Fit to be tied: conformation-directed macrocyclization of peptoid foldamers

Covalent macrocyclic constraints can be readily installed on N-substituted glycine "peptoid" oligomer substrates. Cu(I)-catalyzed [3+2] cycloaddition reactions were conducted on solid support to ligate peptoid side chain azide and alkyne functionalities. Intramolecular macrocycle formation is facilitated by preorganizing the reactive groups across one turn of the helical secondary structure. These results confirm that conformational ordering can be exploited to assist the macrocyclization of folded oligomers.     

Synthesis of new <Emphasis Type="Italic">p</Emphasis>-<Emphasis Type="Italic">tert</Emphasis>-butylcalix[4]arene derivatives containing photopolymerizable 1,3-butadiyne fragments

Successive functionalization of p-tert-butylcalix[4]arene afforded a bifunctional derivative containing photopolymerizable pentacosa-10,12-diynoic acid fragments on the upper rim and propargyl groups on the lower rim of the macrocycle having a cone structure. The functionalization can be readily accomplished via copper-catalyzed azide–alkyne cycloaddition under mild conditions.     

Recent Advances in Macrocyclic Drugs and Microwave-Assisted and/or Solid-Supported Synthesis of Macrocycles

Macrocycles represent attractive candidates in organic synthesis and drug discovery. Since 2014, nineteen macrocyclic drugs, including three radiopharmaceuticals, have been approved by FDA for the treatment of bacterial and viral infections, cancer, obesity, immunosuppression, etc. As such, new synthetic methodologies and high throughput chemistry (e.g., microwave-assisted and/or solid-phase synthesis) to access various macrocycle entities have attracted great interest in this chemical space. This article serves as an update on our previous review related to macrocyclic drugs and new synthetic strategies toward macrocycles (Molecules, 2013, 18, 6230). In this work, I first reviewed recent FDA-approved macrocyclic drugs since 2014, followed by new advances in macrocycle synthesis using high throughput chemistry, including microwave-assisted and/or solid-supported macrocyclization strategies. Examples and highlights of macrocyclization include macrolactonization and macrolactamization, transition-metal catalyzed olefin ring-closure metathesis, intramolecular C–C and C–heteroatom cross-coupling, copper- or ruthenium-catalyzed azide–alkyne cycloaddition, intramolecular S_NAr or S_N2 nucleophilic substitution, condensation reaction, and multi-component reaction-mediated macrocyclization, and covering the literature since 2010.     

“Click” chemistry for in situ formation of thermoresponsive P(NIPAAm‐co‐HEMA)‐based hydrogels

The strategy for in situ chemical gelation of poly(N‐isopropylacrylamide‐co‐hydroxylethyl methacrylate) [P(NIPAAm‐co‐HEMA)]‐based polymers was demonstrated. Two types of new P(NIPAAm‐co‐HEMA) derivatives with alkyne and azide pendant groups, respectively, were prepared. When the solutions of the two derivatives were mixed together, a crosslinking reaction, a type of Huisgen's 1,3‐dipolar azide‐alkyne cycloaddition, in the presence of Cu(I) catalyst occurs. The morphology, equilibrium swelling ratio, swelling kinetics, and temperature response kinetics of the in situ gelated hydrogels were studied. In comparison with the conventional PNIPAAm hydrogel, because of the spatial hindrance of polymeric chains, the resulted hydrogels had a macroporous structure as well as a fast shrinking rate. The strategy described here presents a potential alternative to the traditional synthesis techniques for the in situ formation of thermoresponsive hydrogels. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 5263–5277, 2008     

