Dual-mechanism therapy for chronic rhinosinusitis via siRNA targeting of bacterial 16S rRNA and disruption of CFTR-pathogen interactions

OBJECTIVE(S): This study aimed to develop a dual-mechanism therapeutic strategy for Chronic Rhinosinusitis (CRS) associated with Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) mutations. Specifically, we sought to (1) Design siRNAs targeting conserved regions of the bacterial 16S rRNA gene to reduce pathogen viability and (2) Investigate the interaction between mutant CFTR (PDB: 1XMJ) and a bacterial ribosomal component (PDB: 8SR6) to identify novel inhibitory pathways. METHODS: Computational algorithms were used to design siRNAs complementary to 10 target sites on the 16S rRNA gene. Molecular docking and dynamics simulations analyzed the interaction between mutant CFTR (1XMJ) and the 16S rRNA-associated protein (8SR6). In vitro validation included siRNA transfection into Pseudomonas aeruginosa biofilms and Surface Plasmon Resonance (SPR) assays to quantify 1XMJ-8SR6 binding. Human sinonasal epithelial cells with CFTR mutations were used to model CRS pathophysiology. RESULTS: Multiple siRNA candidates targeting conserved regions of the 16S rRNA gene were identified, exhibiting favorable GC content and predicted high silencing efficacy. Three siRNAs demonstrated >70% silencing efficacy against 16S rRNA, reducing bacterial viability by 60% in biofilms. Docking simulations revealed strong binding affinity (KD = 2.3 nM) between mutant CFTR (1XMJ) and 8SR6, localized to a hotspot region critical for bacterial adhesion. CONCLUSION: The dual targeting of bacterial 16S rRNA via siRNA and disruption of CFTR-pathogen protein interactions presents a promising strategy for CRS treatment, particularly in CFTR-mutation-associated cases. This approach could mitigate antibiotic resistance by directly silencing bacterial genes while modulating host-pathogen crosstalk. Further in vivo validation is warranted to advance translational potential. LEVEL OF EVIDENCE: Level III (Experimental study with laboratory validation).