ε-Poly-l-lysine: A Naturally Occurring Biodegradable Polypeptide for Selective Detection of 5-Nitroimidazole Antibiotics in Animal Products and Living Cells via Fluorescence.

The 5-nitroimidazole (5-NI) class of antibiotics, such as metronidazole, ornidazole, secnidazole, and tinidazole, are widely used to prevent bacterial infection in humans and livestock industries. However, their overuse contaminates the farmed animal products and water bodies. Hence, a selective, sensitive, and cost-effective method to detect 5-NI antibiotics is the need of the hour. Herein, we report a rapid, inexpensive, and efficient sensing system to detect 5-NI drugs using an as-prepared solution of ε-poly-l-lysine (ε-PL), a naturally occurring and biodegradable homopolypeptide that has an intrinsic fluorescence via clustering-triggered emission. The low nanomolar detection limit (3.25-3.97 nM) for the aforementioned representative 5-NI drugs highlights the sensitivity of the system, outperforming most of the reported sensors alike. The resulting fluorescence quenching was found to be static in nature. Importantly, excellent recovery (100.26-104.41%) was obtained for all real samples and animal products tested. Visual detection was demonstrated by using paper strips and silica gel for practical applications. Furthermore, ε-PL could detect 5-NI antibiotics in living 3T3-L1 mouse fibroblast cells via cellular imaging. Taken together, the present work demonstrates the detection of 5-NI antibiotics using a biocompatible natural polypeptide, ε-PL, and represents a simple and inexpensive analytical tool for practical application.

Dansyl-tagged xanthate ester as a capping agent to synthesize fluorescent silver nanoparticles with binding affinity toward serum albumin.

Developing multifunctional nanomaterials with distinct photochemical properties, such as high quantum yield, improved photostability, and good biocompatibility is critical for a wide range of biomedical applications. Motivated by this, we designed and synthesized a dansyl-tagged xanthate-based capping agent (DX) for the synthesis of fluorescent silver nanoparticles (AgNPs). The capping agent DX was characterized by 1 H and 13 C-NMR, LC-MS, and FT-IR. The synthesized DX-capped fluorescent AgNPs were thoroughly characterized by UV-visible spectroscopy, fluorescence spectroscopy, field emission scanning electron microscope (FE-SEM), transmission electron microscope (TEM), dynamic light scattering (DLS), and zeta potential. The fluorescent AgNPs showed distinct surface plasmon resonance absorption at λmax = 414 nm, fluorescence at λmax = 498 nm, quantum yield = 0.24, zeta potential = +18.6 mV, average size = 18.2 nm. Furthermore, the biological activity of the fluorescent AgNPs was validated by its interaction with the most abundant protein in the blood, that is, BSA (Bovine serum albumin) and HSA (Human serum albumin) with binding constant of 2.34 × 104 M-1 and 2.14 × 104 M-1 respectively. Interestingly, fluorescence resonance energy transfer (FRET) was observed between the fluorescent AgNPs and BSA/HSA with a FRET efficiency of 77.23% and 56.36%, respectively, indicating strong interaction between fluorescent AgNPs and BSA/HSA.

Sequence-Defined Tertiary Amine-Based Oligomer Employing a Scalable, Support-Free, and Protection/Deprotection-Free Iterative Strategy.

Sequence-defined oligomers (SDOs) with their unique monomeric sequence and customizable nature are attracting the attention of researchers globally. The structural and functional diversity attainable in SDOs makes this platform promising, albeit with challenges in the synthesis. Herein, we report the design and synthesis of a novel class of SDO by incorporating tertiary amines into the backbone from commercially available inexpensive materials. Tertiary amines were selected due to their various material and biomedical applications. Even though the synthesis and purification of amine compounds are challenging, their various significant applications, such as pharmaceuticals, catalysts, surfactants, corrosion inhibitors, dye intermediates, polymer additives, rubber accelerators, gas treating agents, agriculture, and analytical chemistry, make them fascinating. The synthetic strategy that is designed here is extremely efficient and economical for the scalable synthesis of the SDO and is support-free, protection-deprotection chemistry-free, and catalyst/template-free. Most importantly, no extra design and synthesis of the monomer is required here. The key reactions employed for the SDO synthesis are (i) transformation of the hydroxy group to a halide and (ii) substitution of the halide by the secondary amine units. Including the purifying processes, the multigram synthesis of 4-mer was completed in 12-14 h. The synthetic strategy was established by synthesizing two different sequences of SDOs. The SDOs are characterized by 1H NMR and LC-MS. The tandem MS (MS/MS) experiment was conducted in order to validate the sequences over the SDO chain. Furthermore, the SDO platform was advanced in two ways: (i) by increasing the chain length via attaching a linker, which provides a rapid method for increasing the tertiary amine over the SDO chain, and (ii) postsynthetic modification of SDO with other functional groups, including guanidine for biological importance and a well-known fluorophore dansyl group for material significance.