Quantum chemical estimation of the macrocyclization of 1,4-dithiine

Ab initio quantum chemical methods are employed to study the spatial and electronic structure of a 1,4-dithiine molecule. Calculations are performed with electron correlation treatment by MP2 and B3LYP methods in 6-311++G(d,p) and 6-311G basis sets. It is found that the macrocyclization of 1,4-dithiine is energetically favorable. The addition of each subsequent dithiine ring decreases the relative energy of the system by ??0.5÷2.3 kcal/mol. The cycle consisting of 7 dithiine rings is the most comfortable from the standpoint of the internal strain of the macrocycle. With an increase in the number of rings up to 10, the macrocycle starts to break into 4-, 5-, 6-, or 7-membered fragments. The formation of a nanotube based on a 7-membered macrocycle is energetically favorable. The inner diameter of this nanotube is 6.9     

An Alkyne‐Appended,Click‐Ready PtII Complex with an Unusual Arrangement in the Solid State

To better understand the range of cellular interactions of Pt^II‐based chemotherapeutics, robust and efficient methods to track and analyze Pt targets are needed. A powerful approach is to functionalize Pt^II compounds with alkyne or azide moieties for post‐treatment conjugation through the azide–alkyne cycloaddition (click) reaction. Herein, we report an alkyne‐appended cis‐diamine Pt^II compound, cis‐[Pt(2‐(5‐hexynyl)amido‐1,3‐propanediamine)Cl₂] ( 1 ), the X‐ray crystal structure of which exhibits a combination of unusual radially distributed CH/π(CC) interactions, Pt Pt bonding, and NH:O/NH:Cl hydrogen bonds. In solution, 1 exhibits no Pt alkyne interactions and binds readily to DNA. Subsequent click reactivity with nonfluorescent dansyl azide results in a 70‐fold fluorescence increase. This result demonstrates the potential for this new class of alkyne‐modified Pt compound for the comprehensive detection and isolation of Pt‐bound biomolecules.     

An Alkyne‐Appended,Click‐Ready PtII Complex with an Unusual Arrangement in the Solid State

To better understand the range of cellular interactions of Pt^II‐based chemotherapeutics, robust and efficient methods to track and analyze Pt targets are needed. A powerful approach is to functionalize Pt^II compounds with alkyne or azide moieties for post‐treatment conjugation through the azide–alkyne cycloaddition (click) reaction. Herein, we report an alkyne‐appended cis‐diamine Pt^II compound, cis‐[Pt(2‐(5‐hexynyl)amido‐1,3‐propanediamine)Cl₂] ( 1 ), the X‐ray crystal structure of which exhibits a combination of unusual radially distributed CH/π(C?C) interactions, Pt? Pt bonding, and NH:O/NH:Cl hydrogen bonds. In solution, 1 exhibits no Pt? alkyne interactions and binds readily to DNA. Subsequent click reactivity with nonfluorescent dansyl azide results in a 70‐fold fluorescence increase. This result demonstrates the potential for this new class of alkyne‐modified Pt compound for the comprehensive detection and isolation of Pt‐bound biomolecules.     

Preparation and orthogonal postmodification of dual‐clickable polymer precursors bearing both aldehyde and alkyne groups

A new styrenic monomer 2‐propargyloxy‐5‐vinylbenzaldehyde (PVB) containing both aldehyde and alkyne reactive groups was designed for the synthesis and subsequent orthogonal postfunctionalization of dual‐clickable polymer precursor. Reversible addition‐fragmentation chain transfer polymerization of PVB afforded a structurally well‐defined polymer poly(2‐propargyloxy‐5‐vinylbenzaldehyde) (PPVB) bearing alkyne and aldehyde functionalities that are reactive towards azide ‐ and aminooxy‐containing molecules, respectively. Therefore, the resulting PPVB can be served as a dual‐clickable polymer scaffold for construction of multiple functional polymers via orthogonal alkyne–azide and aldehyde–aminooxy click reactions. Postpolymerization modification of PPVB sequentially with aminooxy‐terminated poly(ethylene oxide)s (H₂NO‐PEO) and azide‐functionalized imidazolium‐type ionic liquid (N₃‐IL·TFSI, having bis(trifluoromethane)sulfonamide, TFSI, counter‐anion) yielded an interesting multicomponent graft polymer PPVB‐g‐(PEO‐and‐IL·TFSI). After anion exchange of hydrophobic TFSI counter‐anion by bromide (Br) anion, the resulting graft copolymer PPVB‐g‐(PEO‐and‐IL·Br) becomes soluble in water, and its imidazolium units can capture negatively charged tetraphenylethylene disulfonate derivative (TPE‐2 ) guest molecule via electrostatic complexation to form in situ self‐assembled fluorescent nanoaggregates with colloidal stability imparted by hydrophilic PEO chains. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 2650–2656     

