Sequence-Defined Backbone Modifications Regulate Antibacterial Activity of OligoTEAs

The Functionality of Membrane-Inserting Proteins and Peptides: Curvature Sensing, Generation, and Pore Formation

Proteins and peptides with hydrophobic and amphiphilic segments are responsible for many biological functions. The sensing and generation of membrane curvature are the functions of several protein domains or motifs. While some specific membrane proteins play an essential role in controlling the curvature of distinct intracellular membranes, others participate in various cellular processes such as clathrin-mediated endocytosis, where several proteins sort themselves at the neck of the membrane bud. A few membrane-inserting proteins form nanopores that permeate selective ions and water to cross the membrane. In addition, many natural and synthetic small peptides and protein toxins disrupt the membrane by inducing nonspecific pores in the membrane. The pore formation causes cell death through the uncontrolled exchange between interior and exterior cellular contents. In this article, we discuss the insertion depth and orientation of protein/peptide helices, and their role as a sensor and inducer of membrane curvature as well as a pore former in the membrane. We anticipate that this extensive review will assist biophysicists to gain insight into curvature sensing, generation, and pore formation by membrane insertion.

Mechanism of Action and Resistance Evasion of an Antimicrobial Oligomer against Multidrug-Resistant Gram-Negative Bacteria

The last resort for treating multidrug-resistant (MDR) Pseudomonas aeruginosa and other MDR Gram-negative bacteria is a class of antibiotics called the polymyxins; however, polymyxin-resistant isolates have emerged. In response, antimicrobial peptides (AMPs) and their synthetic mimetics have been investigated as alternative therapeutic options. Oligothioetheramides (oligoTEAs) are a class of synthetic, sequence-defined oligomers composed of N-allylacrylamide monomers and an abiotic dithiol backbone that is resistant to serum degradation. Characteristic of other AMP mimetics, the precise balance between charge and hydrophobicity has afforded cationic oligoTEAs potent antimicrobial activity, particularly for the compound BDT-4G, which consists of a 1,4-butanedithiol backbone and guanidine pendant groups, the latter of which provides a cationic charge at physiological pH. However, the activity and mechanism of cationic oligoTEAs against MDR Gram-negative isolates have yet to be fully investigated. Herein, we demonstrated the potent antimicrobial activity of BDT-4G against clinical isolates of P. aeruginosa with a range of susceptibility profiles, assessed the kinetics of bactericidal activity, and further elucidated its mechanism of action. Activity was also evaluated against a panel of polymyxin-resistant isolates, including intrinsically-resistant species. We demonstrate that BDT-4G can evade some of the mechanisms conferring resistance to polymyxin B and thus may have therapeutic potential.

Using precision polymer chemistry for plastics traceability and governance

Resolving the anonymity of plastic materials is critical for safeguarding the well-being of our natural environments and human health.

Uniform soluble support for the large-scale synthesis of sequence-defined macromolecules

A monodisperse soluble support is used as an effective tool for the large-scale, liquid-phase synthesis of sequence-defined macromolecules. This uniform support allows for direct characterisation and leads to a single peak in mass spectrometry.

PEGylated Oligothioetheramide Prodrugs Activated by Host Serum Proteases

Due to the increasing prominence of antibiotic resistance, novel drug discovery and delivery approaches targeting bacteria are essential. In this work we evaluate a prodrug design to improve the cytotoxic profile of polycationic oligothioetheramides (oligoTEAs), which are promising antimicrobials. Herein we chemically modify the oligoTEA, PDT-4G, with a polyethylene glycol (PEG) and show that 1, 2, and 5 kDa PEGs mitigate cytotoxicity. As PEGylation reduces antibacterial activity, we evaluate two peptide linkers which, unlike oligoTEAs, are susceptible to proteolytic cleavage in serum. To gain insight into the prodrug reactivation, two linkers were tested, the 5-residue peptide sequence LMPTG, and the dipeptide sequence VC-PABC. In the presence of 20 % serum, prodrugs made with the VC-PABC linker successfully inhibited bacterial growth. Overall, we observed reactivation of oligoTEAs facilitated by serum protease cleavage of the peptide linkers. This work opens the door to the future design of antimicrobial prodrugs with tunable release profiles.

