Predicting Antimicrobial Activity of Conjugated Oligoelectrolyte Molecules via Machine Learning.

New antibiotics are needed to battle growing antibiotic resistance, but the development process from hit, to lead, and ultimately to a useful drug takes decades. Although progress in molecular property prediction using machine-learning methods has opened up new pathways for aiding the antibiotics development process, many existing solutions rely on large data sets and finding structural similarities to existing antibiotics. Challenges remain in modeling unconventional antibiotic classes that are drawing increasing research attention. In response, we developed an antimicrobial activity prediction model for conjugated oligoelectrolyte molecules, a new class of antibiotics that lacks extensive prior structure-activity relationship studies. Our approach enables us to predict the minimum inhibitory concentration for E. coli K12, with 21 molecular descriptors selected by recursive elimination from a set of 5305 descriptors. This predictive model achieves an R2 of 0.65 with no prior knowledge of the underlying mechanism. We find the molecular representation optimum for the domain is the key to good predictions of antimicrobial activity. In the case of conjugated oligoelectrolytes, a representation reflecting the three-dimensional shape of the molecules is most critical. Although it is demonstrated with a specific example of conjugated oligoelectrolytes, our proposed approach for creating the predictive model can be readily adapted to other novel antibiotic candidate domains.

Photoswitchable Conjugated Oligoelectrolytes for a Light-Induced Change of Membrane Morphology.

The synthesis of a new conjugated oligoelectrolyte (COE), namely DSAzB, is described, which contains a conjugated core bearing a diazene moiety in the center of its electronically delocalized structure. Similar to structurally related phenylenevinylene-based COEs, DSAzB readily intercalates into model and natural lipid bilayer membranes. Photoinduced isomerization transforms the linear trans COE into a bent or C-shape form. It is thereby possible to introduce DSAzB into the bilayer of a cell and disrupt its integrity by irradiation with light. This leads to controlled permeabilization of membranes, as demonstrated by the release of calcein from DMPG/DMPC vesicles and by propidium iodide influx experiments on S. epidermidis. Both experiments support that the permeabilization is selective for the light stimulus, highly efficient, and repeatable. Target-selective and photoinduced actions demonstrated by DSAzB may have broad applications in biocatalysis and related biotechnologies.

An anti-mycobacterial conjugated oligoelectrolyte effective against Mycobacterium abscessus.

Infections caused by nontuberculous mycobacteria have increased more than 50% in the past two decades and more than doubled in the elderly population. Mycobacterium abscessus (Mab), one of the most prevalent of these rapidly growing species, is intrinsically resistant to numerous antibiotics. Current standard-of-care treatments are not satisfactory, with high failure rate and notable adverse effects. We report here a potent anti-Mab compound from the flexible molecular framework afforded by conjugated oligoelectrolytes (COEs). A screen of structurally diverse, noncytotoxic COEs identified a lead compound, COE-PNH2, which was bactericidal against replicating, nonreplicating persisters and intracellular Mab.COE-PNH2 had low propensity for resistance development, with a frequency of resistance below 1.25 × 10-9 and showed no detectable resistance upon serial passaging. Mechanism of action studies were in line with COE-PNH2 affecting the physical and functional integrity of the bacterial envelope and disrupting the mycomembrane and associated essential bioenergetic pathways. Moreover, COE-PNH2 was well-tolerated and efficacious in a mouse model of Mab lung infection. This study highlights desirable in vitro and in vivo potency and safety index of this COE structure, which represents a promising anti-mycobacterial to tackle an unmet medical need.

Non-photosynthetic bacteria produce photocurrent mediated by NADH.

In recent years, the concern from the global climate change has driven an urgent need to develop clean energy technologies that do not involve combustion process that emit carbon into the atmosphere. A promising concept is microbial fuel cells that utilize bacteria as electron donors in a bio-electrochemical cell performing a direct electron transfer via conductive protein complexes or by secretion of redox active metabolites such as quinone or phenazine derivatives. In the case of photosynthetic bacteria (cyanobacteria) electrons can also be extracted from the photosynthetic pathway mediated mostly by NADH and NADPH. In this work, we show for the first time that the intact non-photosynthetic bacteria Escherichia coli can produce photocurrent that is enhanced upon addition of an exogenous electron mediator. Furthermore, we apply 2D-fluorescence measurement to show that NADH is released from the bacterial cells, which may apply as a native electron mediator in microbial fuel cells.

Structural modulation of membrane-intercalating conjugated oligoelectrolytes decouples outer membrane permeabilizing and antimicrobial activities.

We report a series of membrane-intercalating conjugated oligoelectrolytes (MICOEs) to probe how structural features impact bacterial membrane integrity and antibiotic activity. Minimum inhibitory concentrations (MICs) and outer membrane (OM) permeability correlated to different structural parameters suggesting that the antimicrobial mechanism is not related to OM permeabilization. However, lipid order parameters and MICs correlated to the same structural feature suggesting a possible link.

Amidine-Based Cationic Conjugated Oligoelectrolytes with Antimicrobial Activity against Pseudomonas aeruginosa Biofilms.