Hairpin DNA‐Dependent Click Conjugation of Oligonucleotides for Electrochemical Monitoring of Copper(II)

A new electrochemical sensing platform was designed for sensitive detection of copper(II) (Cu²⁺) based on click conjugation of two short oligonucleotides by using methylene blue‐functionalized hairpin DNA as the template. The analyte (Cu²⁺) was in situ reduced to Cu⁺ by sodium ascorbate, which catalyzed the click conjugation between two single‐stranded oligonucleotides one was labelled with a 5′‐alkyne and the other with 3′‐azide group via the Cu⁺‐catalyzed azide‐alkyne cycloaddition. The newly formed long‐chain oligonucleotide induced the conformational change of hairpin DNA to open the hairpin, resulting in methylene blue far away from the electrode for the decrease of redox current. Under optimal conditions, the decrease in the electronic signal was directly proportional to target Cu²⁺ concentration, and allowed the detection of Cu²⁺ at a concentration as low as 1.23 nM. Our strategy also displayed high selectivity for Cu²⁺ against other metal ions owing to the highly specific Cu⁺‐catalyzed click chemistry reaction, and was applicable for monitoring of Cu²⁺ in drinking water with satisfactory results.     

Copper(I)‐Catalyzed Interrupted Click/Sulfenylation Cascade: One‐Pot Synthesis of Sulfur Cycle Fused 1,2,3‐Triazoles

Herein, we report a practical protocol for the synthesis of sulfur cycle fused 1,2,3‐triazoles through a copper(I)‐catalyzed tandem click/intramolecular sulfenylation reaction. The reaction proceeded via a copper‐catalyzed alkyne azide cycloaddition, followed by interception of the in situ formed cuprate‐triazole intermediate with p‐toluenesulfonothioate. This reaction shows broad substrate scope, complete regioselectivity, and excellent functional group tolerance under mild reaction conditions.     

In‐situ Generated and Premade 1‐Copper(I) Alkynes in Cycloadditions

The copper(I)‐catalyzed azide‐alkyne cycloaddition (CuAAC) was discovered in 2002, which has become the most remarkable example for “click chemistry” to date. In CuAAC reaction, 1‐copper(I) alkyne has been recognized to be a key intermediate. However, many contradictory experimental results for this intermediate were reported in literature. For example, only the in‐situ generated 1‐copper(I) alkyne was used, while the premade 1‐copper(I) alkyne proved to be inefficient under the standard conditions. The kinetic studies indicated that CuAAC reaction had a strict second‐order dependence on Cu(I) and the DFT studies demonstrated that 1‐copper(I) alkyne intermediate should be a dinuclear copper(I) complex. But these results were inconsistent with the structure of the premade 1‐copper(I) alkyne. Although hundreds of structurally different ligands were reported to significantly enhance the efficiency of CuAAC reaction, their functions were assigned to prevent the oxidation and the disproportionation of Cu(I) ion. Based on the investigation of the references and our works, we proposed that the in‐situ generated 1‐copper(I) alkyne in CuAAC reaction is not identical with the premade 1‐copper(I) alkyne. The ligands may play dual roles to activate the 1‐copper(I) alkyne by blocking the polymerization of the in‐situ formed 1‐copper(I) alkynes and dissociating the polymeric structures of the premade 1‐copper(I) alkynes. As a result, we first disclosed that carboxylic acids can function as such activators and a novel carboxylic acid‐catalyzed CuAAC strategy was developed, which has been proven to be the most convenient and highly efficient CuAAC method to date. Furthermore, highly efficient and regioselective methods for the syntheses of 1,4,5‐trisubstituted 1,2,3‐triazoles were developed by using the premade 1‐copper(I) alkynes as substrates, in which the novel function of the premade 1‐copper(I) alkynes as excellent dipolarophiles was first disclosed and applied. In this article, a series of works reported by our group for the in‐situ generated and the premade 1‐copper(I) alkynes in cycloadditions are reviewed.     

