Betainization of Polydopamine/Polyethylenimine Coating for Universal Zwitterionization.

Biofoulants can adhere to multiple surfaces, degrading the performance of medical devices and industrial facilities and/or causing nosocomial infection. The surface immobilization of zwitterionic materials can prevent the initial attachment of the foulants but lacks extensive implementation. Herein, we propose a facile, universal, two-step surface modification strategy to improve fouling resistance. In the first step, the substrates were immersed in a codeposition solution containing dopamine and branched polyethylenimine (PEI) to form a "primer" layer (PDA/PEI). In the second step, the primer layers were treated with 1,3-propane sultone to betainize primary/secondary/tertiary amine moieties of PEI, generating zwitterions on substrates. After betainization, PS-grafted PDA/PEI (PDA/PEI/S) via a ring-opening alkylation reaction manifested changes in wettability. X-ray photoelectron spectroscopy revealed the presence of zwitterionic moieties on the PDA/PEI/S surfaces. Further investigations using ellipsometry and atomic force microscopy were conducted to scrutinize the relation among the PEI content, film thickness, primer stability, and betainization. As a result, zwitterion-decorated substrates prepared under optimal conditions can exhibit high resistance against bacterial fouling, achieving a 98.5% reduction in bacterial attachment. In addition, the method shows a substrate-independent property, capable of successfully applying it on organic and inorganic substrates. Finally, the newly developed approach shows excellent biocompatibility, displaying no significant difference compared with blank control samples. Overall, we envision that the facile surface modification strategy can further promote the preparation of zwitterion-decorated materials in the future.

Evaluation of the DNA Alkylation Properties of a Chlorambucil-Conjugated Cyclic Pyrrole-Imidazole Polyamide.

Hairpin pyrrole-imidazole polyamides (hPIPs) and their chlorambucil (Chb) conjugates (hPIP-Chbs) can alkylate DNA in a sequence-specific manner, and have been studied as anticancer drugs. Here, we conjugated Chb to a cyclic PIP (cPIP), which is known to have a higher binding affinity than the corresponding hPIP, and investigated the DNA alkylation properties of the resulting cPIP-Chb using the optimized capillary electrophoresis method and conventional HPLC product analysis. cPIP-Chb conjugate 3 showed higher alkylation activity at its binding sites than did hPIP-Chb conjugates 1 and 2. Subsequent HPLC analysis revealed that the alkylation site of conjugate 3, which was identified by capillary electrophoresis, was reliable and that conjugate 3 alkylates the N3 position of adenine as do hPIP-Chbs. Moreover, conjugate 3 showed higher cytotoxicity against LNCaP prostate cancer cells than did conjugate 1 and cytotoxicity comparable to that of conjugate 2. These results suggest that cPIP-Chbs could be novel DNA alkylating anticancer drugs.

Reagent-Based Diversity-Oriented Synthesis of Triazolo[1,5-a][1,4]diazepine Derivatives from Polymer-Supported Homoazidoalanine.

Herein, we report the synthesis of skeletally different triazolo[1,5-a][1,4]diazepines starting from immobilized homoazidoalanine. After sulfonylation with 2/4-nitrobenzenesulfonyl chlorides and Mitsunobu alkylation with various alkynols, the corresponding N-substituted nitrobenzenesulfonamides were obtained. Their catalyst-free Huisgen cycloaddition provided immobilized and functionalized triazolo[1,5-a][1,4]diazepines as the key intermediates for further modification. Using the concept of diversity-oriented, reagent-based synthesis, the key intermediates were subsequently converted to heterocycles bearing [5 + 7 + 5], [5 + 7 + 6], and [5 + 7 + 7] scaffolds. Furthermore, the synthesis of spirocyclic triazolodiazepines was developed.

Quantifying Interferent Effects on Molecularly Imprinted Polymer Sensors for Per- and Polyfluoroalkyl Substances (PFAS).

