Applications In Chemical Biology Research Articles

Profiling Sulfur(VI) Fluorides as Reactive Functionalities for Chemical Biology Tools and Expansion of the Ligandable Proteome.

Here, we report a comprehensive profiling of sulfur(VI) fluorides (SVI-Fs) as reactive groups for chemical biology applications. SVI-Fs are reactive functionalities that modify lysine, tyrosine, histidine, and serine sidechains. A panel of SVI-Fs were studied with respect to hydrolytic stability and reactivity with nucleophilic amino acid sidechains. The use of SVI-Fs to covalently modify carbonic anhydrase II (CAII) and a range of kinases was then investigated. Finally, the SVI-F panel was used in live cell chemoproteomic workflows, identifying novel protein targets based on the type of SVI-F used. This work highlights how SVI-F reactivity can be used as a tool to expand the liganded proteome.

Machine Learning Directed Aptamer Search from Conserved Primary Sequences and Secondary Structures.

Computer-aided prediction of aptamer sequences has been focused on primary sequence alignment and motif comparison. We observed that many aptamers have a conserved hairpin, yet the sequence of the hairpin can be highly variable. Taking such secondary structure information into consideration, a new algorithm combining conserved primary sequences and secondary structures is developed, which combines three scores based on sequence abundance, stability, and structure, respectively. This algorithm was used in the prediction of aptamers from the caffeine and theophylline selections. In the late rounds of the selections, when the libraries were converged, the predicted sequences matched well with the most abundant sequences. When the libraries were far from convergence and the sequences were deemed challenging for traditional analysis methods, this algorithm still predicted aptamer sequences that were experimentally verified by isothermal titration calorimetry. This algorithm paves a new way to look for patterns in aptamer selection libraries and mimics the sequence evolution process. It will help shorten the aptamer selection time and promote the biosensor and chemical biology applications of aptamers.

Tri-part NanoLuc as a new split technology with potential applications in chemical biology: a mini-review.

For several decades, researchers have been using protein-fragment complementation assay (PCA) approaches for biosensing to study protein-protein interaction for a variety of aims, including viral infection, cellular apoptosis, G protein coupled receptor (GPCR) signaling, drug and substrate screening, and protein aggregation and protein editing by CRISPR/Cas9. As a reporter, NanoLuc (NLuc), a smaller and the brightest engineered luciferase derived from deep-sea shrimp Oplophorus gracilirostris, has been found to have many benefits over other luminescent enzymes in PCA. Inspired by the split green fluorescent protein (GFP) and its β-barrel structure, two split NLuc consisting of peptide fragments have been reported including the binary and ternary NLuc systems. NanoBiT® (large fragment + peptide) has been used extensively. In contrast, tripart split NLuc (large fragment + 2 peptides) has been applied and hardly used, while it has some advantages over NanoBiT in some studies. Nevertheless, tripart NLuc has some drawbacks and challenges to overcome but has several potential characteristics to become a multifunctional and powerful tool. In this review, several aspects of tripart NLuc are studied and a brief comparison with NanoBiT® is given.

Recent advances in the synthesis of chiral α-tertiary amines via transition-metal catalysis.

The significance of chiral α-tertiary amines in medicinal chemistry and drug development has been unquestionably established in the last few decades. α-Tertiary amines are attractive structural motifs for natural products, bioactive molecules and pharmaceuticals and are preclinical candidates. Their syntheses have been the focus of intensive research, and the development of new methods has continued to attract more and more attention. In this review, we present the progress in the last decade in the development of synthetic methods for the assembly of chiral ATAs via transition-metal catalysis. To date, the effective approaches in this area could be categorized into three strategies: enantioselective direct and indirect Mannich addition to ketimines; umpolung asymmetric alkylation of imine derivatives; and asymmetric C-N cross-coupling of tertiary alkyl electrophiles. Several related developing strategies for the synthesis of ATAs, such as hydroamination of alkenes, HAT amination approaches and the C-C coupling of α-aminoalkyl fragments, are also described in this article. These strategies have emerged as attractive C-C and C-N bond-forming protocols for enantioselective construction of chiral α-tertiary amines, and to some extent are complementary to each other, showing the prospect of application in medicinal chemistry and chemical biology.