Alkene–Tetrazine Ligation for Imaging Cellular DNA

5‐Vinyl‐2′‐deoxyuridine (VdU) is the first reported metabolic probe for cellular DNA synthesis that can be visualized by using an inverse electron demand Diels–Alder reaction with a fluorescent tetrazine. VdU is incorporated by endogenous enzymes into the genomes of replicating cells, where it exhibits reduced genotoxicity compared to 5‐ethynyl‐2′‐deoxyuridine (EdU). The VdU–tetrazine ligation reaction is rapid (k≈0.02 M ^?1 s^?1) and chemically orthogonal to the alkyne–azide “click” reaction of EdU‐modified DNA. Alkene–tetrazine ligation reactions provide the first alternative to azide–alkyne click reactions for the bioorthogonal chemical labeling of nucleic acids in cells and facilitate time‐resolved, multicolor labeling of DNA synthesis.     

Cover Picture: Angew. Chem. Int. Ed. 6/2002

The cover picture shows the electric eel, Electrophorus electricus, a source for commercially available acetylcholinesterase. In an experiment described by K. B. Sharpless and M. G. Finn and co‐workers on pp. 1053–1057, a femtomolar inhibitor was assembled by the enzyme from a collection of building blocks containing azide and alkyne functional groups, shown floating in solution. The templated 1,3‐dipolar cycloaddition reaction, producing the inhibitor, is represented by the flare of light at the center of the image.     

Cu (I) Catalyzed One Pot SN‐Click Reactions of Halogenated Coumarins and 1‐aza‐coumarins

A one pot three component, copper catalyzed azide‐alkyne cycloaddition reaction has been employed for the synthesis of bis‐coumarinyl triazoles ( A – D ) using 4‐chloro, 4‐bromomethyl, 3‐bromoacetyl and 4‐bromomethyl‐1‐aza‐coumarins ( I – IV ), sodium azide, and coumarin propargyl ethers ( V – IX ) in moderate yields.     

Photochemical Bromination of 2,5-Dimethylbenzoic Acid as Key Step of an Improved Alkyne-Functionalized Blue Box Synthesis**

Cyclobis(paraquat-p-phenylene), also known as “blue box”, is a highly electron-deficient macrocycle, widely used as a molecular receptor for small electron-rich molecules. Inserting a reactive functional group onto the molecular structure of this cyclophane is paramount for its inclusion into complex architectures. To this aim, including an alkyne moiety would be ideal, because it can participate in click reactions. However, the synthesis of such alkyne-functionalized cyclophane suffers from several drawbacks: the use of toxic and expensive CCl₄, the need for high-pressure reactors, and overall low yield. We have revised the existing synthesis of this cyclophane derivative bearing an alkyne moiety, to overcome all these limitations. In particular, photochemical radical bromination is adopted to obtain a sensitive intermediate. We demonstrated that the synthesized host molecule can be functionalized via click reactions and take part in radical-radical interactions. Our work makes a key functionalized paraquat macrocycle more accessible, facilitating the development of novel redox-responsive systems.     