Per- and polyfluoroalkyl substances (PFAS) are emerging as harmful environmental micropollutants. Generally, PFAS species are quantified by mass spectrometry, for which a collected sample is taken to a centralized facility. Robust techniques to quantify PFAS in the field are necessary to diagnose environmental contamination at the earliest onset of pollution. Here, we developed a molecularly imprinted polymer (MIP) electrode for the detection of perfluorooctanesulfonate (PFOS) and explored the MIP surface and the effects of interfering molecules. MIPs were formed by the anodic deposition of o-phenylenediamine (o-PD) in the presence of PFOS template molecules on a glassy carbon macroelectrode. The performance of the resulting MIP electrode was evaluated by the current obtained from the oxidation of ferrocene carboxylic acid as the electrochemical probe. The MIP electrode was able to detect PFOS with a detection limit of 0.05 nM, which is lower than the health advisory limit of 0.14 nM reported by the U.S. EPA. To better understand PFOS association into the MIP, a Langmuir binding model was developed based on the changes in electrochemical responses of the MIP. Fitting the model to the experimental data gave an association constant (KA) of 4.95 × 1012 over a PFOS concentration range of 0 to 0.05 nM. The binding isotherm of other commonly found substances in contaminated water sources such as chloride, humic acid, perfluorooctanoic acid (PFOA), and perfluorobutanesulfonate (PFBS) was also investigated. In the case of chloride and humic acid, the calculated KA values of 9.05 × 107 and 6.01 × 105, respectively, indicate relatively weak adsorption of these species on the MIP. However, PFOA, which is the carboxylate analog of PFOS, revealed a very close KA value (3.41 × 1012) to PFOS. A greater KA value (1.43 × 1013) was obtained for PFBS, which possesses the same functional group and a smaller molecular size compared to PFOS. The presented platform emphasizes the necessity to develop new strategies to make MIP sensors more specific if practical applications are to be pursued.

DNA Alkylation of the RUNX-Binding Sequence by CBI-PI Polyamide Conjugates*.

Many types of molecular targeted drugs that inhibit cancer growth by acting on specific molecules have been developed. The runt-related transcription factor (RUNX) family, which induces cancer development by binding to a specific DNA sequence, has attracted attention as a new target for cancer treatment. We have developed Chb-M', which targets the RUNX-binding sequence. Chb-M' was developed by conjugating pyrrole-imidazole (PI) polyamides and chlorambucil as an anticancer agent. It was recently reported that Chb-M' had a remarkable anticancer effect in vivo. In this study, to explore the possibility of an alternative structure, we designed a new series of CBI-PI polyamides, in which seco-CBI was applied as a DNA-alkylating agent. We examined the characteristics of the CBI-PI polyamides targeting the RUNX-binding sequence and found that these conjugates have great potential for cancer treatment.

A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA.

The methyltransferase enzymes can be applied to deliver a range of modifications to pre-determined sites on large DNA molecules with exceptional specificity and efficiency. To date, however, a limited number of modifications have been delivered in this way because of the complex chemical synthesis that is needed to produce a cofactor analogue carrying a specific function, such as a fluorophore. Here, we describe a method for the direct transfer of a series of functional compounds (seven fluorescent dyes, biotin and polyethylene glycol) to the DNA duplex. Our approach uses a functional cofactor analogue, whose final preparative step is performed alongiside the DNA modification reaction in a single pot, with no purification needed. We show that fluorophore conjugation efficiency in these mixtures is significantly improved compared to two-step labeling approaches. Our experiments highlight the remarkable malleability and selectivity of the methyltransferases tested. Additional analysis using high resolution localization of the fluorophore distribution indicates that target sites for the methyltransferase are predominantly labeled on a single strand of their palindromic site and that a small and randomly-distributed probability of off-site labeling exists.

Molecular Characteristics of DNA-Alkylating PI Polyamides Targeting RUNX Transcription Factors.