Application of Chemical Biology to Reveal the Function of O-GlcNAcylation in Diseases: Research Tools and Tactics

Application of Chemical Biology to Reveal the Function of O-GlcNAcylation in Diseases: Research Tools and Tactics

Synthetic routes to trifluoromethylphenyl diazirine photolabeling reagents containing an alkyne substituent (TPDYNE) for chemical biology applications.

The trifluoromethylphenyl diazirine (TPD) group is widely used in photoaffinity labeling studies. The TPDYNE group (TPD with an additional alkyne substituent on the phenyl ring) enables the use of click chemistry in conjunction with photoaffinity labeling and expands the utility of the TPD group. New methods for preparing previously known as well as new TPDYNE reagents are reported. Additional methods for preparation of a TPDYNE precursor from which the TPDYNE group can be generated once the precursor is attached to the molecule of interest are also described. Procedures for attaching the TPDYNE or TPDYNE precursor to carboxyl, amino, hydroxyl and alkyne groups are demonstrated using steroids as examples.

Exploring Photoredox‐Catalyzed (Re)functionalizations with Core‐Modified Benziodoxolones

AbstractAlkynes and nitriles are valuable building blocks in organic synthesis and also have multiple applications in chemical biology and materials science. Due to the high availability of tertiary alcohols, developing methods for their conversion into alkynes and nitriles is particularly attractive. In a previous communication, our group has reported the conversion of alcohols into alkynes through cesium oxalates based on the powerful combination of photochemistry with Ethynyl BenziodoXolones (EBXs). Herein, we report further investigations into this transformation, including our findings on the effect that backbone modification of EBXs has on the deoxyalkynylation of cesium oxalates. In addition, we disclose preliminary data on the development of new deoxycyanation and dethioalkynylation processes. We also report the serendipitous discovery of the C−H alkynylation of 1,2‐dichloroethane.

Caging of a Strongly Pairing Fluorescent Thymidine Analog with Soft Nucleophiles.

Controlling the pairing strength of nucleobases in DNA through reactions with compounds found inside the cell is a formidable challenge. Here we report how a thiazolyl substituent turns a strongly pairing ethynylpyridone C-nucleoside into a reactive residue in oligonucleotides. The thiazolyl-bearing pyridone reacts with soft nucleophiles, such as glutathione, but not with hard nucleophiles like hydroxide or carbonate. The addition products pair much more weakly with adenine in a complementary strand than the starting material, and also change their fluorescence. This makes oligonucleotides containing the new deoxynucleoside interesting for controlled release. Due to its reactivity toward N, P, S, and Se-nucleophiles, and the visual signal accompanying chemical conversion, the fluorescent nucleotide reported here may also have applications in chemical biology, sensing and diagnostics.

Multifunctionalized Metal Chalcogenides and Their Roles in Catalysis and Biomedical Applications

AbstractChalcogenides are more frequently used to refer sulfides, selenides, tellurides and polonides rather than oxides and all the elements in group 16 of the periodic table are chalcogens. The synthesis of transition metal chalcogenides (TMCs) and their composites involved a wide range of techniques like one pot heat up, hydrothermal, solvothermal, precipitation, co‐precipitation and biological procedures. In light of the possibility of photo‐induced charge‐transfer events leading to intra‐ensemble charge separation, the integration of TMCs onto a strong electron‐accepting material such as graphene which provides unique TMC/graphene consisted of great significance. Electrochemical water splitting is a promising technology for converting, storing and transporting hydrogen energy in a sustainable manner. Because of their unique physical and chemical properties, as well as their low cost, transition metal chalcogenides are fascinating replacements for catalysts in catalytic water splitting. Transition metal chalcogenides have worldwide attention in recent decades due to their applications in chemical sensors, biological and environmental monitoring applications from biosensors to therapeutic treatment agents.