Applications of Discrete Synthetic Macromolecules in Life and Materials Science: Recent and Future Trends

In the last decade, the field of sequence-defined polymers and related ultraprecise, monodisperse synthetic macromolecules has grown exponentially. In the early stage, mainly articles or reviews dedicated to the development of synthetic routes toward their preparation have been published. Nowadays, those synthetic methodologies, combined with the elucidation of the structure-property relationships, allow envisioning many promising applications. Consequently, in the past 3 years, application-oriented papers based on discrete synthetic macromolecules emerged. Hence, material science applications such as macromolecular data storage and encryption, self-assembly of discrete structures and foldamers have been the object of many fascinating studies. Moreover, in the area of life sciences, such structures have also been the focus of numerous research studies. Here, it is aimed to highlight these recent applications and to give the reader a critical overview of the future trends in this area of research.

Geared Toward Applications: A Perspective on Functional Sequence-Controlled Polymers

Sequence-controlled polymers are an emerging class of synthetic polymers with a regulated sequence of monomers. In the past decade, tremendous progress has been made in the synthesis of polymers with the sophisticated sequence control approaching the level manifested in biopolymers. In contrast, the exploration of novel functions that can be achieved by controlling synthetic polymer sequences represents an emerging focus in polymer science. This Viewpoint will survey recent advances in the functional applications of sequence-controlled polymers and provide a perspective on the challenges and outlook for pursuing future applications of this fascinating class of macromolecules.

Design of a PEGylated Antimicrobial Prodrug with Species-Specific Activation

The rise of multidrug-resistant (MDR) "superbugs" has created an urgent need to develop new classes of antimicrobial agents to target these organisms. Oligothioetheramides (oligoTEAs) are a unique class of antimicrobial peptide (AMP) mimetics with one promising compound, BDT-4G, displaying potent activity against MDR Pseudomonas aeruginosa clinical isolates. Despite widely demonstrated potency, BDT-4G and other AMP mimetics have yet to enjoy broad preclinical success against systemic infections, primarily due to their cytotoxicity. In this work, we explore a prodrug strategy to render BDT-4G inactive until it is exposed to an enzyme secreted by the targeted bacteria. The prodrug consists of polyethylene glycol (PEG) conjugated to BDT-4G by a peptide substrate. PEG serves to inactivate and reduce the toxicity of BDT-4G by masking its cationic charge and antimicrobial activity is recovered following site-specific cleavage of the short peptide linker by LasA, a virulence factor secreted by P. aeruginosa. This approach concurrently reduces cytotoxicity by greater than 1 order of magnitude in vitro and provides species specificity through the identity of the cleavable linker.

Sequence-controlled and sequence-defined polypeptoids via the Ugi reaction: synthesis and sequence-driven properties

Ugi reaction offers opportunities to facilely access unprecedented sequence control and sequence-driven properties in polypeptoids.

Sequence-defined oligomer as a modular platform for selective sub-picomolar detection and removal of Hg2+

A modular synthetic platform for selective sensing and removal of Hg2+ was developed.

Dual sequence definition increases the data storage capacity of sequence-defined macromolecules

Sequence-defined macromolecules offer applications in the field of data storage. Challenges include synthesising precise and pure sequences, reading stored information and increasing data storage capacity. Herein, the synthesis of dual sequence-defined oligomers and their application for data storage is demonstrated. While applying the well-established Passerini three-component reaction, the degree of definition of the prepared monodisperse macromolecules is improved compared to previous reports by utilising nine specifically designed isocyanide monomers to introduce backbone definition. The monomers are combined with various aldehyde components to synthesise dual-sequence defined oligomers. Thus, the side chains and the backbones of these macromolecules can be varied independently, exhibiting increased molecular diversity and hence data storage capacity per repeat unit. In case of a dual sequence-defined pentamer, 33 bits are achieved in a single molecule. The oligomers are obtained in multigram scale and excellent purity. Sequential read-out by tandem ESI-MS/MS verifies the high data storage capacity of the prepared oligomers per repeat unit in comparison to other sequence defined macromolecules.