Synthesis and Diversification of Macrocyclic Alkynediyl Sulfide Peptides

The synthesis of rare macrocyclic alkynediyl sulfides by a Cu-catalyzed C_sp−S cross-coupling is presented. The catalytic protocol (Cu(MeCN)₄PF₆/dtbbpy) promotes macrocyclization of peptides, dipeptides and tripeptides at ambient temperature (14 examples, 23→73 % yields) via thiols and bromoalkynes, and is chemoselective with regards to terminal alkynes. Importantly, the underexplored alkynediyl sulfide functionality incorporates a rigidifying structural element and opens new opportunities for diversification of macrocyclic frameworks through S oxidation, halide addition and azide–alkyne cycloaddition chemistries to integrate sulfones, halides or valuable fluorophores (7 examples, 37→92 % yields).     

Benedict's solution/ vitamin C: An alternative catalytic protocol for the synthesis of regioselective‐1,4‐disubstituted‐1H‐1,2,3‐triazoles at room temperature

A novel and highly efficient method for the synthesis of 1,4‐disubstituted‐1H‐1,2,3‐triazoles by copper‐catalyzed azide‐alkyne cycloaddition has been developed. This economic and sustainable protocol uses a readily available Benedict's solution/Vitamin C catalyst system affording a wide range of 1,4‐disubstituted‐1H‐1,2,3‐triazoles under mild conditions.     

Azidopropylvinylsulfonamide as a New Bifunctional Click Reagent for Bioorthogonal Conjugations: Application for DNA–Protein Cross‐Linking

N‐(3‐Azidopropyl)vinylsulfonamide was developed as a new bifunctional bioconjugation reagent suitable for the cross‐linking of biomolecules through copper(I)‐catalyzed azide–alkyne cycloaddition and thiol Michael addition reactions under biorthogonal conditions. The reagent is easily clicked to an acetylene‐containing DNA or protein and then reacts with cysteine‐containing peptides or proteins to form covalent cross‐links. Several examples of bioconjugations of ethynyl‐ or octadiynyl‐modified DNA with peptides, p53 protein, or alkyne‐modified human carbonic anhydrase with peptides are given.     

Macrocyclization of bis-indole quinolines for selective stabilization of G-quadruplex DNA structures

The recognition of G-quadruplex (G4) DNA structures as important regulatory elements in biological mechanisms, and the connection between G4s and the evolvement of different diseases, has sparked interest in developing small organic molecules targeting G4s. However, such compounds often lack drug-like properties and selectivity. Here, we describe the design and synthesis of a novel class of macrocyclic bis-indole quinolines based on their non-macrocyclic lead compounds. The effects of the macrocyclization on the ability to interact with G4 DNA structures were investigated using biophysical assays and molecular dynamic simulations. Overall, this revealed compounds with potent abilities to interact with and stabilize G4 structures and a clear selectivity for both G4 DNA over dsDNA and for parallel/hybrid G4 topologies, which could be attributed to the macrocyclic structure. Moreover, we obtained knowledge about the structure–activity relationship of importance for the macrocyclic design and how structural modifications could be made to construct improved macrocyclic compounds. Thus, the macrocyclization of G4 ligands can serve as a basis for the optimization of research tools to study G4 biology and potential therapeutics targeting G4-related diseases.

Macrocyclization improves the selectivity, affinity, and ability to stabilize G4 DNA structures.     

Screening of Three Transition Metal‐Mediated Reactions Compatible with DNA‐Encoded Chemical Libraries

The construction of DNA‐encoded chemical libraries (DECLs) crucially relies on the availability of chemical reactions, which are DNA‐compatible and which exhibit high conversion rates for a large number of diverse substrates. In this work, we present our optimization and validation procedures for three copper and palladium‐catalyzed reactions (Suzuki cross‐coupling, Sonogashira cross‐coupling, and copper(I)‐catalyzed alkyne‐azide cycloaddition (CuAAC)), which have been successfully used by our group for the construction of large encoded libraries.