Ali Shivaee
1 
, Samira Asadi Gharibdusti
2, Farkhondeh Pooresmaeil
3, Najmeh Ardeshiri
4, Bahareh Hajikhani
5* , Behnam Hasannejad-Asl
* 1 Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
2 Faculty of Basic Sciences, Department of Biology, Tehran East Branch, Islamic Azad University, Tehran, Iran
3 Cancer Immunology and Immunotherapy Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
4 Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
5 Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Siences, Tehran, Iran
6 Arthropod-Borne Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
Abstract
Introduction: Klebsiella pneumoniae is a major cause of severe pneumonia where dysregulated inflammation contributes to tissue injury. Glycyrrhiza glabra (as known licorice) has long been used in traditional medicine to relieve respiratory conditions such as cough, bronchitis, and pneumonia-like symptoms, suggesting the presence of bioactive constituents with immunomodulatory and anti-inflammatory potential.
Methods: We analyzed single-cell RNA sequencing (scRNA-seq) data (GSE220594) from K. pneumoniae–infected and control samples to define differentially expressed genes (DEGs) across immune cell populations. Gene ontology (GO) and pathway enrichment analyses were then used to characterize immune response pathways. Subsequently, quantitative structure–activity relationship (QSAR) modeling was combined with molecular docking to clarify which licorice-derived phytochemicals might interact with potential key inflammatory triggers identified by DEG signatures. Top ligands were further assessed by all-atom molecular dynamics (MD) simulations to evaluate binding stability and structural dynamics of the ligand–receptor complexes.
Results: We identified 2,633 DEGs across major immune cell subsets. Enrichment analysis suggested strong involvement in cytokine-mediated signaling and host defense responses to bacterial and viral infection. Notably, Guanylate-Binding Protein 5 (GBP5) and its downstream inflammasome-related partners were significantly upregulated, potentially contributing to excessive inflammatory activation. Using QSAR and molecular docking, APIGENIN, NEOISOLIQUIRITIN, and NEOLIQUIRITIN from licorice root emerged as candidate anti-inflammatory compounds, with predicted binding free energies of −7.0, −6.7, and −6.0 kcal/mol against GBP5, respectively. Short MD simulations suggested that the APIGENIN–GBP5 complex is stable, hinting at a possible role in modulating inflammasome activation; however, experimental validation is needed.
Conclusion: This computational investigation suggests that licorice-derived phytochemicals can potentially modulate excessive inflammatory signaling during K. pneumoniae–induced pneumonia. The study provides a foundation for future experimental validation and the development of plant-based adjuvant therapies targeting inflammation in bacterial pneumonia.