Selective and sensitive fluorescent staining of serum albumin in protein gel electrophoresis via sequence-defined oligo-dithiocarbamate.

This work presents a fluorescent sequence-defined oligo dithiocarbamate platform with a dansyl appendage for interaction studies with a range of proteins including BSA, HSA, proteinase, trypsin, lysozyme, hemoglobin, and amylase. The platform involves six distinct sequence-defined oligomers (SDOs), each offering varied functionalities - dithiocarbamate (DTC), ester, and amide - within the backbone and side chains; different architectures (linear and branched); and introduction of polar or non-polar groups. Fluorescence titration experiments and molecular docking were used to explore the interaction between the synthesized SDOs and the listed proteins. This analysis identified two promising candidates, particularly SDOs 1 and 2, based on higher FRET efficiency, indicating a stronger interaction with serum albumins. SDO 1, demonstrating the highest FRET, was utilized for specific and sensitive staining of serum albumin in native-polyacrylamide gel electrophoresis (Native-PAGE), providing selective fluorescent staining with a 25 times lower concentration of staining agent compared to conventional Coomassie blue staining. This innovative approach serves as an alternative tool for gel staining, especially for selective fluorescent staining of BSA and HSA.

Dansyl-triazole-based fluorescent macrocycle for selective detection of nitro-antibiotic drugs and protein interaction.

A novel dansyl-triazole-based fluorescent macrocycle with high Stokes shift and positive solvatochromism was developed. This is an excellent fluorescence sensor for selective detection of nitro-containing antibiotics and other nitro-heteroaromatics. Detection was possible in real samples/paper strips in submicromolar concentration. The interaction of the macrocycle with multiple proteins exhibited its bioactivity.

Superfast Capture of Iodine from Air, Water, and Organic Solvent by Potential Dithiocarbamate-Based Organic Polymer.

Organic polymers are widely explored due to their high stability, scalability, and more facile modification properties. We developed cost-effective dithiocarbamate-based organic polymers synthesized using diamides, carbon disulfide, and diamines to apply for environmental remediation. The sequestration of radioiodine is a serious concern to tackle when dealing with nuclear power for energy requirements. However, many of the current sorbents have the problem of slower adsorption for removing iodine. In this report, we discuss the utilization of an electron-rich dithiocarbamate-based organic polymer for the removal of iodine in a very short time and with high uptake. Our material showed 2.8 g/g uptake of vapor iodine in 1 h, 915.19 mg/g uptake of iodine from cyclohexane within 5 s, 93% removal of saturated iodine from water in 1 min, and 1250 mg/g uptake of triiodide ions from water within 30 s. To the best of our knowledge, the iodine capture was faster than previously observed for any existing material. The material was fully recyclable when applied for up to four cycles. Hence, this dithiocarbamate-based polymer can be a promising system for the fast removal of various forms of iodine and, thus, enhance environmental security.

Aza-Oxa-Triazole Based Macrocycles with Tunable Properties: Design, Synthesis, and Bioactivity.

A modular platform for the synthesis of tunable aza-oxa-based macrocycles was established. Modulations in the backbone and the side-chain functional groups have been rendered to achieve the tunable property. These aza-oxa-based macrocycles can also differ in the number of heteroatoms in the backbone and the ring size of the macrocycles. For the proof of concept, a library of macrocycles was synthesized with various hanging functional groups, different combinations of heteroatoms, and ring sizes in the range of 17-27 atoms and was characterized by NMR and mass spectrometry. In light of the importance of the copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction and the significance of triazole groups for various applications, we employed the click-reaction-based macrocyclization. The competence of the synthesized macrocycles in various biomedical applications was proven by studying the interactions with the serum albumin proteins; bovine serum albumin and human serum albumin. It was observed that some candidates, based on their hanging functional groups and specific backbone atoms, could interact well with the protein, thus improving the bioactive properties. On the whole, this work is a proof-of-concept to explore the backbone- and side-chain-tunable macrocycle for different properties and applications.

