Cationic Amphiphiles with Specificity against Gram-Positive and Gram-Negative Bacteria: Chemical Composition and Architecture Combat Bacterial Membranes

Combinatorial Screening of Cationic Lipidoids Reveals How Molecular Conformation Affects Membrane-Targeting Antimicrobial Activity

The search for next-generation antibacterial compounds that overcome the development of resistance can be facilitated by identifying how to target the cell membrane of bacteria. Understanding the key molecular features that enable interactions with lipids and lead to membrane disruption is therefore crucial. Here, we employ a library of lipid-like compounds (lipidoids) comprising modular structures with tunable hydrophobic and hydrophilic architecture to shed light on how the chemical functionality and molecular shape of synthetic amphiphilic compounds determine their activity against bacterial membranes. Synthesized from combinations of 8 different polyamines as headgroups and 13 acrylates as tails, 104 different lipidoids are tested for activity against a model Gram-positive bacterial strain (Bacillus subtilis). Results from the combinatorial screening assay show that lipidoids with the most potent antimicrobial properties (down to 2 μM) have intermediate tail hydrophobicity (i.e., c log P values between 3 and 4) and lower headgroup charge density (i.e., longer spacers between charged amines). However, the most important factor appeared to be the ability of a lipidoid to self-assemble into an inverse hexagonal liquid crystalline phase, as observed by small-angle X-ray scattering (SAXS) analysis. The lipidoids active at lowest concentrations, which induced the most significant membrane damage during propidium iodide (PI) permeabilization assays, were those that aggregated into highly curved inverse hexagonal liquid crystal phases. These observations suggest that the introduction of strong curvature stress into the membrane is one way to maximize membrane disruption and lipidoid antimicrobial activity. Lipidoids that demonstrated the ability to furnish this phase consisted of either (i) branched or linear headgroups with shorter linear tails or (ii) cyclic headgroups with 4 bulky nonlinear tails. On the contrary, lipidoids previously observed to adopt disc-like conformations that pack into bicontinuous cubic phases were significantly less effective against B. subtilis. The discovery of these structure-property relationships demonstrates that it is not simply a balance of hydrophobic and hydrophilic moieties that govern membrane-active antibacterial activity, but also their intrinsic curvature and collective behavior.

Harnessing the Role of Bacterial Plasma Membrane Modifications for the Development of Sustainable Membranotropic Phytotherapeutics

Membrane-targeted molecules such as cationic antimicrobial peptides (CAMPs) are amongst the most advanced group of antibiotics used against drug-resistant bacteria due to their conserved and accessible targets. However, multi-drug-resistant bacteria alter their plasma membrane (PM) lipids, such as lipopolysaccharides (LPS) and phospholipids (PLs), to evade membrane-targeted antibiotics. Investigations reveal that in addition to LPS, the varying composition and spatiotemporal organization of PLs in the bacterial PM are currently being explored as novel drug targets. Additionally, PM proteins such as Mla complex, MPRF, Lpts, lipid II flippase, PL synthases, and PL flippases that maintain PM integrity are the most sought-after targets for development of new-generation drugs. However, most of their structural details and mechanism of action remains elusive. Exploration of the role of bacterial membrane lipidome and proteome in addition to their organization is the key to developing novel membrane-targeted antibiotics. In addition, membranotropic phytochemicals and their synthetic derivatives have gained attractiveness as popular herbal alternatives against bacterial multi-drug resistance. This review provides the current understanding on the role of bacterial PM components on multidrug resistance and their targeting with membranotropic phytochemicals.

Staphylococcus aureus-targeting peptide/surfactant assemblies for antibacterial therapy

To address the challenge from microbial resistance, this work developed a surfactant with 18-carbon single hydrocarbon chain and multi-amine head groups (C18N3). After assembling with Staphylococcus aureus-targeting peptide (CARG), the obtained C18N3/CARG assemblies exhibited excellent antimicrobial activities against Staphylococcus aureus and methicillin-resistant Staphylococcus aureus in vitro and in vivo, in which the targeting peptide CARG bonded specifically to Staphylococcus aureus and C18N3 killed bacteria with a mechanism of membrane disruption. Importantly, C18N3 could also work as a β-lactamase inhibitor to overcome the bacterial resistance to β-lactam antibiotics through noncompetitive inhibition. The combination of β-lactam antibiotic and C18N3/CARG assemblies more effectively suppressed methicillin-resistant Staphylococcus aureus in vitro and in vivo relative to equivalent dose of free antibiotic or C18N3. Thus, the antibacterial platform of antibiotic-carrying surfactant assemblies bearing bacteria-targeted peptides, in which C18N3 performed dual function, antibacterial agent and β-lactamase inhibitor, may help fight against the difficult-to-treat infections.

Nuisance compounds in cellular assays

Compounds that exhibit assay interference or undesirable mechanisms of bioactivity ("nuisance compounds") are routinely encountered in cellular assays, including phenotypic and high-content screening assays. Much is known regarding compound-dependent assay interferences in cell-free assays. However, despite the essential role of cellular assays in chemical biology and drug discovery, there is considerably less known about nuisance compounds in more complex cell-based assays. In our view, a major obstacle to realizing the full potential of chemical biology will not just be difficult-to-drug targets or even the sheer number of targets, but rather nuisance compounds, due to their ability to waste significant resources and erode scientific trust. In this review, we summarize our collective academic, government, and industry experiences regarding cellular nuisance compounds. We describe assay design strategies to mitigate the impact of nuisance compounds and suggest best practices to efficiently address these compounds in complex biological settings.

