysis in aqueous and biological environments: harnessing the power of metal carbenes

Translating the power of transition metal catalysis to the native habitats of enzymes can significantly expand the possibilities of interrogating or manipulating natural biological systems, including living cells and organisms. This is especially relevant for organometallic reactions that have shown great potential in the field of organic synthesis, like the metal-catalyzed transfer of carbenes. While, at first sight, performing metal carbene chemistry in aqueous solvents, and especially in biologically relevant mixtures, does not seem obvious, in recent years there has been a growing number of reports demonstrating the feasibility of the task. Either using small molecule metal catalysts or artificial metalloenzymes, a number of carbene transfer reactions that tolerate aqueous and biorelevant media are being developed. This review intends to summarize the most relevant contributions, and establish the state of the art in this emerging research field.

Functionalization of DNA-Tagged Alkenes with Diazo Compounds via Photocatalysis

To explore potential chemical space using DNA-encoded library (DEL) technology, the development of various types of robust DNA-compatible reactions is urgently needed. Diazo compounds, which serve as valuable building blocks and important synthons in synthetic chemistry, have been rarely applied in DEL synthesis, probably because of their potential modifications of the bases and phosphate backbone of DNA. Herein we report two cases of DNA-compatible reactions with alkenes and diazo compounds, providing corresponding hydroalkylation and cyclopropanation products in moderate to excellent yields. Notably, these transformations not only provide new access to C(sp³)-C(sp³) bond formation in DELs with excellent functional group tolerance but also represent practical ligation methods to introduce functionalized molecules into DNA.

Synthesis of Nucleobase-Modified Oligonucleotides by Post-Synthetic Modification in Solution

Oligonucleotides containing modified nucleobases have applications in various technologies. In general, to synthesize oligonucleotides with different nucleobase structures, each modified phosphoramidite monomer needs to be prepared over multiple steps and then introduced onto the oligonucleotides, which is time-consuming and inefficient. Post-synthetic modification is a powerful strategy for preparing many types of modified oligonucleotides, especially nucleobase-modified ones. Depending on the stage of modification, post-synthetic modification can be divided into two stages: "solid-phase modification," wherein an oligonucleotide attaches to the resin, and "solution-phase modification," wherein an oligonucleotide detaches itself from the resin. In this review, we focus on post-synthetic modification in solution for the synthesis of nucleobase-modified oligonucleotides, except the modifications to linkers for conjugation. Moreover, the reactions are summarized for each modified position of the nucleobases.

Exporting Metal-Carbene Chemistry to Live Mammalian Cells: Copper-Catalyzed Intracellular Synthesis of Quinoxalines Enabled by N-H Carbene Insertions

Implementing catalytic organometallic transformations in living settings can offer unprecedented opportunities in chemical biology and medicine. Unfortunately, the number of biocompatible reactions so far discovered is very limited, and essentially restricted to uncaging processes. Here, we demonstrate the viability of performing metal carbene transfer reactions in live mammalian cells. In particular, we show that copper (II) catalysts can promote the intracellular annulation of alpha-keto diazocarbenes with ortho-amino arylamines, in a process that is initiated by an N-H carbene insertion. The potential of this transformation is underscored by the in cellulo synthesis of a product that alters mitochondrial functions, and by demonstrating cell selective biological responses using targeted copper catalysts. Considering the wide reactivity spectrum of metal carbenes, this work opens the door to significantly expanding the repertoire of life-compatible abiotic reactions.

Selective alkylation of parallel G-quadruplex structure

The selective alkylation of nucleic acids is important for a medicinal approach and biological study. We now report a novel selective alkylation of the parallel G-quadruplex structure using the conjugate of the macrocyclic hexaoxazole L2G2-6OTD-1M1PA and vinyl-quinazolinone-S(O)Me (6OTD-VQ-S(O)Me).

