insight - Computational Biology - # Elucidating Antibiotic Mechanism of Action using Multi-Omics and Proteome Integral Solubility Alteration

Proteome Integral Solubility Alteration Reveals Antibiotic Mechanism of Action for Novel Nitro-Benzoxadiazole Compounds against Helicobacter pylori

Q: How could the multi-omics and PISA-based approach be extended to study the mechanism of action of other antimicrobial compounds, including those with unknown targets

The multi-omics and PISA-based approach can be extended to study the mechanism of action of other antimicrobial compounds, including those with unknown targets, by following a systematic workflow. First, the compounds of interest can be tested on the target bacteria at their respective minimum inhibitory concentrations (MIC) to induce cellular responses. Subsequently, the bacteria can be subjected to multi-omics analysis, including transcriptomics and proteomics, to identify changes in gene expression and protein abundance induced by the compounds. The data obtained from these analyses can then be integrated to identify potential pathways and targets affected by the compounds. In the case of compounds with unknown targets, the PISA assay can be employed to determine intracellular targets by assessing changes in protein solubility upon drug treatment. By combining the results from the PISA assay with the multi-omics data, it is possible to deconvolute the mechanism of action of the compounds and identify potential targets. This integrated approach provides a comprehensive understanding of how antimicrobial compounds interact with bacterial cells and can be applied to unravel the mode of action of novel compounds with unknown targets.

Q: What are the potential limitations and challenges in applying this integrated approach to clinical samples or in vivo models to validate the findings

Applying the integrated multi-omics and PISA-based approach to clinical samples or in vivo models to validate the findings poses several limitations and challenges. One major limitation is the complexity of clinical samples, which may contain a diverse microbial population and host factors that can influence the results. Additionally, the variability in sample collection, processing, and storage can introduce confounding factors that may affect the accuracy and reproducibility of the data. Another challenge is the translation of findings from in vitro studies to in vivo models. In vivo models may not fully recapitulate the complex interactions that occur in a clinical setting, making it challenging to validate the results obtained from laboratory studies. Furthermore, ethical considerations and regulatory requirements must be taken into account when conducting studies in human subjects or animal models. Technical challenges, such as the need for specialized equipment and expertise to perform multi-omics analyses and the high cost associated with these techniques, can also hinder the application of this integrated approach to clinical samples or in vivo models. Standardizing protocols and ensuring quality control measures are in place are essential to overcome these challenges and generate reliable and reproducible data for validation studies.

Q: Could the insights gained from this study on the regulation of virulence factors like CagA be leveraged to develop novel therapeutic strategies against H. pylori infection and associated diseases

The insights gained from this study on the regulation of virulence factors like CagA in H. pylori infection can be leveraged to develop novel therapeutic strategies against the bacterium and associated diseases. Targeting virulence factors, such as CagA, which play a crucial role in the pathogenicity of H. pylori, can lead to the development of more effective and targeted antimicrobial therapies. By understanding how compounds interact with virulence factors and disrupt their function, it is possible to design drugs that specifically inhibit these factors, thereby reducing the pathogenicity of the bacterium. Furthermore, the identification of essential proteins and pathways targeted by the compounds can guide the development of combination therapies that target multiple pathways simultaneously, reducing the likelihood of resistance development. By leveraging the knowledge gained from this study, researchers can design innovative treatment strategies that not only eradicate H. pylori infection but also mitigate the associated diseases, such as gastric cancer, that result from chronic infection with the bacterium.

Core Concepts

A multi-omics approach integrating transcriptomics, proteomics, and Proteome Integral Solubility Alteration (PISA) assay was used to uncover the mechanism of action of novel nitro-benzoxadiazole compounds against the priority pathogen Helicobacter pylori.

Abstract

The study aimed to understand the mechanism of action of a series of novel nitro-benzoxadiazole compounds developed as inhibitors of the essential H. pylori protein flavodoxin. The researchers employed a multi-omics approach combining transcriptomics, proteomics, and the Proteome Integral Solubility Alteration (PISA) assay to delineate the intracellular targets and pathways affected by these compounds.

The key findings are:

Transcriptomics and proteomics analysis revealed widespread changes in gene expression and protein levels upon treatment with the compounds, with limited correlation between mRNA and protein levels.
The PISA assay, applied for the first time in bacteria, identified several key intracellular targets of the compounds, including the virulence factor CagA, cell division proteins FtsA and FtsZ, and the chaperone protein trigger factor.
Weighted Correlation Network Analysis (WGCNA) of the transcriptomics data identified co-expression modules associated with the compounds, revealing pathways related to ATP synthesis, gene expression, and virulence that were affected.
Functional validation experiments demonstrated that the compounds induced oxidative stress, DNA damage, and reduced oxygen consumption, consistent with the identified targets and pathways.