DNA Strand Displacement with Base Pair Stabilizers: Purine-2,6-Diamine and 8-Aza-7-Bromo-7-Deazapurine-2,6-Diamine Oligonucleotides Invade Canonical DNA and New Fluorescent Pyrene Click Sensors Monitor the Reaction.

Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides (1 and 2) were implemented in isothermal DNA strand displacement reactions. Nucleoside 1 is a weak stabilizer of dA-dT base pairs, nucleoside 2 evokes strong stabilization. Strand displacement reactions used single-stranded invaders with single and multiple incorporations of stabilizers. Displacement is driven by negative enthalpy changes between target and displaced duplex. Toeholds are not required. Two new environmental sensitive fluorescent pyrene sensors were developed to monitor the progress of displacement reactions. Pyrene was connected to the nucleobase in the invader or to a dendritic linker in the output strand. Both new sensors were constructed by click chemistry; phosphoramidites and oligonucleotides were prepared. Sensors show monomer or excimer emission. Fluorescence intensity changes when the displacement reaction progresses. Our work demonstrates that strand displacement with base pair stabilizers is applicable to DNA, RNA and to related biopolymers with applications in chemical biology, nanotechnology and medicinal diagnostics.

Rapid Electrophilic Cysteine Arylation with Pyridinium Salts.

Here, we present a series of fluorinated cationic reagents that enable rapid arylation of cysteine under mild conditions compatible with proteins and peptides. The highly polarized C-F bond and attractive nucleophile-electrophile Coulombic interactions substantially accelerate cysteine arylation, leading to unusually high rate constants on the order of 100 M-1·s-1 and allowing for equimolar labeling of substrates at micromolar concentrations. The synthetic modularity of this approach promotes the direct coupling of structurally diverse phenol-containing functional motifs to cysteine residues of biomacromolecules with high efficiency. This user-friendly chemistry enables fast bond formation between commonly used bioconjugation partners, thus greatly streamlining the synthetic chemistry workflow, and can be easily developed as convenient kits for chemical biology and medicinal chemistry applications.

5]-Helistatins: Tubulin-Binding Helicenes with Antimitotic Activity.

Helicenes are high interest synthetic targets with unique conjugated helical structures that have found important technological applications. Despite this interest, helicenes have had limited impact in chemical biology. Herein, we disclose a first-in-class antimitotic helicene, helistatin 1 (HA-1), where the helicene scaffold acts as a structural mimic of colchicine, a known antimitotic drug. The synthesis proceeds via sequential Pd-catalyzed coupling reactions and a π-Lewis acid cycloisomerization mediated by PtCl2. HA-1 was found to block microtubule polymerization in both cell-free and live cell assays. Not only does this demonstrate the feasibility of using helicenes as bioactive scaffolds against protein targets, but also suggests wider potential for the use of helicenes as isosteres of biaryls or cis-stilbenes-themselves common drug and natural product scaffolds. Overall, this study further supports future opportunities for helicenes for a range of chemical biological applications.

Affinity Bioorthogonal Chemistry (ABC) Tags for Site‐Selective Conjugation, On‐Resin Protein‐Protein Coupling, and Purification of Protein Conjugates

AbstractThe site‐selective functionalization of proteins has broad application in chemical biology, but can be limited when mixtures result from incomplete conversion or the formation of protein containing side products. It is shown here that when proteins are covalently tagged with pyridyl‐tetrazines, the nickel‐iminodiacetate (Ni‐IDA) resins commonly used for His‐tags can be directly used for protein affinity purification. These Affinity Bioorthogonal Chemistry (ABC) tags serve a dual role by enabling affinity‐based protein purification while maintaining rapid kinetics in bioorthogonal reactions. ABC‐tagging works with a range of site‐selective bioconjugation methods with proteins tagged at the C‐terminus, N‐terminus or at internal positions. ABC‐tagged proteins can also be purified from complex mixtures including cell lysate. The combination of site‐selective conjugation and clean‐up with ABC‐tagged proteins also allows for facile on‐resin reactions to provide protein‐protein conjugates.

