Synthesis of DIBAC analogues with excellent SPAAC rate constants

A Short Review of Research Progress on the Synthesis Approaches of Aza-Dibenzocyclooctyne Derivatives

Cyclooctyne molecules have found wide applications in the strain-promoted azide-alkyne cycloaddition (SPAAC) reactions, which avoid the biotoxicity caused by the use of Cu(I) catalysts. Among the various cyclooctyne systems, dibenzocyclooctyne (DBCO) series have displayed the highest reaction activity. However, the synthesis processes of such structures are time-consuming, which to some extent limit their large-scale development and application. This review has summarized current synthesis routes of two DBCO molecules, aza-dibenzocyclooctyne (DIBAC) and biarylazacyclooctynone (BARAC).

New Derivatives of the Multi-Stage Active Malaria Box Compound MMV030666 and Their Antiplasmodial Potencies

MMV's Malaria Box compound MMV030666 shows multi-stage activity against various strains of Plasmodium falciparum and lacks resistance development. To evaluate the importance of its diarylether partial structure, diarylthioethers and diphenylamines with varying substitution patterns were prepared. A number of evident structure-activity relationships were revealed. Physicochemical and pharmacokinetic parameters were determined experimentally (passive permeability) or calculated. Compared to the lead compound a diarylthioether was more active and less cytotoxic resulting in an excellent selectivity index of 850. In addition, pharmacokinetic and physicochemical parameters were improved.

Fast and Efficient Postsynthetic DNA Labeling in Cells by Means of Strain-Promoted Sydnone-Alkyne Cycloadditions

Sydnones are highly stable mesoionic 1,3-dipoles that react with cyclooctynes through strain-promoted sydnone-alkyne cycloaddition (SPSAC). Although sydnones have been shown to be valuable bioorthogonal chemical reporters for the labeling of proteins and complex glycans, nucleic acids have not yet been tagged by SPSAC. Evaluation of SPSAC kinetics with model substrates showed fast reactions with cyclooctyne probes (up to k=0.59 M-1  s-1 ), and two different sydnones were effectively incorporated into both 2'-deoxyuridines at position 5, and 7-deaza-2'-deoxyadenosines at position 7. These modified nucleosides were synthetically incorporated into single-stranded DNAs, which were successfully postsynthetically labeled with cyclooctyne probes both in vitro and in cells. These results show that sydnones are versatile bioorthogonal tags and have the premise to become essential tools for tracking DNA and potentially RNA in living cells.

Synthesis and Structure-Activity Relationships of New 2-Phenoxybenzamides with Antiplasmodial Activity

The 2-phenoxybenzamide 1 from the Medicines for Malaria Venture Malaria Box Project has shown promising multi-stage activity against different strains of P. falciparum. It was successfully synthesized via a retrosynthetic approach. Subsequently, twenty-one new derivatives were prepared and tested for their in vitro activity against blood stages of the NF54 strain of P. falciparum. Several insights into structure-activity relationships were revealed. The antiplasmodial activity and cytotoxicity of compounds strongly depended on the substitution pattern of the anilino partial structure as well as on the size of substituents. The diaryl ether partial structure had further impacts on the activity. Additionally, several physicochemical and pharmacokinetic parameters were calculated (log P, log D₇.₄ and ligand efficiency) or determined experimentally (passive permeability and CYP3A4 inhibition). The tert-butyl-4-{4-[2-(4-fluorophenoxy)-3-(trifluoromethyl)benzamido]phenyl}piperazine-1-carboxylate possesses high antiplasmodial activity against P. falciparum NF54 (PfNF54 IC₅₀ = 0.2690 µM) and very low cytotoxicity (L-6 cells IC₅₀ = 124.0 µM) resulting in an excellent selectivity index of 460. Compared to the lead structure 1 the antiplasmodial activity was improved as well as the physicochemical and some pharmacokinetic parameters.