The runt-related transcription factor (RUNX) family has been associated with cancer development. The binding of RUNX family members to specific DNA sequences is hypothesized to promote the expression of downstream genes and cause cancer proliferation. On the basis of this proposed mechanism of cancer growth, we developed conjugate 1, which inhibits the binding of RUNX to its target DNA. Conjugate 1 is a DNA-alkylating pyrrole-imidazole (PI) polyamide conjugate containing chlorambucil as an anticancer agent. Conjugate 1 was reported to have a marked anticancer effect in mouse models of acute myeloid leukemia. Although the effectiveness of 1 has been demonstrated in vivo, the detailed mechanism by which it alkylates DNA is unknown. Here, we chemically elucidated the molecular characteristics of conjugate 1 to confirm its potential as a RUNX-inhibiting drug. We also generated an alternative conjugate 2, which targets the same DNA sequence, by replacing one pyrrole with ß-alanine. Comparison of the characteristics of conjugates 1 and 2 suggested that reaction selectivity and binding affinity to the RUNX-binding sequence were improved by the introduction of ß-alanine. These findings indicate the possibility of DNA-alkylating PI polyamides as candidates for cancer chemotherapeutics.

Adequate Reducing Conditions Enable Conjugation of Oxidized Peptides to Polymers by One-Pot Thiol Click Chemistry.

Thiol(-click) chemistry has been extensively investigated to conjugate (bio)molecules to polymers. Handling of cysteine-containing molecules may however be cumbersome, especially in the case of fast-oxidizing coiled-coil-forming peptides. In the present study, we investigated the practicality of a one-pot process to concomitantly reduce and conjugate an oxidized peptide to a polymer. Three thiol-based conjugation chemistries (vinyl sulfone (VS), maleimide, and pyridyldithiol) were assayed along with three reducing agents (tris(2-carboxyethyl)phosphine (TCEP), dithiothreitol, and ß-mercaptoethanol). Seven out of the nine possible combinations significantly enhanced the conjugation yield, provided that an adequate concentration of reductant was used. Among them, the coincubation of an oxidized peptide with TCEP and a VS-modified polymer displayed the highest level of conjugation. Our results also provide insights into two topics that currently lack consensus: TCEP is stable in 10 mM phosphate buffered saline and it reacts with thiol-alkylating agents at submillimolar concentrations, and thus should be carefully used in order to avoid interference with thiol-based conjugation reactions.

Immobilization by Surface Conjugation of Cyclic Peptides for Effective Mimicry of the HCV-Envelope E2 Protein as a Strategy toward Synthetic Vaccines.

Mimicry of the binding interface of antibody-antigen interactions using peptide-based modulators (i.e., epitope mimics) has promising applications for vaccine design. These epitope mimics can be synthesized in a streamlined and straightforward fashion, thereby allowing for high-throughput analysis. The design of epitope mimics is highly influenced by their spatial configuration and structural conformation. It is widely assumed that for proper mimicry sufficient conformational constraints have to be implemented. This paper describes the synthesis of bromide derivatives functionalized with a flexible TEG linker equipped with a thiol-moiety that could be used to support cyclic or linear peptides. The cyclic and linear epitope mimics were covalently conjugated via the free thiol-moiety on maleimide-activated plate surfaces. The resulting covalent, uniform, and oriented coated surface of cyclic or linear epitope mimics were subjected to an ELISA to investigate the effect of peptide cyclization with respect to mimicry of an antigen-antibody interaction of the HCV E2 glycoprotein. To the best of our knowledge, the benefit of cyclized peptides over linear peptides has been clearly demonstrated here for the first time. Cyclic epitope mimics, and not the linear epitope mimics, demonstrated specificity toward their monoclonal antibodies HC84.1 and V3.2, respectively. The described strategy for the construction of epitope mimics shows potential for high-throughput screening of key binding residues by simply changing the amino acid sequences within synthetic peptides. In this way, leucine-438 has been identified as a key binding residue for binding monoclonal antibody V3.2.

Exploiting Macromolecular Design To Optimize the Antibacterial Activity of Alkylated Cationic Oligomers.