From Sequence-Defined Macromolecules to Macromolecular Pin Codes

Dynamic sequence-defined oligomers carrying a chemically written pin code are obtained through a strategy combining multicomponent reactions with the thermoreversible addition of 1,2,4-triazoline-3,5-diones (TADs) to indole substrates. The precision oligomers are specifically designed to be encrypted upon heating as a result of the random reshuffling of the TAD-indole covalent bonds within the backbone, thereby resulting in the scrambling of the encoded information. The encrypted pin code can eventually be decrypted following a second heating step that enables the macromolecular pin code to be deciphered using 1D electrospray ionization-mass spectrometry (ESI-MS). The herein introduced concept of encryption/decryption represents a key advancement compared with current strategies that typically use uncontrolled degradation to erase and tandem mass spectrometry (MS/MS) to analyze, decipher, and read-out chemically encrypted information. Additionally, the synthesized macromolecules are coated onto a high-value polymer material, which demonstrates their potential application as coded product tags for anti-counterfeiting purposes.

Thiol-Ene Networks from Sequence-Defined Polyurethane Macromers

To date, scalability limitations have hindered the exploration and application of sequence-defined polymers in areas such as synthetic plastics, fibers, rubbers, coatings, and composites. Additionally, the impact of sequence on the properties of cross-linked networks remains largely unknown. To address the need for synthetic methods to generate sequence-defined materials in gram quantities, we developed a strategy involving inexpensive and readily functional vanillin-based monomers to assemble sequence-defined polyurethane oligomers via sequential reductive amination and carbamation. Three oligomers were synthesized with monomer sequence precisely dictated by the placement of reactive side chains during the reductive amination reaction. Avoiding excessive chromatographic purification and solid- or liquid-phase supports enabled synthesis of sequence-defined oligomers on the gram-scale. Remarkably, sequence was shown to influence network topology upon cross-linking, as evidenced by sequence-dependent rubbery moduli values. This work provides one of the first examples of a scalable synthetic route toward sequence-defined thermosets that exhibit sequence-dependent properties.

Sequence-defined nucleobase containing oligomers via reversible addition–fragmentation chain transfer single monomer addition

Nucleobase acrylate monomers have been synthesized and monodisperse tetramers with any order of bases are created via single monomer insertion reactions in a RAFT process.

Antibiotic Discovery with Synthetic Fermentation: Library Assembly, Phenotypic Screening, and Mechanism of Action of β-Peptides Targeting Penicillin-Binding Proteins

In analogy to biosynthetic pathways leading to bioactive natural products, synthetic fermentation generates mixtures of molecules from simple building blocks under aqueous, biocompatible conditions, allowing the resulting cultures to be directly screened for biological activity. In this work, a novel β-peptide antibiotic was successfully identified using the synthetic fermentation platform. Phenotypic screening was carried out in an initially random fashion, allowing simple identification of active cultures. Subsequent deconvolution, focused screening, and structure-activity relationship studies led to the identification of a potent antimicrobial peptide, showing strong selectivity for our model system Bacillus subtilis over human HEK293 cells. To determine the antibacterial mechanism of action, a peptide probe bearing a photoaffinity tag was readily synthesized through the use of appropriate synthetic fermentation building blocks and utilized for target identification using a quantitative mass spectrometry-based strategy. The chemoproteomic approach led to the identification of a number of bacterial membrane proteins as prospective targets. These findings were validated through binding affinity studies with penicillin-binding protein 4 using microscale thermophoresis, with the bioactive peptide showing a dissociation constant ( K_d) in the nanomolar range. Through these efforts, we provide a proof of concept for the synthetic fermentation approach presented here as a new strategy for the phenotypic discovery of novel bioactive compounds.