Automation and data-driven design of polymer therapeutics

Polymers are uniquely suited for drug delivery and biomaterial applications due to tunable structural parameters such as length, composition, architecture, and valency. To facilitate designs, researchers may explore combinatorial libraries in a high throughput fashion to correlate structure to function. However, traditional polymerization reactions including controlled living radical polymerization (CLRP) and ring-opening polymerization (ROP) require inert reaction conditions and extensive expertise to implement. With the advent of air-tolerance and automation, several polymerization techniques are now compatible with well plates and can be carried out at the benchtop, making high throughput synthesis and high throughput screening (HTS) possible. To avoid HTS pitfalls often described as "fishing expeditions," it is crucial to employ intelligent and big data approaches to maximize experimental efficiency. This is where the disruptive technologies of machine learning (ML) and artificial intelligence (AI) will likely play a role. In fact, ML and AI are already impacting small molecule drug discovery and showing signs of emerging in drug delivery. In this review, we present state-of-the-art research in drug delivery, gene delivery, antimicrobial polymers, and bioactive polymers alongside data-driven developments in drug design and organic synthesis. From this insight, important lessons are revealed for the polymer therapeutics community including the value of a closed loop design-build-test-learn workflow. This is an exciting time as researchers will gain the ability to fully explore the polymer structural landscape and establish quantitative structure-property relationships (QSPRs) with biological significance.

Triple, Mutually Orthogonal Bioorthogonal Pairs through the Design of Electronically Activated Sulfamate-Containing Cycloalkynes

Interest in mutually exclusive pairs of bioorthogonal labeling reagents continues to drive the design of new compounds that are capable of fast and predictable reactions. The ability to easily modify S-, N-, and O-containing cyclooctynes (SNO-OCTs) enables electronic tuning of various SNO-OCTs to influence their cycloaddition rates with Type I-III dipoles. As opposed to optimizations based on just one specific dipole class, the electrophilicity of the alkynes in SNO-OCTs can be manipulated to achieve divergent reactivities and furnish mutually orthogonal dual ligation systems. Significant reaction rate enhancements of a difluorinated SNO-OCT derivative, as compared to the parent scaffold, were noted, with the second-order rate constant in cycloadditions with diazoacetamides exceeding 5.13 M-1 s-1. Computational and experimental studies were employed to inform the design of triple ligation systems that encompass three orthogonal reactivities. Finally, polar SNO-OCTs are rapidly internalized by mammalian cells and remain functional in the cytosol for live-cell labeling, highlighting their potential for diverse in vitro and in vivo applications.

One-pot thiol-amine bioconjugation to maleimides: simultaneous stabilisation and dual functionalisation

Maleimide chemistry is widely used in the site-selective modification of proteins. However, hydrolysis of the resultant thiosuccinimides is required to provide robust stability to the bioconjugates. Herein, we present an alternative approach that affords simultaneous stabilisation and dual functionalisation in a one pot fashion. By consecutive conjugation of a thiol and an amine to dibromomaleimides, we show that aminothiomaleimides can be generated extremely efficiently. Furthermore, the amine serves to deactivate the electrophilicity of the maleimide, precluding further reactivity and hence generating stable conjugates. We have applied this conjugation strategy to peptides and proteins to generate stabilised trifunctional conjugates. We propose that this stabilisation-dual modification strategy could have widespread use in the generation of diverse conjugates.

Hepatitis C Virus Helicase Binding Activity Monitored through Site-Specific Labeling Using an Expanded Genetic Code

