Fluorescence quenchers for hydrazone and oxime orthogonal bioconjugation

Planar Chiral p,p'-Terphenyl-Based Cyclophanes with Remarkable Enantiomer Stability: Synthesis, Theoretical Investigations, and Complexation Studies

Design of conformationally stable compounds with planar chirality is a topic of great interest mainly because of their potential applications as enantioselective ligands or other functional materials. Herein, we present the design and synthesis of novel planar chiral cyclophanes, obtained by ortho, ortho″ anchoring of the p,p'-terphenyl unit, with bridges of different lengths and rigidities, along with their nuclear magnetic resonance, mass spectrometry, and X-ray characterizations. We investigated the influence of the structural particularities of the bridges over the stability of the enantiomers, by means of nuclear magnetic resonance and chiral high-performance liquid chromatography as well as by density functional theory calculations. We also demonstrated the ability of one of the cyclophanes to preferentially bind arginine with Ka > 110 M-1 (ΔG > -11 kJ mol-1) in acetonitrile solutions containig 10 % water, in the presence of other amino acids.

Molecular Engineering of E. coli Bacterioferritin: A Versatile Nanodimensional Protein Cage

Currently, intense interest is focused on the discovery and application of new multisubunit cage proteins and spherical virus capsids to the fields of bionanotechnology, drug delivery, and diagnostic imaging as their internal cavities can serve as hosts for fluorophores or bioactive molecular cargo. Bacterioferritin is unusual in the ferritin protein superfamily of iron-storage cage proteins in that it contains twelve heme cofactors and is homomeric. The goal of the present study is to expand the capabilities of ferritins by developing new approaches to molecular cargo encapsulation employing bacterioferritin. Two strategies were explored to control the encapsulation of a diverse range of molecular guests compared to random entrapment, a predominant strategy employed in this area. The first was the inclusion of histidine-tag peptide fusion sequences within the internal cavity of bacterioferritin. This approach allowed for the successful and controlled encapsulation of a fluorescent dye, a protein (fluorescently labeled streptavidin), or a 5 nm gold nanoparticle. The second strategy, termed the heme-dependent cassette strategy, involved the substitution of the native heme with heme analogs attached to (i) fluorescent dyes or (ii) nickel-nitrilotriacetate (NTA) groups (which allowed for controllable encapsulation of a histidine-tagged green fluorescent protein). An in silico docking approach identified several small molecules able to replace the heme and capable of controlling the quaternary structure of the protein. A transglutaminase-based chemoenzymatic approach to surface modification of this cage protein was also accomplished, allowing for future nanoparticle targeting. This research presents novel strategies to control a diverse set of molecular encapsulations and adds a further level of sophistication to internal protein cavity engineering.

Orthogonal Chemical Reporter Strategy Enables Sensitive and Specific SERS Detection of Hydrazine Derivatives

Hydrazine and its derivatives are well-known environmental hazards and biological carcinogens; therefore, there is a great need for a powerful workflow solution for protecting the public from unexpected exposure to toxic contaminants. Recently, functional surface-enhanced Raman scattering (SERS) exhibits enormous benefits in sensing trace biochemical substances due to its fingerprint-like identification of individual molecules, making it an ideal method for detecting and quantifying hydrazine. Herein, for the first time, we integrated the orthogonal chemical reporter strategy with SERS to build an intelligent hydrazine detection platform (orthogonal chemical SERS, ocSERS), in which 4-mercaptobenzaldehyde was incorporated on a nanoimprinted gold nanopillar array, which acted as an orthogonal coupling partner of hydrazine to form Raman active benzaldehyde hydrazone, allowing for sensitively detecting hydrazine with a detection limit of 10^-13 M in complex circumstances. Particularly, ocSERS could effectively identify the carcinogen N-nitrosodimethylamine (NDMA) after its reduction to dimethylhydrazine (UDMH), enabling ultrasensitive detection of UDMH (10^-13 M). Importantly, ocSERS could not only monitor elevated levels of NDMA in ranitidine due to improper storage but also quantify NDMA in urine and blood after oral administration of NDMA-containing drugs, thereby preventing NDMA overexposure. Therefore, ocSERS represents the first click SERS sensor and may open up a new analytical field.