There is growing interest in synthetic polymers which co-opt the structural features of naturally occurring antimicrobial peptides. However, our understanding of how macromolecular architecture affects antibacterial activity remains limited. To address this, we investigated whether varying architectures of a series of block and statistical co-oligomers influenced antibacterial and hemolytic activity. Cu(0)-mediated polymerization was used to synthesize oligomers constituting 2-(Boc-amino)ethyl acrylate units and either diethylene glycol ethyl ether acrylate (DEGEEA) or poly(ethylene glycol) methyl ether acrylate units with varying macromolecular architecture; subsequent deprotection produced primary amine functional oligomers. Further guanylation provided an additional series of antimicrobial candidates. Both chemical composition and macromolecular architecture were shown to affect antimicrobial activity. A broad spectrum antibacterial oligomer (containing guanidine moieties and DEGEEA units) was identified that possessed promising activity (MIC = 2 µg mL-1) toward both Gram-negative and Gram-positive bacteria. Bacterial membrane permeabilization was identified as an important contributor to the mechanism of action.

Organocatalytic Enantioselective Vinylogous Aldol Reaction of 5-Alkyl-4-Nitroisoxazoles to Paraformaldehyde.

An organocatalytic asymmetric aldol reaction of 5-alkyl-4-nitroisoxazoles to paraformaldehyde has been developed. By using a chiral dipeptide-based urea-amide-guanidinium as the phase-transfer catalyst, the transformations were promoted by sodium acetate, leading to a range of enantio-enriched isoxazole derivatives in high yields with moderate to excellent enantioselectivities. This work represents the first example of constructing chiral C-C bonds at the α-position of 5-alkyl-4-nitroisoxazoles. The viability of readily accessing chiral fungicides from the obtained aldol products demonstrates the important utility of this method.

Fast, irreversible modification of cysteines through strain releasing conjugate additions of cyclopropenyl ketones.

A method of cysteine alkylation using cyclopropenyl ketones is described. Due to the significant release of cyclopropene strain energy, reactions of thiols with cyclopropenyl ketones are both fast and irreversible and give rise to stable conjugate addition adducts. The resulting cyclopropenyl ketones have a low molecular weight and allow for simple attachment of amides via N-hydroxysuccinimide (NHS)-esters. While cyclopropenyl ketones do display slow background reactivity toward water, labeling by thiols is much more rapid. The reaction of a cyclopropenyl ketone with glutathione (GSH) proceeds with a rate of 595 M-1 s-1 in PBS at pH 7.4, which is considerably faster than α-halocarbonyl labeling reagents, and competitive with maleimide/thiol couplings. The method has been demonstrated in protein conjugation, and an arylthiolate conjugate was shown to be stable upon prolonged incubation in either GSH or human plasma. Finally, cyclopropenyl ketones were used to create PEG-based hydrogels that are stable to prolonged incubation in a reducing environment.

The synthesis of mono-alkyl phosphates and their derivatives: an overview of their nature, preparation and use, including synthesis under plausible prebiotic conditions.

Nucleic acids, phospholipids and other organic phosphates play central roles in biological pathways. n-Alkyl phosphates and their derivatives have been recognized as amphiphilic molecules for nearly two centuries. In the last 50 years, n-alkyl phosphate derivatives such as di-alkyl phosphates, mono-alkyl phosphatidyl ethanol amines and mono-alkyl phosphocholines have become predominant compounds with applications in different areas, from food chemistry to life science. The aim of this review is to summarize the most relevant progress made in the field of the synthesis of these molecules and to provide a concise perspective on the use of these amphiphiles as possible prebiotic membrane constituents. The first part of the review is dedicated to the analysis of the most relevant syntheses carried out in recent years with respect to those reported from the second half of the nineteenth century. The second part is dedicated to a description of the latest reports on prebiotic synthesis of mono-alkyl phosphates. In this part, the authors did not report the phosphorylation of other relevant biomolecules, such as nucleosides, which have been excellently reviewed elsewere.

Antiobesity and emetic effects of a short-length peptide YY analog and its PEGylated and alkylated derivatives.