Programmable site-selective labeling of oligonucleotides based on carbene catalysis

Site-selective modification of oligonucleotides serves as an indispensable tool in many fields of research including research of fundamental biological processes, biotechnology, and nanotechnology. Here we report chemo- and regioselective modification of oligonucleotides based on rhodium(I)-carbene catalysis in a programmable fashion. Extensive screening identifies a rhodium(I)-catalyst that displays robust chemoselectivity toward base-unpaired guanosines in single and double-strand oligonucleotides with structurally complex secondary structures. Moreover, high regioselectivity among multiple guanosines in a substrate is achieved by introducing guanosine-bulge loops in a duplex. This approach allows the introduction of multiple unique functional handles in an iterative fashion, the utility of which is exemplified in DNA-protein cross-linking in cell lysates.

Transition-Metal-Mediated Modification of Biomolecules

The site-selective modification of biomolecules has grown spectacularly in recent years. The presence of a large number of functional groups in a biomolecule makes its chemo- and regioselective modification a challenging goal. In this context, transition-metal-mediated reactions are emerging as a powerful tool owing to their unique reactivity and good functional group compatibility, allowing highly efficient and selective bioconjugation reactions that operate under mild conditions. This Minireview focuses on the current state of organometallic chemistry for bioconjugation, highlighting the potential of transition metals for the development of chemoselective and site-specific methods for functionalization of peptides, proteins and nucleic acids. The importance of the selection of ligands attached to the transition metal for conferring the desired chemoselectivity will be highlighted.

Selective Functionalization of Aliphatic Amines via Myoglobin-catalyzed Carbene N-H Insertion

Engineered myoglobins have recently gained attention for their ability to catalyze a variety of abiological carbene transfer reactions including the functionalization of amines via carbene insertion into N-H bonds. However, the scope of myoglobin and other hemoprotein-based biocatalysts in the context of this transformation has been largely limited to aniline derivatives as the amine substrates and ethyl diazoacetate as the carbene donor reagent. In this report, we describe the development of an engineered myoglobin-based catalyst useful for promoting carbene N-H insertion reactions across a broad range of substituted benzylamines and α-diazo acetates with high efficiency (82-99% conversion), elevated catalytic turnovers (up to 7,000), and excellent chemoselectivity for the desired single insertion product (up to 99%). The scope of this transformation could be extended to cyclic aliphatic amines. These studies expand the biocatalytic toolbox available for the selective formation of C-N bonds, which are ubiquitous in many natural and synthetic bioactive compounds.

Reactive OFF-ON type alkylating agents for higher-ordered structures of nucleic acids

Higher-ordered structure motifs of nucleic acids, such as the G-quadruplex (G-4), mismatched and bulge structures, are significant research targets because these structures are involved in genetic control and diseases. Selective alkylation of these higher-order structures is challenging due to the chemical instability of the alkylating agent and side-reactions with the single- or double-strand DNA and RNA. We now report the reactive OFF-ON type alkylating agents, vinyl-quinazolinone (VQ) precursors with a sulfoxide, thiophenyl or thiomethyl group for the OFF-ON control of the vinyl reactivity. The stable VQ precursors conjugated with aminoacridine, which bind to the G-4 DNA, selectively reacted with a T base on the G-4 DNA in contrast to the single- and double-strand DNA. Additionally, the VQ precursor reacted with the T or U base in the AP-site, G-4 RNA and T-T mismatch structures. These VQ precursors would be a new candidate for the T or U specific alkylation in the higher-ordered structures of nucleic acids.

Selective alkylation of T-T mismatched DNA using vinyldiaminotriazine-acridine conjugate

The alkylation of the specific higher-order nucleic acid structures is of great significance in order to control its function and gene expression. In this report, we have described the T–T mismatch selective alkylation with a vinyldiaminotriazine (VDAT)–acridine conjugate. The alkylation selectively proceeded at the N3 position of thymidine on the T–T mismatch. Interestingly, the alkylated thymidine induced base flipping of the complementary base in the duplex. In a model experiment for the alkylation of the CTG repeats DNA which causes myotonic dystrophy type 1 (DM1), the observed reaction rate for one alkylation increased in proportion to the number of T–T mismatches. In addition, we showed that primer extension reactions with DNA polymerase and transcription with RNA polymerase were stopped by the alkylation. The alkylation of the repeat DNA will efficiently work for the inhibition of replication and transcription reactions. These functions of the VDAT–acridine conjugate would be useful as a new biochemical tool for the study of CTG repeats and may provide a new strategy for the molecular therapy of DM1.