Rapid and Sequential Dual Oxime Ligation Enables De Novo Formation of Functional Synthetic Membranes from Water-Soluble Precursors

Cell membranes define the boundaries of life and primarily consist of phospholipids. Living organisms assemble phospholipids by enzymatically coupling two hydrophobic tails to a soluble polar head group. Previous studies have taken advantage of micellar assembly to couple single-chain precursors, forming non-canonical phospholipids. However, biomimetic nonenzymatic coupling of two alkyl tails to a polar head-group remains challenging, likely due to the sluggish reaction kinetics of the initial coupling step. Here we demonstrate rapid de novo formation of biomimetic liposomes in water using dual oxime bond formation between two alkyl chains and a phosphocholine head group. Membranes can be generated from non-amphiphilic, water-soluble precursors at physiological conditions using micromolar concentrations of precursors. We demonstrate that functional membrane proteins can be reconstituted into synthetic oxime liposomes from bacterial extracts in the absence of detergent-like molecules.

Discovery of Potent and Selective Inhibitors against Protein-Derived Electrophilic Cofactors

Electrophilic cofactors are widely distributed in nature and play important roles in many physiological and disease processes, yet they have remained blind spots in traditional activity-based protein profiling (ABPP) approaches that target nucleophiles. More recently, reverse-polarity (RP)-ABPP using hydrazine probes identified an electrophilic N-terminal glyoxylyl (Glox) group for the first time in secernin-3 (SCRN3). The biological function(s) of both the protein and Glox as a cofactor has not yet been pharmacologically validated because of the lack of selective inhibitors that could disrupt and therefore identify its activity. Here, we present the first platform for analyzing the reactivity and selectivity of an expanded nucleophilic probe library toward main-chain carbonyl cofactors such as Glox and pyruvoyl (Pyvl) groups. We first applied the library proteome-wide to profile and confirm engagement with various electrophilic protein targets, including secernin-2 (SCRN2), shown here also to possess a Glox group. A broadly reactive indole ethylhydrazine probe was used for a competitive in vitro RP-ABPP assay to screen for selective inhibitors against such cofactors from a set of commercially available nucleophilic fragments. Using Glox-containing SCRN proteins as a case study, naphthyl hydrazine was identified as a potent and selective SCRN3 inhibitor, showing complete inhibition in cell lysates with no significant cross-reactivity detected for other enzymes. Moving forward, this platform provides the fundamental basis for the development of selective Glox inhibitors and represents a starting point to advance small molecules that modulate electrophile-dependent function.

Chemistry of Peptide-Oligonucleotide Conjugates: A Review

Peptide-oligonucleotide conjugates (POCs) represent one of the increasingly successful albeit costly approaches to increasing the cellular uptake, tissue delivery, bioavailability, and, thus, overall efficiency of therapeutic nucleic acids, such as, antisense oligonucleotides and small interfering RNAs. This review puts the subject of chemical synthesis of POCs into the wider context of therapeutic oligonucleotides and the problem of nucleic acid drug delivery, cell-penetrating peptide structural types, the mechanisms of their intracellular transport, and the ways of application, which include the formation of non-covalent complexes with oligonucleotides (peptide additives) or covalent conjugation. The main strategies for the synthesis of POCs are viewed in detail, which are conceptually divided into (a) the stepwise solid-phase synthesis approach and (b) post-synthetic conjugation either in solution or on the solid phase, especially by means of various click chemistries. The relative advantages and disadvantages of both strategies are discussed and compared.