The study showcases how the integration of multi-omics data and the PISA assay can provide a comprehensive understanding of the mechanism of action of antimicrobial compounds, enabling the development of more effective and targeted therapies against priority pathogens like H. pylori.

Customize Summary

Rewrite with AI

Generate Citations

Translate Source

To Another Language

Generate MindMap

from source content

Visit Source

biorxiv.org

Stats

The minimum inhibitory concentrations (MICs) of the compounds are provided in Figure 2(A).
Compound IV: MIC = 0.5 μg/mL
Compound IVa: MIC = 0.5 μg/mL
Compound IVb: MIC = 1 μg/mL
Compound IVj: MIC = 0.25 μg/mL
Compound IVk: MIC = 0.5 μg/mL

Quotes

"Antimicrobial resistance is responsible for an alarming number of deaths, estimated at 5 million per year."
"Understanding the molecular alterations induced by medications is critical for the design of multi-targeting treatments capable of eradicating the infection and mitigating its pathogenicity."
"This study introduces a comprehensive method for understanding drug mechanisms and optimizing the development of multi-targeting antimicrobial therapies."

Key Insights Distilled From

Merging Multi-OMICs with Proteome Integral Solubility Alteration Unveils Antibiotic Mode of Action

by Sancho,J., M... at www.biorxiv.org 09-11-2023

https://www.biorxiv.org/content/10.1101/2023.09.07.556692v2

Deeper Inquiries

How could the multi-omics and PISA-based approach be extended to study the mechanism of action of other antimicrobial compounds, including those with unknown targets

The multi-omics and PISA-based approach can be extended to study the mechanism of action of other antimicrobial compounds, including those with unknown targets, by following a systematic workflow. First, the compounds of interest can be tested on the target bacteria at their respective minimum inhibitory concentrations (MIC) to induce cellular responses. Subsequently, the bacteria can be subjected to multi-omics analysis, including transcriptomics and proteomics, to identify changes in gene expression and protein abundance induced by the compounds. The data obtained from these analyses can then be integrated to identify potential pathways and targets affected by the compounds.
In the case of compounds with unknown targets, the PISA assay can be employed to determine intracellular targets by assessing changes in protein solubility upon drug treatment. By combining the results from the PISA assay with the multi-omics data, it is possible to deconvolute the mechanism of action of the compounds and identify potential targets. This integrated approach provides a comprehensive understanding of how antimicrobial compounds interact with bacterial cells and can be applied to unravel the mode of action of novel compounds with unknown targets.

What are the potential limitations and challenges in applying this integrated approach to clinical samples or in vivo models to validate the findings

Applying the integrated multi-omics and PISA-based approach to clinical samples or in vivo models to validate the findings poses several limitations and challenges. One major limitation is the complexity of clinical samples, which may contain a diverse microbial population and host factors that can influence the results. Additionally, the variability in sample collection, processing, and storage can introduce confounding factors that may affect the accuracy and reproducibility of the data.
Another challenge is the translation of findings from in vitro studies to in vivo models. In vivo models may not fully recapitulate the complex interactions that occur in a clinical setting, making it challenging to validate the results obtained from laboratory studies. Furthermore, ethical considerations and regulatory requirements must be taken into account when conducting studies in human subjects or animal models.
Technical challenges, such as the need for specialized equipment and expertise to perform multi-omics analyses and the high cost associated with these techniques, can also hinder the application of this integrated approach to clinical samples or in vivo models. Standardizing protocols and ensuring quality control measures are in place are essential to overcome these challenges and generate reliable and reproducible data for validation studies.

Could the insights gained from this study on the regulation of virulence factors like CagA be leveraged to develop novel therapeutic strategies against H. pylori infection and associated diseases

The insights gained from this study on the regulation of virulence factors like CagA in H. pylori infection can be leveraged to develop novel therapeutic strategies against the bacterium and associated diseases. Targeting virulence factors, such as CagA, which play a crucial role in the pathogenicity of H. pylori, can lead to the development of more effective and targeted antimicrobial therapies. By understanding how compounds interact with virulence factors and disrupt their function, it is possible to design drugs that specifically inhibit these factors, thereby reducing the pathogenicity of the bacterium.
Furthermore, the identification of essential proteins and pathways targeted by the compounds can guide the development of combination therapies that target multiple pathways simultaneously, reducing the likelihood of resistance development. By leveraging the knowledge gained from this study, researchers can design innovative treatment strategies that not only eradicate H. pylori infection but also mitigate the associated diseases, such as gastric cancer, that result from chronic infection with the bacterium.