Pseudomonas aeruginosa is an opportunistic Gram-negative bacterium that can cause high-morbidity infections. Due to its robust, flexible genome and ability to form biofilms, it can evade and rapidly develop resistance to antibiotics. Cationic conjugated oligoelectrolytes (COEs) have emerged as a promising class of antimicrobials. Herein, we report a series of amidine-containing COEs with high selectivity for bacteria. From this series, we identified 1b as the most active compound against P. aeruginosa (minimum inhibitory concentration (MIC) = 2 µg/mL) with low cytotoxicity (IC50 (HepG2) = 1024 µg/mL). The activity of 1b was not affected by known drug-resistant phenotypes of 100 diverse P. aeruginosa isolates. Moreover, 1b is bactericidal with a low propensity for P. aeruginosa to develop resistance. Furthermore, 1b is also able to inhibit biofilm formation at subinhibitory concentrations and kills P. aeruginosa in established biofilms. The in vivo efficacy of 1b was demonstrated in biofilm-associated murine wound infection models.

Amide Moieties Modulate the Antimicrobial Activities of Conjugated Oligoelectrolytes against Gram-negative Bacteria.

Cationic conjugated oligoelectrolytes (COEs) are a class of compounds that can be tailored to achieve relevant in vitro antimicrobial properties with relatively low cytotoxicity against mammalian cells. Three distyrylbenzene-based COEs were designed containing amide functional groups on the side chains. Their properties were compared to two representative COEs with only quaternary ammonium groups. The optimal compound, COE2-3C-C3-Apropyl, has an antimicrobial efficacy against Escherichia coli with an MIC=2 µg mL-1 , even in the presence of human serum albumin low cytotoxicity (IC50 =740 µg mL-1 ) and minimal hemolytic activity. Moreover, we find that amide groups increase interactions between COEs and a bacterial lipid mimic based on calcein leakage assay and allow COEs to readily permeabilize the cytoplasmic membrane of E. coli. These findings suggest that hydrogen bond forming moieties can be further applied in the molecular design of antimicrobial COEs to further improve their selectivity towards bacteria.

Molecular design of antimicrobial conjugated oligoelectrolytes with enhanced selectivity toward bacterial cells.

A series of cationic conjugated oligoelectrolytes (COEs) was designed to understand how variations in molecular dimensions impact the relative activity against bacteria and mammalian cells. These COEs kept a consistent distyrylbenzene framework but differed in the length of linker between the core and the cationic site and the length of substitute on the quaternary ammonium functioned group. Their antimicrobial efficacy, mammalian cell cytotoxicity, hemolytic activity, and cell association were determined. We find that hydrophobicity is a factor that controls the degree of COE association to cells, but in vitro efficacy and cytotoxicity depend on more subtle structural features. COE2-3C-C4butyl was found to be the optimal structure with a minimum inhibitory concentration (MIC) of 4 µg mL-1 against E. coli K12, low cytotoxicity against HepG2 cells and negligible hemolysis of red blood cells, even at 1024 µg mL-1. A time-kill kinetics study of COE2-3C-C4butyl against E. coli K12 demonstrates bactericidal activity. These findings provide the first systematic investigation of how COEs may be modulated to achieve low mammalian cell cytotoxicity with the long-range perspective of finding candidates suitable for developing a broad-spectrum antimicrobial agent.

Living Bioelectrochemical Composites.

Composites, in which two or more material elements are combined to provide properties unattainable by single components, have a historical record dating to ancient times. Few include a living microbial community as a key design element. A logical basis for enabling bioelectronic composites stems from the phenomenon that certain microorganisms transfer electrons to external surfaces, such as an electrode. A bioelectronic composite that allows cells to be addressed beyond the confines of an electrode surface can impact bioelectrochemical technologies, including microbial fuel cells for power production and bioelectrosynthesis platforms where microbes produce desired chemicals. It is shown that the conjugated polyelectrolyte CPE-K functions as a conductive matrix to electronically connect a three-dimensional network of Shewanella oneidensis MR-1 to a gold electrode, thereby increasing biocurrent ≈150-fold over control biofilms. These biocomposites spontaneously assemble from solution into an intricate arrangement of cells within a conductive polymer matrix. While increased biocurrent is due to more cells in communication with the electrode, the current extracted per cell is also enhanced, indicating efficient long-range electron transport. Further, the biocomposites show almost an order-of-magnitude lower charge transfer resistance than CPE-K alone, supporting the idea that the electroactive bacteria and the conjugated polyelectrolyte work synergistically toward an effective bioelectronic composite.

A Chain-Elongated Oligophenylenevinylene Electrolyte Increases Microbial Membrane Stability.

A novel conjugated oligoelectrolyte (COE) material, named S6, is designed to have a lipid-bilayer stabilizing topology afforded by an extended oligophenylenevinylene backbone. S6 intercalates biological membranes acting as a hydrophobic support for glycerophospholipid acyl chains. Indeed, Escherichia coli treated with S6 exhibits a twofold improvement in butanol tolerance, a relevant feature to achieve within the general context of modifying microorganisms used in biofuel production. Filamentous growth, a morphological stress response to butanol toxicity in E. coli, is observed in untreated cells after incubation with 0.9% butanol (v/v), but is mitigated by S6 treatment. Real-time fluorescence imaging using giant unilamellar vesicles reveals the extent to which S6 counters membrane instability. Moreover, S6 also reduces butanol-induced lipopolysaccharide release from the outer membrane to further maintain cell integrity. These findings highlight a deliberate effort in the molecular design of a chain-elongated COE to stabilize microbial membranes against environmental challenges.