Förster resonance energy transfer (FRET) and applications thereof

FRET is a nonradiative process of energy transfer that is based on the dipole-dipole interactions between molecules that are fluorescent. Transfer of energy takes place rapidly from a donor molecule to an acceptor molecule in juxtaposition such as 0 to 10 nm without photonic radiation. FRET has occupied a center stage in biotechnology and biological studies. It is used to gain information on conformation changes in single molecules. The pharmaceutical industry has also developed large fluorescence detection systems with very small sample sizes, at the level of single molecules, using fluorescence correlation spectroscopy.

Quantification of Aldehydes on Polymeric Microbead Surfaces via Catch and Release of Reporter Chromophores

Aldehyde moieties on 2D-supports or micro- and nanoparticles can function as anchor groups for the attachment of biomolecules or as reversible binding sites for proteins on cell surfaces. The use of aldehyde-based materials in bioanalytical and medical settings calls for reliable methods to detect and quantify this functionality. We report here on a versatile concept to quantify the accessible aldehyde moieties on particle surfaces through the specific binding and subsequent release of small reporter molecules such as fluorescent dyes and nonfluorescent chromophores utilizing acylhydrazone formation as a reversible covalent labeling strategy. This is representatively demonstrated for a set of polymer microparticles with different aldehyde labeling densities. Excess reporter molecules can be easily removed by washing, eliminating inaccuracies caused by unspecific adsorption to hydrophobic surfaces. Cleavage of hydrazones at acidic pH assisted by a carbonyl trap releases the fluorescent reporters rapidly and quasi-quantitatively and allows for their fluorometric detection at low concentration. Importantly, this strategy separates the signal-generating molecules from the bead surface. This circumvents common issues associated with light scattering and signal distortions that are caused by binding-induced changes in reporter fluorescence as well as quenching dye-dye interactions on crowded particle surfaces. In addition, we demonstrate that the release of a nonfluorescent chromophore via disulfide cleavage and subsequent quantification by absorption spectroscopy gives comparable results, verifying that both assays are capable of rapid and sensitive quantification of aldehydes on microbead surfaces. These strategies enable a quantitative comparison of bead batches with different functionalization densities, and a qualitative prediction of their coupling efficiencies in bioconjugations, as demonstrated in reductive amination reactions with Streptavidin.

Efficient Synthesis of a Wide-Range Absorbing Azaphthalocyanine Dark Quencher and Its Application to Dual-Labeled Oligonucleotide Probes for Quantitative Real-Time Polymerase Chain Reactions

Unsymmetrical dialkylamino-substituted zinc azaphthalocyanine (AzaPc) exhibits unique spectral and photophysical properties for dark quenchers of fluorescence in DNA hybridization probes. The panchromatic light absorption of AzaPc from 300 nm up to at least 700 nm and its lack of fluorescence make it an ideal candidate for a universal dark quencher. To prove this experimentally, oligodeoxyribonucleotide probes were labeled at the 3'-end by this AzaPc and at the 5'-end by a fluorophore used in the polymerase chain reaction (PCR)-that is, fluorescein, CAL Fluor Red 610, and Cy5. AzaPc showed a significantly higher quenching efficiency compared to the commercially available dark quenchers (BHQ-1, BHQ-2, BBQ-650) in a developed model of TaqMan PCR assay. The AzaPc-labeled probe proved to also be useful in a practical PCR assay for the quantification of the SLCO2B1 transporter gene expression. The constructed calibration curves indicated linearity in the range from 10² to 10⁷ of target copies.

Borylated oximes: versatile building blocks for organic synthesis

Herein, we demonstrate the synthesis and functionalization of α-boryl aldoximes from α-boryl aldehydes, with no sign of C-to-N boryl migration. Selective modification of the oxime functionality enables access to a wide range of borylated compounds, such as borylated heterocycles and N-acetoxyamides. By reducing the α-boryl aldoximes, MIDA deprotection yields the corresponding β-boryl hydroxylamines. As part of this study, we also demonstrate the utility of the boryl aldoxime motif in peptide conjugation.