Towards Enantiomerically Pure Unnatural α-Amino Acids via Photoredox Catalytic 1,4-Additions to a Chiral Dehydroalanine.

Chemo- and diastereoselective 1,4-conjugate additions of anionic and radical C-nucleophiles to a chiral bicyclic dehydroalanine (Dha) are described. Of particular importance, radical carbon photolysis by a catalytic photoredox process using a simple method with a metal-free photocatalyst provides exceptional yields and selectivities at room temperature. Moreover, these 1,4-conjugate additions offer an excellent starting point for synthesizing enantiomerically pure carbon-β-substituted unnatural α-amino acids (UAAs), which could have a high potential for applications in chemical biology.

Membrane Permeating Macrocycles: Design Guidelines from Machine Learning.

The ability to predict cell-permeable candidate molecules has great potential to assist drug discovery projects. Large molecules that lie beyond the Rule of Five (bRo5) are increasingly important as drug candidates and tool molecules for chemical biology. However, such large molecules usually do not cross cell membranes and cannot access intracellular targets or be developed as orally bioavailable drugs. Here, we describe a random forest (RF) machine learning model for the prediction of passive membrane permeation rates developed using a set of over 1000 bRo5 macrocyclic compounds. The model is based on easily calculated chemical features/descriptors as independent variables. Our random forest (RF) model substantially outperforms a multiple linear regression model based on the same features and achieves better performance metrics than previously reported models using the same underlying data. These features include: (1) polar surface area in water, (2) the octanol-water partitioning coefficient, (3) the number of hydrogen-bond donors, (4) the sum of the topological distances between nitrogen atoms, (5) the sum of the topological distances between nitrogen and oxygen atoms, and (6) the multiple molecular path count of order 2. The last three features represent molecular flexibility, the ability of the molecule to adopt different conformations in the aqueous and membrane interior phases, and the molecular "chameleonicity." Guided by the model, we propose design guidelines for membrane-permeating macrocycles. It is anticipated that this model will be useful in guiding the design of large, bioactive molecules for medicinal chemistry and chemical biology applications.

Photoswitchable, Water‐Soluble Bisazobenzene Cross‐Linkers with Enhanced Properties for Biological Applications

AbstractPhotoswitchable cross‐linkers are light‐responsive molecules that can be attached at two locations to a target biomolecule to modulate its activity. Under irradiation, the cross‐linker changes the distance between the residues it spans, affecting the structure and function of the labeled target. Efficient photocontrol is enabled especially by cross‐linkers with large end‐to‐end length change upon switching. The design of water‐soluble azobenzene‐based cross‐linkers for applications in chemical biology remains challenging due to major issues regarding synthesis and purification. Furthermore, the solubility and photochemical properties of the reported systems are frequently not suitable in aqueous media. Herein we report two water‐soluble bisazobenzene cross‐linkers with extended half‐lives and high photostationary state isomer distributions that can be achieved upon irradiation. We present molecules that enable cross‐linking of biomolecular residues within one target, or are bridging two proteins to allow the study of protein–protein interactions, which paves the way for light‐based manipulation of under‐explored biological targets.

Redox-Controlled Chemical Protein Synthesis: Sundry Shades of Latency.