A versatile strategy for the synthesis of sequence-defined peptoids with side-chain and backbone diversity via amino acid building blocks

Designing artificial macromolecules with absolute sequence order is still a long-term challenge in polymer chemistry as opposed to natural biopolymers with perfectly defined sequences like proteins and DNA. Herein, we combined amino acid building blocks and iterative Ugi reactions for the de novo design and synthesis of sequence-defined peptoids. The highly efficient strategy provided excellent yields and enables multigram-scale synthesis of perfectly defined peptoids. This new strategy furnishes the broad structural diversity of side chains, as well as backbones. Importantly, the overall hydrophobicity and lower critical solution temperature (LCST) behaviours of these precisely defined peptoids can be logically altered by variation of the sequence. By following the same Ugi chemistry, these peptoids are also conjugated to DNA in a simple way, facilitating the development of novel therapeutics.

Biophysical Characterization of Cationic Antibacterial Oligothioetheramides

Biophysical analysis into the mechanism of action of membrane-disrupting antibiotics such as antimicrobial peptides (AMPs) and AMP mimetics is necessary to improve our understanding of this promising but relatively untapped class of antibiotics. We evaluate the impact of cationic nature, specifically the presence of guanidine versus amine functional groups using sequence-defined oligothioetheramides (oligoTEAs). Relative to amines, guanidine groups demonstrated improved antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). To understand the mechanism of action, we evaluated membrane interactions by performing a propidium iodide assay and fluorescence microscopy of supported MRSA mimetic bilayers treated with oligoTEAs. Both studies demonstrated membrane disruption, while fluorescence microscopy showed the formation of lipid aggregates. We further analyzed the mechanism using surface plasmon resonance with a recently developed two-state binding model with loss. Our biophysical analysis points to the importance of lipid aggregation for antibacterial activity and suggests that guanidine groups improve antibacterial activity by increasing the extent of lipid aggregation. Altogether, these results verify and rationalize the importance of guanidines for enhanced antibacterial activity of oligoTEAs, and present biophysical phenomena for the design and analysis of additional membrane-active antibiotics.

Sequence and Dispersity Are Determinants of Photodynamic Antibacterial Activity Exerted by Peptidomimetic Oligo(thiophene)s

A library of functionalized oligo(thiophene)s with precisely controlled chain length, regioregularity, sequence, and pendant moieties in the side chains was prepared by iterative convergent/divergent organometallic couplings. The cationic and facially amphiphilic structures were designed to mimic the salient physiochemical features of host defense peptides (HDPs) while concurrently exerting a photodynamic mechanism of antibacterial activity. In the dark, the oligothiophenes exert broad-spectrum and rapid bactericidal activity in the micromolar regime, which is the typical range of HDP activity. Under visible light, the antibacterial potency is enhanced by orders of magnitude, leading to potency in the nanomolar concentration range, whereas the toxicity to red blood cells (RBCs) is almost unaffected by the same visible light exposure. We attribute the potent and selective antibacterial activity to a dual mechanism of action that involves bacterial cell binding, combined with reactive oxygen species production in the bound state. Comonomer sequence and chain length dispersity play important roles in dictating the observed biological activities. The most promising candidate compound from a set of screening experiments showed antibacterial activity that is 3 orders of magnitude more potent against bacteria relative to toxicity against RBCs. Importantly, this compound did not induce resistance upon 21 subinhibitory passages, whereas the activity of ciprofloxacin was reduced 32× in the same condition. Cytotoxicity against HeLa cells in vitro is orders of magnitude weaker than antibacterial activity under visible light illumination. Thus, we have established a new class of HDP-mimetic antibacterial compounds with nanomolar activity and cell type selectivity of greater than 1300-fold. These and related compounds may be highly promising candidates in the urgent search for new topical photodynamic antibacterial formulations.

Sequence-defined non-natural polymers: synthesis and applications

Sequence-defined polymer: A promising gateway for the next generation polymeric materials and vast opportunities for new synthetic strategies, functional diversity and its material and biomedical applications.