The mechanism of unwinding catalyzed by the hepatitis C virus nonstructural protein 3 helicase (NS3h) has been a subject of considerable interest, with NS3h serving as a prototypical enzyme in the study of helicase function. Recent studies support an ATP-fueled, inchworm-like stepping of NS3h on the nucleic acid that would result in the displacement of the complementary strand of the duplex during unwinding. Here, we describe the screening of a site of incorporation of an unnatural amino acid in NS3h for fluorescent labeling of the enzyme to be used in single-molecule Förster resonance energy transfer (FRET) experiments. From the nine potential sites identified in NS3h for incorporation of the unnatural amino acid, only one allowed for expression and fluorescent labeling of the recombinant protein. Incorporation of the unnatural amino acid was confirmed via bulk assays to not interfere with unwinding activity of the helicase. Binding to four different dsDNA sequences bearing a ssDNA overhang segment of varying length (either minimal 6 or 7 base length overhang to ensure binding or a long 24 base overhang) and sequence was recorded with the new NS3h construct at the single-molecule level. Single-molecule fluorescence displayed time intervals with anticorrelated donor and acceptor emission fluctuations associated with protein binding to the substrates. An apparent FRET value was estimated from the binding events showing a single FRET value of ∼0.8 for the 6-7 base overhangs. A smaller mean value and a broad distribution was in turn recorded for the long ssDNA overhang, consistent with NS3h exploring a larger physical space while bound to the DNA construct. Notably, intervals where NS3h binding was recorded were exhibited at time periods where the acceptor dye reversibly bleached. Protein induced fluorescence intensity enhancement in the donor channel became apparent at these intervals. Overall, the site-specific fluorescent labeling of NS3h reported here provides a powerful tool for future studies to monitor the dynamics of enzyme translocation during unwinding by single-molecule FRET.

A Dual Wavelength Polymerization and Bioconjugation Strategy for High Throughput Synthesis of Multivalent Ligands

Structure-function relationships for multivalent polymer scaffolds are highly complex due to the wide diversity of architectures offered by such macromolecules. Evaluation of this landscape has traditionally been accomplished case-by-case due to the experimental difficulty associated with making these complex conjugates. Here, we introduce a simple dual-wavelength, two-step polymerize and click approach for making combinatorial conjugate libraries. It proceeds by incorporation of a polymerization friendly cyclopropenone-masked dibenzocyclooctyne into the side chain of linear polymers or the α-chain end of star polymers. Polymerizations are performed under visible light using an oxygen tolerant porphyrin-catalyzed photoinduced electron/energy transfer-reversible addition-fragmentation chain-transfer (PET-RAFT) process, after which the deprotection and click reaction is triggered by UV light. Using this approach, we are able to precisely control the valency and position of ligands on a polymer scaffold in a manner conducive to high throughput synthesis.

Selective Engineering of Linkage-Specific α2,6-N-Linked Sialoproteins Using Sydnone-Modified Sialic Acid Bioorthogonal Reporters

The metabolic oligosaccharide engineering (MOE) strategy using unnatural sialic acids has recently enabled the visualization of the sialome in living systems. However, MOE only reports on global sialylation and dissected information regarding subsets of sialosides is missing. Described here is the synthesis and utilization of sialic acids modified with a sydnone reporter for the metabolic labeling of sialoconjugates. The positioning of the reporter on the sugar significantly altered its metabolic fate. Further in vitro enzymatic assays revealed that the 9-modified neuraminic acid is preferentially accepted by the sialyltransferase ST6Gal-I over ST3Gal-IV, leading to the favored incorporation of the reporter into linkage-specific α2,6-N-linked sialoproteins. This sydnone sugar presents the possibility of investigating the roles of specific sialosides.

Ring Expansion of Alkylidenecarbenes Derived from Lactams, Lactones, and Thiolactones into Strained Heterocyclic Alkynes: A Theoretical Study

Strained cycloalkynes are of considerable interest to theoreticians and experimentalists, and possess much synthetic value as well. Herein, a series of cyclic alkylidenecarbenes—formally obtained by replacing the carbonyl oxygen of four-, five-, and six-membered lactams, lactones, and thiolactones with a divalent carbon—were modeled at the CCSD(T)/cc-pVTZ//B3LYP/6-311+G** and CCSD(T)/cc-pVTZ//CCSD/6-311+G** levels of theory. The singlet carbenes were found to be more stable than the triplets. The strained heterocyclic alkynes formed by ring expansion of these singlet carbenes were also modeled. Interestingly, the C≡C bonds in the five-membered heterocycles, obtained from the rearrangement of β-lactam- and β-lactone-derived alkylidenecarbenes, displayed lengths intermediate between formal double and triple bonds. Furthermore, 2-(1-azacyclobutylidene)carbene was found to be nearly isoenergetic with its ring-expanded isomer, and 1-oxacyclopent-2-yne was notably higher in energy than its precursor carbene. In all other cases, the cycloalkynes were lower in energy than the corresponding carbenes. The transition states for ring-expansion were always lower for the 1,2-carbon shifts than for 1,2-nitrogen or oxygen shifts, but higher than for the 1,2-sulfur shifts. These predictions should be verifiable using carbenes bearing appropriate isotopic labels. Computed vibrational spectra for the carbenes, and their ring-expanded isomers, are presented and could be of value to matrix isolation experiments.