Neuropeptide Y2 receptor (Y2R) agonism is an important anorectic signal and a target of antiobesity drug discovery. Recently, we synthesized a short-length Y2R agonist, PYY-1119 (4-imidazolecarbonyl-[d-Hyp24,Iva25,Pya(4)26,Cha27,36,γMeLeu28,Lys30,Aib31]PYY(23-36), 1) as an antiobesity drug candidate. Compound 1 induced marked body weight loss in diet-induced obese (DIO) mice; however, 1 also induced severe vomiting in dogs at a lower dose than the minimum effective dose administered to DIO mice. The rapid absorption of 1 after subcutaneous administration caused the severe vomiting. Polyethylene glycol (PEG)- and alkyl-modified derivatives of 1 were synthesized to develop Y2R agonists with improved pharmacokinetic profiles, i.e., lower maximum plasma concentration (Cmax) and longer time at maximum concentration (Tmax). Compounds 5 and 10, modified with 20 kDa PEG at the N-terminus and eicosanedioic acid at the Lys30 side chain of 1, respectively, showed high Y2R binding affinity and induced significant body weight reduction upon once-daily administration to DIO mice. Compounds 5 and 10, with their relatively low Cmax and long Tmax, partially attenuated emesis in dogs compared with 1. These results indicate that optimization of pharmacokinetic properties of Y2R agonists is an effective strategy to alleviate emesis induced by Y2R agonism.

Evaluation of alkylating pyrrole-imidazole polyamide conjugates by a novel method for high-throughput sequencer.

N-Methylpyrrole-N-methylimidazole (PI) polyamides are a class of DNA minor groove binders with DNA sequence-specificity. DNA-alkylating PI polyamide conjugates are attractive candidates as anticancer drugs acting through DNA damage and its subsequent inhibition of cell proliferation. One example is a chlorambucil-PI polyamide conjugate targeting the runt-related transcription factor (RUNX) family. RUNX1 has pro-oncogenic properties in acute myeloid leukemia, and recently the chlorambucil-PI polyamide conjugate was demonstrated to have anticancer effects. Herein, we apply another DNA-alkylating agent, seco-CBI, to target the consensus sequence of the RUNX family. Two types of CBI conjugates were prepared and their binding properties were characterized by Bind-n-Seq analysis using a high-throughput sequencer. The sequencing data were analyzed by two methods, MERMADE and our new MR (motif identification with a reference sequence), and the resultant binding motif logos were as predicted from the pairing rules proposed by Dervan et al. This is the first report to employ the MR method on alkylating PI polyamide conjugates. Moreover, cytotoxicity of conjugates 3 and 4 against a human non-small cell lung cancer, A549, were examined to show promising IC50s of 120 nm and 63 nm, respectively. These findings suggest seco-CBI-PI polyamide conjugates are candidates for oncological therapy.

Alkyl-Dimethylpyrazines in Mandibular Gland Secretions of Four Odontomachus Ant Species (Formicidae: Ponerinae).

Ponerine ants are known to contain mixtures of pyrazines in their mandibular glands. We analyzed the mandibular gland contents of four ponerine species (Odontomachus chelifer, O. erythrocephalus, O. ruginodis, and O. bauri) by gas chromatography coupled with mass spectrometry, and found that each species contains specific mixtures of trisubstituted alkylpyrazines among other volatiles. Attempts to identify alkylpyrazines solely by mass spectral interpretation is unrealistic because spectra of positional isomers are indistinguishable. To avoid misidentifications, we synthesized a large number of reference compounds and compared their mass spectral and gas chromatographic properties with those present in the Odontomachus species under investigation. Most of the compounds identified were 2-alkyl-3,5-dimethylpyrazines. Interestingly, when the third substituent was an isopentyl group, the two methyl groups were found to be located at the 2 and 5 ring positions. Using our data, we recognized several misidentifications in previous publications.

Integration of chemical catalysis with extractive fermentation to produce fuels.