Synthetic mimics of cyclic antimicrobial peptides via templated ring-opening metathesis (TROM)

We utilized a templated ring-opening metathesis (TROM) strategy to synthesize a series of precision macrocyclic olefins, each containing two, three or four repeating units of a cyclooctene with pendant carboxylic acid side chains.

A one-pot metal-free protocol for the synthesis of chalcogenated furans from 1,4-enediones and thiols

Transition-metal-free synthesis of chalcogenated furans through the sequential thiol-Michael/Paal–Knorr reaction of 1,4-enediones in the presence of a catalytic amount of p-toluene sulfonic acid has been developed.

Antibacterial isoamphipathic oligomers highlight the importance of multimeric lipid aggregation for antibacterial potency

Cationic charge and hydrophobicity have long been understood to drive the potency and selectivity of antimicrobial peptides (AMPs). However, these properties alone struggle to guide broad success in vivo, where AMPs must differentiate bacterial and mammalian cells, while avoiding complex barriers. New parameters describing the biophysical processes of membrane disruption could provide new opportunities for antimicrobial optimization. In this work, we utilize oligothioetheramides (oligoTEAs) to explore the membrane-targeting mechanism of oligomers, which have the same cationic charge and hydrophobicity, yet show a unique ~ 10-fold difference in antibacterial potency. Solution-phase characterization reveals little difference in structure and dynamics. However, fluorescence microscopy of oligomer-treated Staphylococcus aureus mimetic membranes shows multimeric lipid aggregation that correlates with biological activity and helps establish a framework for the kinetic mechanism of action. Surface plasmon resonance supports the kinetic framework and supports lipid aggregation as a driver of antimicrobial function.

Joseph Brown et al. use oligothioetheramides (oligo TEAs) to show that multimeric lipid aggregation in Staphylococcus aureus mimetic membranes correlates with the biological activity of oligoTEAs. These results may explain why antimicrobial peptides with identical cationic charge and hydrophobicity show different biological activity.

Recent Developments in Solid-Phase Strategies towards Synthetic, Sequence-Defined Macromolecules

Sequence-control in synthetic polymers is an important contemporary research area because it provides the opportunity to create completely novel materials for structure-function studies. This is especially relevant for biomimetic polymers, bioactive and information security materials. The level of control is strongly dependent and inherent upon the polymerization technique utilized. Today, the most established method yielding monodispersity and monomer sequence-definition is solid-phase synthesis. This Focus Review highlights recent advances in solid-phase strategies to access synthetic, sequence-defined macromolecules. Alternatives strategies towards sequence-defined macromolecules are also briefly summarized.

Sensitivity of Antibacterial Activity to Backbone Sequence in Constitutionally Isomeric OligoTEAs

Antimicrobial peptides are promising alternatives to traditional antibiotics but their translational potential is limited due to rapid degradation by serum proteases. Recently, a number of peptidomimetics with backbones resistant to proteolysis have been synthesized and their antimicrobial potential evaluated as a function of their hydrophobic to cationic ratio. However, these mimetics also have a fixed backbone thus making it difficult to isolate the effect of backbone hydrophobic composition and sequence. In this work, advantage is taken of the oligothioetheramide (oligoTEA) synthetic strategy that allows for precise control over backbone and pendant group placement to systematically study the effect of backbone hydrophobic sequence while keeping pendant group constant. Biophysical data acquired with a set of constitutional oligoTEA isomers show that backbone hydrophobic sequence, that is, local hydrophobicity, affects the mode of oligoTEA interaction with lipid bilayers. This differential interaction among the constitutionally isomeric oligoTEAs is manifested in their antibacterial activities and points to the possibility of using backbone hydrophobic sequence to tune antibacterial potency and selectivity.

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.