ConspectusThe last two decades have witnessed the rise in power of chemical protein synthesis to the point where it now constitutes an established corpus of synthetic methods efficiently complementing biological approaches. One factor explaining this spectacular evolution is the emergence of a new class of chemoselective reactions enabling the formation of native peptide bonds between two unprotected peptidic segments, also known as native ligation reactions. In recent years, their application has fueled the production of homogeneous batches of large and highly decorated protein targets with a control of their composition at the atomic level. In doing so, native ligation reactions have provided the means for successful applications in chemical biology, medicinal chemistry, materials science, and nanotechnology research.The native chemical ligation (NCL) reaction has had a major impact on the field by enabling the chemoselective formation of a native peptide bond between a C-terminal peptidyl thioester and an N-terminal cysteinyl peptide. Since its introduction in 1994, the NCL reaction has been made the object of significant improvements and its scope and limitations have been thoroughly investigated. Furthermore, the diversification of peptide segment assembly strategies has been essential to access proteins of increasing complexity and has had to overcome the challenge of controlling the reactivity of ligation partners.One hallmark of NCL is its dependency on thiol reactivity, including for its catalysis. While Nature constantly plays with the redox properties of biological thiols for the regulation of numerous biochemical pathways, such a control of reactivity is challenging to achieve in synthetic organic chemistry and, in particular, for those methods used for assembling peptide segments by chemical ligation. This Account covers the studies conducted by our group in this area. A leading theme of our research has been the conception of controllable acyl donors and cysteine surrogates that place the chemoselective formation of amide bonds by NCL-like reactions under the control of dichalcogenide-based redox systems. The dependency of the redox potential of dichalcogenide bonds on the nature of the chalcogenides involved (S, Se) has appeared as a powerful means for diversifying the systems, while allowing their sequential activation for protein synthesis. Such a control of reactivity mediated by the addition of harmless redox additives has greatly facilitated the modular and efficient preparation of multiple targets of biological relevance. Taken together, these endeavors provide a practical and robust set of methods to address synthetic challenges in chemical protein synthesis.

Fluorogenic Protein Labeling by Generation of Fluorescent Quinoliziniums Using [Cp*RhCl2]2

Fluorogenic labeling has received considerable attention as a result of the high demand in chemical biology and synthetic biology applications. Herein, we develop a new strategy for fluorescent turn-on ligation targeting alkyne- and quinoline-linked peptides and proteins (λem of 515 nm and up to ΦF of 0.20) using the [Cp*RhCl2]2 catalyst. The good conversion, high flexibility, broad utility, ease of use, and mild reaction conditions are great advantages to extend the rhodium-mediated turn-on fluorogenic bioconjugation for further applications.

Chemical Conjugation to Less Targeted Proteinogenic Amino Acids.

Protein bioconjugates are in high demand for applications in biomedicine, diagnostics, chemical biology and bionanotechnology. Proteins are large and sensitive molecules containing multiple different functional groups and in particular nucleophilic groups. In bioconjugation reactions it can therefore be challenging to obtain a homogeneous product in high yield. Numerous strategies for protein conjugation have been developed, of which a vast majority target lysine, cysteine and to a lesser extend tyrosine. Likewise, several methods that involve recombinantly engineered protein tags have been reported. In recent years a number of methods have emerged for chemical bioconjugation to other amino acids and in this review, we present the progress in this area.

Essential Oil of the Plants Growing in the Brazilian Amazon: Chemical Composition, Antioxidants, and Biological Applications.

Essential oils are biosynthesized in the secondary metabolism of plants, and in their chemical composition, they can be identified different classes of compounds with potential antioxidant and biological applications. Over the years in the Amazon, several species of aromatic plants were discovered and used in traditional medicine. The literature has shown that essential oils extracted from amazon species have several biological activities, such as antioxidant, antibacterial, antifungal, cytotoxic, and antiprotozoal activities. These activities are related to the diversified chemical composition found in essential oils that, by synergism, favors its pharmacological action. In light of this vital importance, this study aimed at performing a review of the literature with particular emphasis on the chemical composition and biological activities in studies conducted with species collected in the Amazon, taking into consideration in particular the last 10 years of collection and research.