Nearly one hundred years ago, the fermentative production of acetone by Clostridium acetobutylicum provided a crucial alternative source of this solvent for manufacture of the explosive cordite. Today there is a resurgence of interest in solventogenic Clostridium species to produce n-butanol and ethanol for use as renewable alternative transportation fuels. Acetone, a product of acetone-n-butanol-ethanol (ABE) fermentation, harbours a nucleophilic α-carbon, which is amenable to C-C bond formation with the electrophilic alcohols produced in ABE fermentation. This functionality can be used to form higher-molecular-mass hydrocarbons similar to those found in current jet and diesel fuels. Here we describe the integration of biological and chemocatalytic routes to convert ABE fermentation products efficiently into ketones by a palladium-catalysed alkylation. Tuning of the reaction conditions permits the production of either petrol or jet and diesel precursors. Glyceryl tributyrate was used for the in situ selective extraction of both acetone and alcohols to enable the simple integration of ABE fermentation and chemical catalysis, while reducing the energy demand of the overall process. This process provides a means to selectively produce petrol, jet and diesel blend stocks from lignocellulosic and cane sugars at yields near their theoretical maxima.

Deciphering the genomic targets of alkylating polyamide conjugates using high-throughput sequencing.

Chemically engineered small molecules targeting specific genomic sequences play an important role in drug development research. Pyrrole-imidazole polyamides (PIPs) are a group of molecules that can bind to the DNA minor-groove and can be engineered to target specific sequences. Their biological effects rely primarily on their selective DNA binding. However, the binding mechanism of PIPs at the chromatinized genome level is poorly understood. Herein, we report a method using high-throughput sequencing to identify the DNA-alkylating sites of PIP-indole-seco-CBI conjugates. High-throughput sequencing analysis of conjugate 2: showed highly similar DNA-alkylating sites on synthetic oligos (histone-free DNA) and on human genomes (chromatinized DNA context). To our knowledge, this is the first report identifying alkylation sites across genomic DNA by alkylating PIP conjugates using high-throughput sequencing.

Chemical Design of Non-Ionic Polymer Brushes as Biointerfaces: Poly(2-oxazine)s Outperform Both Poly(2-oxazoline)s and PEG.

The era of poly(ethylene glycol) (PEG) brushes as a universal panacea for preventing non-specific protein adsorption and providing lubrication to surfaces is coming to an end. In the functionalization of medical devices and implants, in addition to preventing non-specific protein adsorption and cell adhesion, polymer-brush formulations are often required to generate highly lubricious films. Poly(2-alkyl-2-oxazoline) (PAOXA) brushes meet these requirements, and depending on their side-group composition, they can form films that match, and in some cases surpass, the bioinert and lubricious properties of PEG analogues. Poly(2-methyl-2-oxazine) (PMOZI) provides an additional enhancement of brush hydration and main-chain flexibility, leading to complete bioinertness and a further reduction in friction. These data redefine the combination of structural parameters necessary to design polymer-brush-based biointerfaces, identifying a novel, superior polymer formulation.

Synthesis of Lipophilic Guanine N-9 Derivatives: Membrane Anchoring of Nucleobases Tailored to Fatty Acid Vesicles.

Covalent or noncovalent surface functionalization of soft-matter structures is an important tool for tailoring their function and stability. Functionalized surfaces and nanoparticles have found numerous applications in drug delivery and diagnostics, and new functionalization chemistry is continuously being developed in the discipline of bottom-up systems chemistry. The association of polar functional molecules, e.g., molecular recognition agents, with soft-matter structures can be achieved by derivatization with alkyl chains, allowing noncovalent anchoring into amphiphilic membranes. We report the synthesis of five new guanine-N9 derivatives bearing alkyl chains with different attachment chemistries, exploiting a synthesis pathway that allows a flexible choice of hydrophobic anchor moiety. In this study, these guanine derivatives were functionalized with C10 chains for insertion into decanoic acid bilayer structures, in which both alkyl chain length and attachment chemistry determined their interaction with the membrane. Incubation of these guanine conjugates, as solids, with a decanoic acid vesicle suspension, showed that ether- and triazole-linked C10 anchors yielded an increased partitioning of the guanine derivative into the membranous phase compared to directly N-9-linked saturated alkyl anchors. Decanoic acid vesicle membranes could be loaded with up to 5.5 mol % guanine derivative, a 6-fold increase over previous limits. Thus, anchor chemistries exhibiting favorable interactions with a bilayer's hydrophilic surface can significantly increase the degree of structure functionalization.