A hydrogel-based in vitro assay for the fast prediction of antibiotic accumulation in Gram-negative bacteria

Richter, Robert; Kamal, Mohamed Ashraf M.; García-Rivera, Mariel A.; Kaspar, Jerome; Junk, Maximilian; Elgaher, Walid A. M.; Srikakulam, Sanjay Kumar; Greß, Alexander; Beckmann, Arnold; Grißmer, Alexander; Meier, Carola; Vielhaber, Michael; Kalinina, Olga; Hirsch, Anna K. H.; Hartmann, Rolf W.; Brönstrup, Mark; Schneider-Daum, Nicole; Lehr, Claus‐Michael

doi:10.1016/j.mtbio.2020.100084

Cited by 10 publications

(19 citation statements)

References 60 publications

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“…A further aim of the consortium is to design and develop informative assays that can provide information about the desired antibacterial effect, together with further characteristics such as target engagement, bacterial penetration characteristics (for example, kinetics of compound permeation through Gram-negative cell envelope models 117 , 118 ) and potential cytotoxicity.…”

Section: Synthetic Hit Compoundsmentioning

confidence: 99%

Towards the sustainable discovery and development of new antibiotics

et al. 2021

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An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations.

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Section: Synthetic Hit Compoundsmentioning

confidence: 99%

Towards the sustainable discovery and development of new antibiotics

et al. 2021

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“…In addition, we are aware that the differences in biophysical characteristics observed in the model membranes compared to those in whole cells have a high influence on permeability. Nevertheless, it has been demonstrated previously that the permeability through much simpler biomaterials qualitatively correlated with respective bacterial accumulation data, [20] demonstrating the high importance of sufficient antibiotic uptake to overall intrabacterial accumulation. (Figure 9) In this study, we found that in vitro permeability coefficients matched in bacterio accumulation best when the permeation model was made of OMV from E. coli BL21 DE3 or E. coli BL21 DE3 Omp8 (Figure 9A,B), while purely PL-containing layers as obtained from liposomes failed to adequately match in vitro permeability with in bacterio accumulation.…”

Section: Comparison Of In Vitro Permeation To In Bacterio Accumulationmentioning

confidence: 68%

“…Such low-concentrated agarose gel has already previously shown no significant separating effect between antibiotics. [20] The gel coating of the vesicle-based models has been investigated by stereomicroscopy and showed throughout all four vesicle types a confluent and concave layer of ≈1 mm minimum thickness (Figure S14, Supporting Information).…”

Section: Preparation Of the Omv-based In Vitro Modelmentioning

confidence: 99%

“…[5][6][7] To help drug developers also optimize their structures toward better cell penetration and enhanced bacterial bioavailability, [8] various approaches have been undertaken, ranging from cell-based assays, [9][10][11][12][13] vesicle swelling assays, [14,15] electrophysiological assays [16,17] to PAMPA-like filter support-based assays coated with different biomaterials. [18][19][20] Only the latter assay type currently offers the opportunity to be employed in high throughput screening. However, the so far employed materials either mimic non-facilitated uptake [18,19] or mainly facilitated uptake [20] while employing either artificial PLs or physiologically irrelevant hydrogels.…”

Section: Introductionmentioning

confidence: 99%

“…[18][19][20] Only the latter assay type currently offers the opportunity to be employed in high throughput screening. However, the so far employed materials either mimic non-facilitated uptake [18,19] or mainly facilitated uptake [20] while employing either artificial PLs or physiologically irrelevant hydrogels. By introducing natural bacterial membrane components such as LPS and porins into such an assay via OMVs, predictive capacity and strain specificity could be increased while the impact of several components on antibiotic translocation can be observed.…”

Section: Introductionmentioning

confidence: 99%

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An Outer Membrane Vesicle‐Based Permeation Assay (OMPA) for Assessing Bacterial Bioavailability

Richter

Kamal

Koch

et al. 2021

Adv Healthcare Materials

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When searching for new antibiotics against Gram-negative bacterial infections, a better understanding of the permeability across the cell envelope and tools to discriminate high from low bacterial bioavailability compounds are urgently needed. Inspired by the phospholipid vesicle-based permeation assay (PVPA), which is designed to predict non-facilitated permeation across phospholipid membranes, outer membrane vesicles (OMVs) of Escherichia coli either enriched or deficient of porins are employed to coat filter supports for predicting drug uptake across the complex cell envelope. OMVs and the obtained in vitro model are structurally and functionally characterized using cryo-TEM, SEM, CLSM, SAXS, and light scattering techniques. In vitro permeability, obtained from the membrane model for a set of nine antibiotics, correlates with reported in bacterio accumulation data and allows to discriminate high from low accumulating antibiotics. In contrast, the correlation of the same data set generated by liposome-based comparator membranes is poor. This better correlation of the OMV-derived membranes points to the importance of hydrophilic membrane components, such as lipopolysaccharides and porins, since those features are lacking in liposomal comparator membranes. This approach can offer in the future a high throughput screening tool with high predictive capacity or can help to identify compound-and bacteria-specific passive uptake pathways.

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Functional Materials to Overcome Bacterial Barriers and Models to Advance Their Development

Bali

Kamal

Mulla

et al. 2023

Adv Funct Materials

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With the emerging problem of antimicrobial resistance, the world is facing a slow but dangerous pandemic. While the discovery of novel antibiotics is reaching a nearly exhaustive end, new concepts for anti‐infective drugs are emerging. So‐called pathoblockers aim to de‐weaponize bacteria rather than just killing them. As the target of these molecules is typically located intracellularly, however, hitherto almost unnoticed biological barriers are emerging such as the biofilm matrix, the bacterial cell envelope, efflux pumps, and eventual bacterial metabolism. This leads to a new paradigm that is to maximize bacterial bioavailability. To overcome the bacterial barriers, especially when further optimization of the active molecules is not possible, functional materials are needed to engineer innovative delivery systems. Those may not only enable novel anti‐infective molecules to reach their targets, but will also improve the bacterial bioavailability of existing anti‐infectives. Additionally, there is a need for better infection models that allow studying drug effects on both the bacteria and the host in a relevant manner as needed for rational anti‐infective drug development.

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A hydrogel-based in vitro assay for the fast prediction of antibiotic accumulation in Gram-negative bacteria

Cited by 10 publications

References 60 publications

Towards the sustainable discovery and development of new antibiotics

Towards the sustainable discovery and development of new antibiotics

An Outer Membrane Vesicle‐Based Permeation Assay (OMPA) for Assessing Bacterial Bioavailability

Functional Materials to Overcome Bacterial Barriers and Models to Advance Their Development

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