Synthetic Applications of Flexible SNO-OCT Strained Alkynes and Their Use in Postpolymerization Modifications

SNO-OCTs are eight-membered heterocyclic alkynes that have fast rates of reactivity with 1,3-dipoles. In contrast to many other reported cycloalkynes, SNO-OCTs contain multiple sites for derivatization, display stability under a variety of common reaction conditions, and offer the opportunity for strain-induced ring-opening following the initial reaction of the alkyne moiety. In this paper, we describe how the unique features of SNO-OCTs can be employed to modify an oxime-bearing styrene copolymer and introduce an array of polar functionalities into the polymer. This can be achieved through both the addition of SNO-OCT to the polymer, as well as in the subsequent opening of the sulfamate ring once it has been installed in the polymer.

2-Aminobenzenesulfonamide-Containing Cyclononyne as Adjustable Click Reagent for Strain-Promoted Azide-Alkyne Cycloaddition

The synthesis of 2-aminobenzenesulfonamide-containing cyclononyne (ABSACN), starting from 2-nitrobenzenesulfonamide and but-2-yne-1,4-diol via Mitsunobu and Nicholas reactions, is described for the development of an adjustable alkyne reagent in click reactions. In a strain-promoted azide-alkyne cycloaddition (SPAAC) reaction, the reactivity of the alkyne is controlled by introducing various N-functionalities. The structure-reactivity relationship is found to be influenced by a transannular hydrogen bond between amino and sulfonyl groups.

Use of Ambient Ionization High-Resolution Mass Spectrometry for the Kinetic Analysis of Organic Surface Reactions

In contrast to homogeneous systems, studying the kinetics of organic reactions on solid surfaces remains a difficult task due to the limited availability of appropriate analysis techniques that are general, high-throughput, and capable of offering quantitative, structural surface information. Here, we demonstrate how direct analysis in real time mass spectrometry (DART-MS) complies with above considerations and can be used for determining interfacial kinetic parameters. The presented approach is based on the use of a MS tag that--in principle--allows application to other reactions. To show the potential of DART-MS, we selected the widely applied strain-promoted alkyne-azide cycloaddition (SPAAC) as a model reaction to elucidate the effects of the nanoenvironment on the interfacial reaction rate.

Strain-Promoted 1,3-Dipolar Cycloaddition of Cycloalkynes and Organic Azides

A nearly forgotten reaction discovered more than 60 years ago-the cycloaddition of a cyclic alkyne and an organic azide, leading to an aromatic triazole-enjoys a remarkable popularity. Originally discovered out of pure chemical curiosity, and dusted off early this century as an efficient and clean bioconjugation tool, the usefulness of cyclooctyne-azide cycloaddition is now adopted in a wide range of fields of chemical science and beyond. Its ease of operation, broad solvent compatibility, 100 % atom efficiency, and the high stability of the resulting triazole product, just to name a few aspects, have catapulted this so-called strain-promoted azide-alkyne cycloaddition (SPAAC) right into the top-shelf of the toolbox of chemical biologists, material scientists, biotechnologists, medicinal chemists, and more. In this chapter, a brief historic overview of cycloalkynes is provided first, along with the main synthetic strategies to prepare cycloalkynes and their chemical reactivities. Core aspects of the strain-promoted reaction of cycloalkynes with azides are covered, as well as tools to achieve further reaction acceleration by means of modulation of cycloalkyne structure, nature of azide, and choice of solvent.

Site-specific conjugation of 8-ethynyl-BODIPY to a protein by [2 + 3] cycloaddition

We report a straightforward synthesis of 8-ethynyl-BODIPY derivatives and their potential as fluorescent labeling compounds using an alkyne–azide click chemistry approach.