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Property space mapping of Pseudomonas aeruginosa permeability to small molecules.

ABSTRACT: Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approach uses mass spectrometric measurements of accumulation of a library of structurally diverse compounds in four isogenic strains of P. aeruginosa with varied permeability barriers. We further developed a machine learning algorithm that generates a deterministic classification model with minimal synonymity between the descriptors. This model predicted good permeators into P. aeruginosa with an accuracy of 89% and precision above 58%. The good permeators are broadly distributed in the property space and can be mapped to six distinct regions representing diverse chemical scaffolds. We posit that this approach can be used for more detailed mapping of the property space and for rational design of compounds with high Gram-negative permeability.

SUBMITTER: Leus IV

PROVIDER: S-EPMC9114115 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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Property space mapping of Pseudomonas aeruginosa permeability to small molecules.

Leus Inga V IV Weeks Jon W JW Bonifay Vincent V Shen Yue Y Yang Liang L Cooper Connor J CJ Nath Dinesh D Duerfeldt Adam S AS Smith Jeremy C JC Parks Jerry M JM Rybenkov Valentin V VV Zgurskaya Helen I HI

Scientific reports 20220517 1

Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approa ...[more]

PMID: 35581346

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Project description:The extremely large number of unique polymer compositions that can be achieved through copolymerisation makes it an attractive strategy for tuning their optoelectronic properties. However, this same attribute also makes it challenging to explore the resulting property space and understand the range of properties that can be realised. In an effort to enable the rapid exploration of this space in the case of binary copolymers, we train a neural network using a tiered data generation strategy to accurately predict the optical and electronic properties of 350 000 binary copolymers that are, in principle, synthesizable from their dihalogen monomers via Yamamoto, or Suzuki-Miyaura and Stille coupling after one-step functionalisation. By extracting general features of this property space that would otherwise be obscured in smaller datasets, we identify simple models that effectively relate the properties of these copolymers to the homopolymers of their constituent monomers, and challenge common ideas behind copolymer design. We find that binary copolymerisation does not appear to allow access to regions of the optoelectronic property space that are not already sampled by the homopolymers, although it conceptually allows for more fine-grained property control. Using the large volume of data available, we test the hypothesis that copolymerisation of 'donor' and 'acceptor' monomers can result in copolymers with a lower optical gap than their related homopolymers. Overall, despite the prevalence of this concept in the literature, we observe that this phenomenon is relatively rare, and propose conditions that greatly enhance the likelihood of its experimental realisation. Finally, through a 'topographical' analysis of the co-polymer property space, we show how this large volume of data can be used to identify dominant monomers in specific regions of property space that may be amenable to a variety of applications, such as organic photovoltaics, light emitting diodes, and thermoelectrics.

Project description:Pseudomonas aeruginosa is a Gram-negative bacterium, which causes opportunistic infections in immuno-compromised individuals. Due to its multiple resistances toward antibiotics, the development of new drugs is required. Interfering with Quorum Sensing (QS), a cell-to-cell communication system, has shown to be highly efficient in reducing P. aeruginosa pathogenicity. One of its QS systems employs Pseudomonas Quinolone Signal (PQS) and 4-hydroxy-2-heptylquinoline (HHQ) as signal molecules. Both activate the transcriptional regulator MvfR (Multiple Virulence Factor Regulator), also called PqsR, driving the production of QS molecules as well as toxins and biofilm formation. The aim of this work was to elucidate the effects of QS inhibitors (QSIs), such as MvfR antagonists and PqsBC inhibitors, on the biosynthesis of the MvfR-regulated small molecules 2'-aminoacetophenone (2-AA), dihydroxyquinoline (DHQ), HHQ, PQS, and 4-hydroxy-2-heptylquinoline-N-oxide (HQNO). The employed synthetic MvfR antagonist fully inhibited pqs small molecule formation showing expected sigmoidal dose-response curves for 2-AA, HQNO, HHQ and PQS. Surprisingly, DHQ levels were enhanced at lower antagonist concentrations followed by a full suppression at higher QSI amounts. This particular bi-phasic profile hinted at the accumulation of a biosynthetic intermediate resulting in the observed overproduction of the shunt product DHQ. Additionally, investigations on PqsBC inhibitors showed a reduction of MvfR natural ligands, while increased 2-AA, DHQ and HQNO levels compared to the untreated cells were detected. Moreover, PqsBC inhibitors did not show any significant effect in PA14 pqsC mutant demonstrating their target selectivity. As 2-AA is important for antibacterial tolerance, the QSIs were evaluated in their capability to attenuate persistence. Indeed, persister cells were reduced along with 2-AA inhibition resulting from MvfR antagonism, but not from PqsBC inhibition. In conclusion, antagonizing MvfR using a dosage capable of fully suppressing this QS system will lead to a favorable therapeutic outcome as DHQ overproduction is avoided and bacterial persistence is reduced.

Dataset Information

Property space mapping of Pseudomonas aeruginosa permeability to small molecules.

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Property space mapping of Pseudomonas aeruginosa permeability to small molecules.

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