Effect of Composition on Antibacterial Activity of Sequence-Defined Cationic Oligothioetheramides

In response to the urgent need for new antibiotic development strategies, antimicrobial peptides and their synthetic mimetics are being investigated as promising alternatives to traditional antibiotics. To facilitate their development into clinically viable candidates, we need to understand what molecular features and physicochemical properties are needed to induce cell death. Within the context of sequence-defined oligothioetheramides (oligoTEAs), we explore the impact of the cationic pendant group and backbone hydrophobicity on the potency and selectivity of antibacterial oligoTEAs. Through antibacterial, cytotoxicity, membrane destabilization, and membrane depolarization assays, we find a strong dependency on the nature of the cationic group and improved selectivity toward bacteria by tuning backbone hydrophobicity. In particular, compounds with the guanidinium headgroup are more potent than those with amines. Finally, we identify a promising oligoTEA, PDT-4G, with enhanced activity in vitro (minimum inhibitory concentration (MIC) ∼ 0.78 μM) and moderate activity in a mouse thigh infection model of methicillin-resistant Staphylococcus aureus. The studies outlined in this work provide insights into the effect of macromolecular physicochemical properties on antibacterial potency. This knowledge base will be vital for researchers engaged in the ongoing development of clinically viable antibacterial agents.

A Versatile Approach to Noncanonical, Dynamic Covalent Single- and Multi-Loop Peptide Macrocycles for Enhancing Antimicrobial Activity

Peptide oligomers offer versatile scaffolds for the formation of potent antimicrobial agents due to their high sequence versatility, inherent biocompatibility, and chemical tunability. Though many methods exist for the formation of peptide-based macrocycles (MCs), increasingly pervasive in commercial antimicrobial therapeutics, the introduction of multiple looped structures into a single peptide oligomer remains a significant challenge. Herein, we report the utilization of dynamic hydrazone condensation for the versatile formation of single-, double-, and triple-loop peptide MCs using simple dialdehyde or dihydrazide small-molecule cross-linkers, as confirmed by MALDI-TOF MS, HPLC, and SDS-PAGE. Furthermore, incorporation of aldehyde-containing side chains onto peptides synthesized from hydrazide C-terminal resins resulted in tunable peptide MC assemblies formed directly upon resin cleavage post solid-phase peptide synthesis. Both of these types of dynamic covalent assemblies produced significant enhancements to overall antimicrobial properties when introduced into a known antimicrobial peptide, buforin II, when compared to the original unassembled sequence.

Sequence-definition from controlled polymerization: the next generation of materials

An overview is given on the state-of-the-art in synthesis of sequence-controlled and sequence-defined oligomers and polymers.

Click and Click-Inspired Chemistry for the Design of Sequence-Controlled Polymers

During the previous decade, many popular chemical reactions used in the area of "click" chemistry and similarly efficient "click-inspired" reactions have been applied for the design of sequence-defined and, more generally, sequence-controlled structures. This combination of topics has already made quite a significant impact on scientific research to date and has enabled the synthesis of highly functionalized and complex oligomeric and polymeric structures, which offer the prospect of many exciting further developments and applications in the near future. This minireview highlights the fruitful combination of these two topics for the preparation of sequence-controlled oligomeric and macromolecular structures and showcases the vast number of publications in this field within a relatively short span of time. It is divided into three sections according to the click-(inspired) reaction that has been applied: copper-catalyzed azide-alkyne cycloaddition, thiol-X, and related thiolactone-based reactions, and finally Diels-Alder-chemistry-based routes are outlined, respectively.

Versatile Platform for the Synthesis of Orthogonally Cleavable Heteromultifunctional Cross-Linkers

Cleavable and heteromultifunctional cross-linkers have proven critical in a wide range of biological applications. Traditional approaches for synthesizing these linkers suffer from various synthetic and functional limitations. In this work, an efficient sequence-defined synthetic methodology, developed for the assembly of oligothioetheramides, was used to address many of these limitations. Four heterotrifunctional cross-linkers with up to two orthogonal internal cleavage sites were synthesized. These linkers were conjugated to a pair of fluorophores that undergo Förster resonance energy transfer (FRET) and a model protein-human transferrin. Orthogonal bond cleavage was validated by mass spectrometry, fluorescent gel electrophoresis, and confocal microscopy. These studies demonstrate the versatility and biological utility of oligothioetheramides as a new class of multifunctional chemical cross-linkers and biologically relevant fluorescent probes.