Design, synthesis and bioactive properties of a class of macrocycles with tunable functional groups and ring size.

The design and synthesis of a versatile class of macrocycles with tunable functional groups and ring size are unfolded. Herein, a synthetic strategy is reported to furnish a new class of macrocycles in multi-gram scale in a two-step reaction. The total time taken for synthesizing a macrocycle is 1.5 h. Dithiocarbamates, an important functional group in biomedical and material sciences, is strategically incorporated in the macrocyclic backbone without metal for the first time. It is noteworthy that when state-of-the-art macrocycle synthesis is in millimolar concentration, this work employs the reaction in molar concentration (0.2-0.4 M). As proof-of-principle, a library of macrocycles was synthesized, varying the functional groups and ring size. The physicochemical properties of macrocycles revealed their druggable nature and are affirmed by protein (serum albumin) interaction study theoretically and experimentally. Diverse functional groups and ring sizes of macrocycles brought about twenty-five-fold difference in binding constant with the model protein.

An in-silico study on selected organosulfur compounds as potential drugs for SARS-CoV-2 infection via binding multiple drug targets.

The emerging paradigm shift from 'one molecule, one target, for one disease' towards 'multi-targeted small molecules' has paved an ingenious pathway in drug discovery in recent years. We extracted this idea for the investigation of drugs for COVID-19. Perceiving the importance of organosulfur compounds, seventy-six known organosulfur compounds were screened and studied for the interaction with multiple SARS-CoV-2 target proteins by molecular dynamics simulation. Lurasidone and its derivatives displayed substantial binding affinity against five proteins (Mpro, PLpro, Spro, helicase and RdRp). The pharmacokinetics, ADMET properties and target prediction studies performed in this work further potentiates the effectiveness against SARS-CoV-2.

Biomimetic Electronic Devices for Measuring Bacterial Membrane Disruption.

Antibiotic discovery has experienced a severe slowdown in terms of discovery of new candidates. In vitro screening methods using phospholipids to model the bacterial membrane provide a route to identify molecules that specifically disrupt bacterial membranes causing cell death. Thanks to the electrically insulating properties of the major component of the cell membrane, phospholipids, electronic devices are highly suitable transducers of membrane disruption. The organic electrochemical transistor (OECT) is a highly sensitive ion-to-electron converter. Here, the OECT is used as a transducer of the permeability of a lipid monolayer (ML) at a liquid:liquid interface, designed to read out changes in ion flux caused by compounds that interact with, and disrupt, lipid assembly. This concept is illustrated using the well-documented antibiotic Polymixin B and the highly sensitive quantitation of permeability of the lipid ML induced by two novel recently described antibacterial amine-based oligothioetheramides is shown, highlighting molecular scale differences in their disruption capabilities. It is anticipated that this platform has the potential to play a role in front-line antimicrobial compound design and characterization thanks to the compatibility of semiconductor microfabrication technology with high-throughput readouts.

Ultrafast Electron Transfer across a Nanocapsular Wall: Coumarins as Donors, Viologen as Acceptor, and Octa Acid Capsule as the Mediator.

Results of our study on ultrafast electron transfer (eT) dynamics from coumarins (coumarin-1, coumarin-480, and coumarin-153) incarcerated within octa acid (OA) capsules as electron donors to methyl viologen dissolved in water as acceptor are presented. Upon photoexcitation, coumarin inside the OA capsule transfers an electron to the acceptor electrostatically attached to the capsule leading to a long-lived radical-ion pair separated by the OA capsular wall. This charge-separated state returns to the neutral ground state via back electron transfer on the nanosecond time scale. This system allows for ultrafast electron transfer processes through a molecular wall from the apolar capsular interior to the highly polar (aqueous) environment on the femtosecond time scale. Employing femtosecond transient absorption spectroscopy, distinct rates of both forward (1-25 ps) and backward eT (700-1200 ps) processes were measured. Further understanding of the energetics is provided using Rehm-Weller analysis for the investigated photoinduced eT reactions. The results provide the rates of the eT across a molecular wall, akin to an isotropic solution, depending on the standard free energy of the reaction. The insights from this work could be utilized in the future design of efficient electron transfer processes across interfaces separating apolar and polar environments.