An artificial metalloenzyme for carbene transfer based on a biotinylated dirhodium anchored within streptavidin

We report an artificial carbenoid transferase which combines a biotinylated dirhodium moiety within streptavidin scaffold.

Copper carbenes alkylate guanine chemoselectively through a substrate directed reaction

Cu(i) carbenes derived from α-diazocarbonyl compounds lead to selective alkylation of the O6 position in guanine (O6-G) in mono- and oligonucleotides. Only purine-type lactam oxygens are targeted - other types of amides or lactams are poorly reactive under conditions that give smooth alkylation of guanine. Mechanistic studies point to N7G as a directing group that controls selectivity. Given the importance of O6-G adducts in biology and biotechnology we expect that Cu(i)-catalyzed O6-G alkylation will be a broadly used synthetic tool. While the propensity for transition metals to increase redox damage is well-appreciated, our results suggest that transition metals might also increase the vulnerability of nucleic acids to alkylation damage.

Diazo Compounds: Versatile Tools for Chemical Biology

Diazo groups have broad and tunable reactivity. That and other attributes endow diazo compounds with the potential to be valuable reagents for chemical biologists. The presence of diazo groups in natural products underscores their metabolic stability and anticipates their utility in a biological context. The chemoselectivity of diazo groups, even in the presence of azido groups, presents many opportunities. Already, diazo compounds have served as chemical probes and elicited novel modifications of proteins and nucleic acids. Here, we review advances that have facilitated the chemical synthesis of diazo compounds, and we highlight applications of diazo compounds in the detection and modification of biomolecules.

Rapid cycloaddition of a diazo group with an unstrained dipolarophile

The cycloaddition of a diazoacetamide with ethyl 4,4,4-trifluorocrotonate proceeds with k = 0.1 M-1s-1. This second-order rate constant rivals those of optimized strain-promoted azide- alkyne cycloadditions, even though the reaction does not release strain. The regioselectivity and a computational distortion/interaction analysis of the reaction energetics are consistent with the formation of an N-H…F-C hydrogen bond in the transition state and the electronic character of the trifluorocrotonate. Analogous reactions with an azidoacetamide dipole or with an acrylate or crotonate dipolarophile were much slower. These findings suggest a new strategy for the design of diazo-selective reagents for chemical biology.

A new strategy for site-specific alkylation of DNA using oligonucleotides containing an abasic site and alkylating probes

Selective chemical reactions with DNA, such as its labelling, are very useful in many applications. In this paper, we discuss a new strategy for the selective alkylation of DNA using an oligonucleotide containing an abasic site and alkylating probes. We designed three probes consisting of 2-AVP as a reactive moiety and three kinds of binding moiety with high affinity to duplex DNA. Among these probes, Hoechst-AVP probe exhibited high selectivity and efficient reactivity to thymine bases at the site opposite an abasic site in DNA. Our method is potentially useful for inducing site-directed reactions aimed at inhibiting polymerase reactions.

1,3-Dipolar Cycloadditions of Diazo Compounds in the Presence of Azides

The diazo group has untapped utility in chemical biology. The tolerance of stabilized diazo groups to cellular metabolism is comparable to that of azido groups. However, chemoselectivity has been elusive, as both groups undergo 1,3-dipolar cycloadditions with strained alkynes. Removing strain and tuning dipolarophile electronics yields diazo group selective 1,3-dipolar cycloadditions that can be performed in the presence of an azido group. For example, diazoacetamide but not its azido congener react with dehydroalanine residues, as in the natural product nisin.

The pKa of Brønsted acids controls their reactivity with diazo compounds

We study the O-alkylation of phosphate groups by alkyl diazo compounds in a range of small molecules and biopolymers.

Bioorthogonal Enzymatic Activation of Caged Compounds

Engineered cytochrome P450 monooxygenase variants are reported as highly active and selective catalysts for the bioorthogonal uncaging of propargylic and benzylic ether protected substrates, including uncaging in living E. coli. observed selectivity is supported by induced-fit docking and molecular dynamics simulations. This proof-of-principle study points towards the utility of bioorthogonal enzyme/protecting group pairs for applications in the life sciences.