Oximes and Hydrazones in Bioconjugation: Mechanism and Catalysis

The formation of oximes and hydrazones is employed in numerous scientific fields as a simple and versatile conjugation strategy. This imine-forming reaction is applied in fields as diverse as polymer chemistry, biomaterials and hydrogels, dynamic combinatorial chemistry, organic synthesis, and chemical biology. Here we outline chemical developments in this field, with special focus on the past ∼10 years of developments. Recent strategies for installing reactive carbonyl groups and α-nucleophiles into biomolecules are described. The basic chemical properties of reactants and products in this reaction are then reviewed, with an eye to understanding the reaction's mechanism and how reactant structure controls rates and equilibria in the process. Recent work that has uncovered structural features and new mechanisms for speeding the reaction, sometimes by orders of magnitude, is discussed. We describe recent studies that have identified especially fast reacting aldehyde/ketone substrates and structural effects that lead to rapid-reacting α-nucleophiles as well. Among the most effective new strategies has been the development of substituents near the reactive aldehyde group that either transfer protons at the transition state or trap the initially formed tetrahedral intermediates. In addition, the recent development of efficient nucleophilic catalysts for the reaction is outlined, improving greatly upon aniline, the classical catalyst for imine formation. A number of uses of such second- and third-generation catalysts in bioconjugation and in cellular applications are highlighted. While formation of hydrazone and oxime has been traditionally regarded as being limited by slow rates, developments in the past 5 years have resulted in completely overturning this limitation; indeed, the reaction is now one of the fastest and most versatile reactions available for conjugations of biomolecules and biomaterials.

Chemoselective Modification of Vinyl DNA by Triazolinediones

A new method for the post-synthetic modification of nucleic acids was developed that involves mixing a phenyl triazolinedione (PTAD) derivative with DNA containing a vinyl nucleobase. The resulting reactions proceeded through step-wise mechanisms, giving either a formal [4+2] cycloaddition product, or, depending on the context of nucleobase, PTAD addition along with solvent trapping to give a secondary alcohol in water. Catalyst-free addition between PTAD and the terminal alkene of 5-vinyl-2'-deoxyuridine (VdU) was exceptionally fast, with a second-order rate constant of 2×10³  m^-1  s^-1 . PTAD derivatives selectively reacted with VdU-containing oligonucleotides in a conformation-selective manner, with higher yields observed for G-quadruplex versus duplex DNA. These results demonstrate a new strategy for copper-free bioconjugation of DNA that can potentially be used to probe nucleic acid conformations in cells.

Synthesis of chemically modified DNA

Naturally occurring DNA is encoded by the four nucleobases adenine, cytosine, guanine and thymine. Yet minor chemical modifications to these bases, such as methylation, can significantly alter DNA function, and more drastic changes, such as replacement with unnatural base pairs, could expand its function. In order to realize the full potential of DNA in therapeutic and synthetic biology applications, our ability to 'write' long modified DNA in a controlled manner must be improved. This review highlights methods currently used for the synthesis of moderately long chemically modified nucleic acids (up to 1000 bp), their limitations and areas for future expansion.

Erythromycin Modification That Improves Its Acidic Stability while Optimizing It for Local Drug Delivery

The antibiotic erythromycin has limited efficacy and bioavailability due to its instability and conversion under acidic conditions via an intramolecular dehydration reaction. To improve the stability of erythromycin, several analogs have been developed—such as azithromycin and clarithromycin—which decrease the rate of intramolecular dehydration. We set out to build upon this prior work by developing a conjugate of erythromycin with improved pH stability, bioavailability, and preferential release from a drug delivery system directly at the low pH of an infection site. To develop this new drug conjugate, adamantane-1-carbohydrazide was covalently attached to erythromycin via a pH-degradable hydrazone bond. Since Staphylococcus aureus infection sites are slightly acidic, the hydrazone bond will undergo hydrolysis liberating erythromycin directly at the infection site. The adamantane group provides interaction with the drug delivery system. This local delivery strategy has the potential of reducing off-target and systemic side-effects. This work demonstrates the synthesis of a pH-cleavable, erythromycin conjugate that retains the inherent antimicrobial activity of erythromycin, has an increased hydrophobicity, and improved stability in acidic conditions; thereby enhancing erythromycin’s bioavailability while simultaneously reducing its toxicity.