Synthesis, Self-Assembly, and Biological Activities of Pyrimidine-Based Cationic Amphiphiles

Pyrimidine-based cationic amphiphiles (PCAms), i.e., di-trifluoroacetic acid salts of N1-[1'-(1″,3″-diglycinatoxy-propane-2″-yl)-1',2',3'-triazole-4'-yl]methyl-N3-alkylpyrimidines have been synthesized utilizing naturally occurring biocompatible precursors, like glycerol, glycine, and uracil/ thymine in good yields. Synthesized PCAms consist of a hydrophilic head group comprising TFA salt of glyceryl 1,3-diglycinate and hydrophobic tail comprising of C-7 and C-12 N3-alkylated uracil or thymine conjugated via a 4-methylene-1,2,3-triazolyl linker. The physicochemical properties of all PCAms, such as critical aggregation concentration, hydrodynamic diameter, shape, and zeta potential (surface charge) were analyzed. These PCAms were also evaluated for their anti-proliferative and anti-tubercular activities. One of the synthesized PCAm exhibited 4- to 75-fold more activity than first-line anti-tubercular drugs streptomycin and isoniazid, respectively, against the multidrug resistant clinical isolate 591 of Mycobacterium tuberculosis.

Cationic amphiphiles against Gardnerella vaginalis resistant strains and bacterial vaginosis-associated pathogens

Antibiotic resistance and infection recurrence are critical issues in treating bacterial vaginosis, the most common vaginal disorder in women of reproductive age. Novel alternatives to traditional antibiotics, such as peptidomimetics, have the potential to address this challenge. Previously, two series of cationic amphiphiles (CAms) were developed with both hydrophilic head groups and non-polar domains, giving them the ability to self-assemble into supramolecular nanostructures with membrane-lytic properties. Those CAms were shown to be effective against biofilms of Gardnerella vaginalis while preserving the commensal microbiota. Two new series of CAms were designed with varying levels of flexibility between the hydrophilic head groups and the hydrophobic domains. Activities against the vaginal pathogen G. vaginalis ranged from 1.3 to 18.5 µM, while the tested vaginal lactobacilli were significantly more tolerant of CAms, with minimal inhibitory concentration values as high as 208 µM. Minimal biofilm bactericidal concentrations of the tested CAms ranged from 21.47 to <388.3 µM, and were lowest against resistant forms of G. vaginalis, while Lactobacillus biofilms were tolerant of concentrations ≥687 µM. Safety aspects of the CAms were also investigated, and they were found to be safe for use against vaginal ectocervical tissue.

Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria

Drug discovery faces a crisis. The industry has used up the "obvious" space in which to find novel drugs for biomedical applications, and productivity is declining. One strategy to combat this is rational approaches to expand the search space without relying on chemical intuition, to avoid rediscovery of similar spaces. In this work, we present proof of concept of an approach to rationally identify a "chemical vocabulary" related to a specific drug activity of interest without employing known rules. We focus on the pressing concern of multidrug resistance in Pseudomonas aeruginosa by searching for submolecules that promote compound entry into this bacterium. By synergizing theory, computation, and experiment, we validate our approach, explain the molecular mechanism behind identified fragments promoting compound entry, and select candidate compounds from an external library that display good permeation ability.

Interplay between Supramolecular and Coordination Interactions in Synthetic Amphiphiles: Triggering Metal Starvation and Anchorage onto MRSA Cell Surface

The present work highlights the implications of supramolecular interaction and metal coordination on the self-assembly behavior and bactericidal potential of salicaldehyde-(C1) and napthaldehyde-based (C2) amphiphiles against methicillin-resistant Staphylococcus aureus (MRSA). LB trough and atomic force microscope (AFM) analysis indicated the propensity of the amphiphiles to form a monolayer as well as spherical aggregates, with the critical micelle concentration (CMC) for C2 (7.0 μM) being lower than C1 (18.5 μM) in water. Formation of an amphiphile-metal complex was evidenced by ESI-MS, FTIR, FETEM-EDX, and ITC analysis. Growth of S. aureus MRSA 100 cells was remarkably impaired in the presence of 5.0 μM C1 or 20 μM C2 as compared to free cells or cells grown in the presence of equivalent levels of amphiphile-metal complexes, suggesting that the amphiphiles perhaps sequester metal and induce metal starvation in MRSA. C1 and C2 rendered superior membrane damage in MRSA and were less toxic to human embryonic kidney (HEK 293) cells as compared to their metal complexes. C1 and C2 rendered a dose-dependent inhibition of S. aureus biofilm formation, while revival of biofilm upon Zn(II) addition suggested that zinc starvation rendered by the amphiphiles may induce biofilm inhibition. C1 imposed a concentration-dependent metal starvation response in MRSA as there was an upregulation of the cntL gene and downregulation of cntA gene, which are involved in synthesis of the zincophore staphylopine (Stp) and transport of the Stp-Zn complex, respectively. ITC analysis revealed that binding of C1 and C2 to staphylococcal lipoteichoic acid (LTA) was stronger than the corresponding Zn(II) complexes, which perhaps accounted for the higher bactericidal potency of the amphiphiles. The study provides a fundamental understanding on how the chemistry-driven multimodal interaction of the amphiphile translates into growth inhibition and metal starvation in MRSA and advances the idea of combating drug resistance in pathogenic bacteria through amphiphiles, which are pluri-active.

Development of an antibacterial surface with a self-defensive and pH-responsive function

In this work, a charge conversion mechanism was introduced to build a bacteria responsive antibacterial surface.