Sequence-Defined Backbone Modifications Regulate Antibacterial Activity of OligoTEAs.

In response to the urgent need for new antibiotic development strategies, antimicrobial peptides (AMPs) and other synthetic polymers are being actively investigated as promising alternatives to traditional antibiotics. Although most AMPs display lytic activity against several types of bacteria, they have poor toxicology profiles and are susceptible to proteolysis in vivo. While many synthetic variants have been created to mimic AMPs by tuning the hydrophobic to cationic ratio of the side-chain groups, few have decoupled the effects of charge from hydrophobicity in discrete systems, and none have investigated the effect of backbone hydrophobicity. We recently developed a rapid and efficient approach for the assembly of synthetic sequence-defined oligothioetheramides (oligoTEAs) that are resistant to protease activity. Our oligoTEA assembly scheme allows direct access to the oligomer backbone, which enables precise tuning of oligoTEA hydrophobicity while keeping charge constant. In this study, we synthesized a new class of antibacterial oligoTEAs (AOTs) with precise control over backbone hydrophobicity and composition. Our studies suggest that AOTs lyse cells via membrane permeabilization and that hydrophobicity and macromolecular conformation are key properties that regulate AOT activity. Some of our AOTs show highly promising antibacterial activity (MIC ∼ 0.5-5 µM) against clinically relevant pathogens in the presence of serum, with little to no toxicity against RBCs and HEK293 cells. Taken together, our data identify design parameters and criteria that may be useful for assembling the next generation of potent and selective AOTs.

Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array.

Scalable, high-throughput DNA sequencing is a prerequisite for precision medicine and biomedical research. Recently, we presented a nanopore-based sequencing-by-synthesis (Nanopore-SBS) approach, which used a set of nucleotides with polymer tags that allow discrimination of the nucleotides in a biological nanopore. Here, we designed and covalently coupled a DNA polymerase to an α-hemolysin (αHL) heptamer using the SpyCatcher/SpyTag conjugation approach. These porin-polymerase conjugates were inserted into lipid bilayers on a complementary metal oxide semiconductor (CMOS)-based electrode array for high-throughput electrical recording of DNA synthesis. The designed nanopore construct successfully detected the capture of tagged nucleotides complementary to a DNA base on a provided template. We measured over 200 tagged-nucleotide signals for each of the four bases and developed a classification method to uniquely distinguish them from each other and background signals. The probability of falsely identifying a background event as a true capture event was less than 1.2%. In the presence of all four tagged nucleotides, we observed sequential additions in real time during polymerase-catalyzed DNA synthesis. Single-polymerase coupling to a nanopore, in combination with the Nanopore-SBS approach, can provide the foundation for a low-cost, single-molecule, electronic DNA-sequencing platform.

Sequence-defined bioactive macrocycles via an acid-catalysed cascade reaction.

Synthetic macrocycles derived from sequence-defined oligomers are a unique structural class whose ring size, sequence and structure can be tuned via precise organization of the primary sequence. Similar to peptides and other peptidomimetics, these well-defined synthetic macromolecules become pharmacologically relevant when bioactive side chains are incorporated into their primary sequence. In this article, we report the synthesis of oligothioetheramide (oligoTEA) macrocycles via a one-pot acid-catalysed cascade reaction. The versatility of the cyclization chemistry and modularity of the assembly process was demonstrated via the synthesis of >20 diverse oligoTEA macrocycles. Structural characterization via NMR spectroscopy revealed the presence of conformational isomers, which enabled the determination of local chain dynamics within the macromolecular structure. Finally, we demonstrate the biological activity of oligoTEA macrocycles designed to mimic facially amphiphilic antimicrobial peptides. The preliminary results indicate that macrocyclic oligoTEAs with just two-to-three cationic charge centres can elicit potent antibacterial activity against Gram-positive and Gram-negative bacteria.

Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array.

DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5'-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotide-based polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time single-molecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods.

Supramolecular Photochemistry in Solution and on Surfaces: Encapsulation and Dynamics of Guest Molecules and Communication between Encapsulated and Free Molecules.

Supramolecular assemblies that help to preorganize reactant molecules have played an important role in the development of concepts related to the control of excited-state processes. This has led to a persistent search for newer supramolecular systems (hosts), and this review briefly presents our work with octa acid (OA) to a host to control excited-state processes of organic molecules. Octa acid, a water-soluble host, forms 1:1, 2:1, and 2:2 (host-guest) complexes with various organic molecules. A majority of the guest molecules are enclosed within a capsule made up of two molecules of OA whereas OA by itself remains as a monomer or aggregates. Luminescence and (1)H NMR spectroscopy help to characterize the structure and dynamics of these host-guest complexes. The guest molecule as well as the host-guest complex as a whole undergoes various types of motion, suggesting that the guests possess freedom inside the confined space of the octa acid capsule. In addition, the confined guests are not isolated but are able to communicate (energy, electron, and spin) with molecules present closer to the capsule. The host-guest complexes are stable even on solid surfaces such as silica, clay, α-Zr phosphate, TiO2, and gold nanoparticles. This opens up new opportunities to explore the interaction between confined guests and active surfaces of TiO2 and gold nanoparticles. In addition, this allows the possibility of performing energy and electron transfer between organic molecules that do not adsorb on inert surfaces of silica, clay, or α-Zr phosphate. The results summarized here, in addition to providing a fundamental understanding of the behavior of molecules in a confined space provided by the host OA, are likely to have a long-range effect on the capture and release of solar energy.

Sequence-defined polymers via orthogonal allyl acrylamide building blocks.

Biological systems have long recognized the importance of macromolecular diversity and have evolved efficient processes for the rapid synthesis of sequence-defined biopolymers. However, achieving sequence control via synthetic methods has proven to be a difficult challenge. Herein we describe efforts to circumvent this difficulty via the use of orthogonal allyl acrylamide building blocks and a liquid-phase fluorous support for the de novo design and synthesis of sequence-specific polymers. We demonstrate proof-of-concept via synthesis and characterization of two sequence-isomeric 10-mer polymers. (1)H NMR and LCMS were used to confirm their chemical structure while tandem MS was used to confirm sequence identity. Further validation of this methodology was provided via the successful synthesis of a sequence-specific 16-mer polymer incorporating nine different monomers. This strategy thus shows promise as an efficient approach for the assembly of sequence-specific functional polymers.

Synthetic versus natural receptors: supramolecular control of chemical sensing in fish.

The encapsulation of odorants by the synthetic receptor cucurbit[7]uril (CB[7]) reduces the response of olfactory receptors in Mozambique tilapia (Oreochromis mossambicus) in vivo. For example, the olfactory receptor response to the odorant adamantan-1-amine, as measured by electro-olfactography, was suppressed by 92% in the presence of CB[7]. A reduction in olfactory response of 88% was observed for pentane-1,5-diamine (cadaverine), an odorant associated with carrion avoidance in some fish. The results reveal how the association constants and the concentrations of natural and synthetic receptors play a determinant role and show that synthetic receptors can be used to remove bioactive molecules from fish olfaction.

Phototransformation of benzimidazole and thiabendazole inside cucurbit[8]uril.

The phototransformation of benzimidazole (BZ) and of the benzimidazole pesticide thiabendazole (TBZ) was investigated in aqueous solution in the absence and presence of the supramolecular host cucurbit[8]uril (CB8). ESI-MS and NMR reveal that both compounds form stable 1 : 2 host-guest complexes with CB8 (BZ2@CB8, TBZ2@CB8). The phototransformation of free BZ leads to dehydrodimerization, while for TBZ the photoreactivity leads to BZ, benzimidazole-2-carboximide and 2-acetylbenzimidazole. Inside CB8, BZ undergoes photohydrolysis to form 2-aminoformanilide, while for TBZ2@CB8 additional photoproducts were observed which are pH dependent. At pH 1.2 photolysis of TBZ2@CB8 leads to new red-shifted photoproducts with extended π conjugation.