Rhodium(II) Proximity-Labeling Identifies a Novel Target Site on STAT3 for Inhibitors with Potent Anti-Leukemia Activity

Nearly 40 % of children with acute myeloid leukemia (AML) suffer relapse arising from chemoresistance, often involving upregulation of the oncoprotein STAT3 (signal transducer and activator of transcription 3). Herein, rhodium(II)-catalyzed, proximity-driven modification identifies the STAT3 coiled-coil domain (CCD) as a novel ligand-binding site, and we describe a new naphthalene sulfonamide inhibitor that targets the CCD, blocks STAT3 function, and halts its disease-promoting effects in vitro, in tumor growth models, and in a leukemia mouse model, validating this new therapeutic target for resistant AML.

Catalytic carbene transfer allows the direct customization of cyclic purine dinucleotides

We describe a simple method for the direct modification of nucleobases in cyclic purine dinucleotides, important signalling molecules in both prokaryotes and eukaryotes. The method tolerates all members of the cyclic dinucleotide family and could be used to modulate their function or introduce useful side-chains such as fluorophores and photo-crosslinking groups.

Catalysts for RNA and DNA modification

To study DNAs and RNAs it is often necessary to chemically modify them. Nature's strategy for nucleic acid modification is to use selective catalysts, and chemists have begun to emulate this conceptual approach. In this review we present a summary of catalytic approaches toward the construction of modified RNAs and DNAs and outline our opinions on where new research is needed.

Molecular recognition in protein modification with rhodium metallopeptides

Chemical manipulation of natural, unengineered proteins is a daunting challenge which tests the limits of reaction design. By combining transition-metal or other catalysts with molecular recognition ideas, it is possible to achieve site-selective protein reactivity without the need for engineered recognition sequences or reactive sites. Some recent examples in this area have used ruthenium photocatalysis, pyridine organocatalysis, and rhodium(II) metallocarbene catalysis, indicating that the fundamental ideas provide opportunities for using diverse reactivity on complex protein substrates and in complex cell-like environments.

Selective chemical modification of DNA with alkoxy- and benzyloxyamines

DNA is modified selectively at cytosine with benzyloxyamine and -derivatives carrying handles for click reactions.

Progress towards bioorthogonal catalysis with organometallic compounds

The catalysis of bioorthogonal transformations inside living organisms is a formidable challenge--yet bears great potential for future applications in chemical biology and medicinal chemistry. We herein disclose highly active organometallic ruthenium complexes for bioorthogonal catalysis under biologically relevant conditions and inside living cells. The catalysts uncage allyl carbamate protected amines with unprecedented high turnover numbers of up to 270 cycles in the presence of water, air, and millimolar concentrations of thiols. By live-cell imaging of HeLa cells and with the aid of a caged fluorescent probe we could reveal a rapid development of intense fluorescence within the cellular cytoplasm and therefore support the proposed bioorthogonality of the catalysts. In addition, to illustrate the manifold applications of bioorthogonal catalysis, we developed a method for catalytic in-cell activation of a caged anticancer drug, which efficiently induced apoptosis in HeLa cells.

A general method for artificial metalloenzyme formation through strain-promoted azide-alkyne cycloaddition

Strain-promoted azide-alkyne cycloaddition (SPAAC) can be used to generate artificial metalloenzymes (ArMs) from scaffold proteins containing a p-azido-L-phenylalanine (Az) residue and catalytically active bicyclononyne-substituted metal complexes. The high efficiency of this reaction allows rapid ArM formation when using Az residues within the scaffold protein in the presence of cysteine residues or various reactive components of cellular lysate. In general, cofactor-based ArM formation allows the use of any desired metal complex to build unique inorganic protein materials. SPAAC covalent linkage further decouples the native function of the scaffold from the installation process because it is not affected by native amino acid residues; as long as an Az residue can be incorporated, an ArM can be generated. We have demonstrated the scope of this method with respect to both the scaffold and cofactor components and established that the dirhodium ArMs generated can catalyze the decomposition of diazo compounds and both Si-H and olefin insertion reactions involving these carbene precursors.