Selective Chemical Labeling of Natural T Modifications in DNA

We present a chemical method to selectively tag and enrich thymine modifications, 5-formyluracil (5-fU) and 5-hydroxymethyluracil (5-hmU), found naturally in DNA. Inherent reactivity differences have enabled us to tag 5-fU chemoselectively over its C modification counterpart, 5-formylcytosine (5-fC). We rationalized the enhanced reactivity of 5-fU compared to 5-fC via ab initio quantum mechanical calculations. We exploited this chemical tagging reaction to provide proof of concept for the enrichment of 5-fU containing DNA from a pool that contains 5-fC or no modification. We further demonstrate that 5-hmU can be chemically oxidized to 5-fU, providing a strategy for the enrichment of 5-hmU. These methods will enable the mapping of 5-fU and 5-hmU in genomic DNA, to provide insights into their functional role and dynamics in biology.

A genetically encoded aldehyde for rapid protein labelling

Using a mutant pyrrolysyl-tRNA synthetase-tRNA(Pyl)(CUA) pair, 3-formyl-phenylalanine is genetically incorporated into proteins at amber mutation sites in Escherichia coli. This non-canonical amino acid readily reacts with hydroxylamine dyes, leading to rapid and site-selective protein labelling.

Selective chemical modification of DNA with alkoxy- and benzyloxyamines

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

Synthesis of Hydrophilic Aminooxy Linkers and Multivalent Cores for Chemoselective Aldehyde/Ketone Conjugation

A series of three linear and two trivalent aminooxy-containing hydrophilic linkers and cores were synthesized. The five molecules contain from one to three aminooxy groups, and all but one contain an ether for enhanced aqueous solubility. These unique and versatile molecules can be utilized in the chemoselective conjugation of aldehyde/ketone-containing molecules, including reducing sugars, under mild aqueous conditions, and give rise to oxime-containing conjugates useful in a wide variety of applications and studies. The value of these aminooxy-based molecules and the ease and speed of preparation of both monovalent and multivalent oxime-linked molecules is demonstrated in two examples using the disaccharide cellobiose; one with a linear linker, and the second with a trivalent core.

Enhanced catalysis of oxime-based bioconjugations by substituted anilines

The conjugation of biomolecules by chemoselective oxime ligation is of great interest for the site-specific modification of proteins, peptides, nucleic acids, and carbohydrates. These conjugations proceed optimally at a reaction pH of 4-5, but some biomolecules are not soluble or stable under these conditions. Aniline can be used as a nucleophilic catalyst to enhance the rate of oxime formation, but even in its presence, the reaction rate at neutral pH can be slower than desired, particularly at low reagent concentrations and/or temperature. Recently, alternative catalysts with improved properties were reported, including anthranilic acid derivatives for small molecule ligations, as well as m-phenylenediamine at high concentrations for protein conjugations. Here, we report that p-substituted anilines containing an electron-donating ring substituent are superior catalysts of oxime-based conjugations at pH 7. One such catalyst, p-phenylenediamine, was studied in greater detail. This catalyst was highly effective at neutral pH, even at the low concentration of 2 mM. In a model oxime ligation using aminooxy-functionalized PEG, catalysis at pH 7 resulted in a 120-fold faster rate of protein PEGylation as compared to an uncatalyzed reaction, and 19-fold faster than the equivalent aniline-catalyzed reaction. p-Phenylenediamine (10 mM) was also an effective catalyst under acidic conditions and was more efficient than aniline throughout the pH range 4-7. This catalyst allows efficient oxime bioconjugations to proceed under mild conditions and low micromolar concentrations, as demonstrated by the PEGylation of a small protein.

Thioamide quenching of fluorescent probes through photoinduced electron transfer: mechanistic studies and applications

Previously we have shown that thioamides can be incorporated into proteins as minimally perturbing fluorescence-quenching probes to study protein dynamics, folding, and aggregation. Here, we show that the spontaneity of photoinduced electron transfer between a thioamide and an excited fluorophore is governed by the redox potentials of each moiety according to a Rehm-Weller-type model. We have used this model to predict thioamide quenching of various common fluorophores, and we rigorously tested more than a dozen examples. In each case, we found excellent agreement between our theoretical predictions and experimental observations. In this way, we have been able to expand the scope of fluorophores quenched by thioamides to include dyes suitable for microscopy and single-molecule studies, including fluorescein, Alexa Fluor 488, BODIPY FL, and rhodamine 6G. We describe the photochemistry of these systems and explore applications that demonstrate the utility of thioamide quenching of fluorescein to studying protein folding and proteolysis.

Fast hydrazone reactants: electronic and acid/base effects strongly influence rate at biological pH

Kinetics studies with structurally varied aldehydes and ketones in aqueous buffer at pH 7.4 reveal that carbonyl compounds with neighboring acid/base groups form hydrazones at accelerated rates. Similarly, tests of a hydrazine with a neighboring carboxylic acid group show that it also reacts at an accelerated rate. Rate constants for the fastest carbonyl/hydrazine combinations are 2-20 M(-1) s(-1), which is faster than recent strain-promoted cycloaddition reactions.

Synthesis of dabsyl-appended cyclophanes and their heterodimer formation with pyrene-appended cyclophanes

As a quencher-type host, dabsyl-appended cyclophanes bearing positively and negatively charged side chains (1a and 1b, respectively) were synthesized. Formation of cyclophane heterodimers of 1a with anionic fluorescent cyclophane bearing a pyrene moiety 2b was confirmed by fluorescence titration experiments. The 1:1 binding constant (K) of 1a toward 2b was calculated to be 1.6 × 10(5) M(-1). On the other hand, almost no complexation affinity of 1a toward cationic analogue of fluorescent cyclophane 2a was confirmed by the identical methods, indicating that electrostatic interactions became effective in the formation of cyclophane heterodimers. In addition, van't Hoff analysis applied to the temperature-dependent K values for the heterodimer formation gave negative enthalpy (ΔH) and entropy changes (ΔS). The large and negative ΔH values as well as small and also negative ΔS values showed that the complexation is an exothermic and enthalpy-controlled but not entropy-driven process. A similar trend of molecular recognition was also confirmed for formation of cyclophane heterodimers of 1b with 2a by the identical methods.

Water-soluble organocatalysts for hydrazone and oxime formation

The formation of oximes and hydrazones is widely used in chemistry and biology as a molecular conjugation strategy for achieving ligation, attachment, and bioconjugation. However, the relatively slow rate of reaction has hindered its utility. Here, we report that simple, commercially available anthranilic acids and aminobenzoic acids act as superior catalysts for hydrazone and oxime formation, speeding the reaction considerably over the traditional aniline-catalyzed reaction at neutral pH. This efficient nucleophilic catalysis, involving catalyst-imine intermediates, allows rapid hydrazone/oxime formation even with relatively low concentrations of the two reactants. The most efficient catalysts are found to be 5-methoxyanthranilic acid and 3,5-diaminobenzoic acid; we find that they can enhance rates by factors of as much as 1-2 orders of magnitude over the aniline-catalyzed reaction. Evidence based on a range of differently substituted arylamines suggests that the ortho-carboxylate group in the anthranilate catalysts serves to aid in intramolecular proton transfer during imine and hydrazone formation.