DEVELOPMENT OF APTAMER-BASED ENTRY INHIBITORS TARGETING CONSERVED HOST RECEPTORS OF RESPIRATORY VIRUSES

Respiratory viruses represent a significant public health challenge, with both seasonal and emerging pathogens capable of causing severe disease, especially in vulnerable populations. Among these, Human Rhinoviruses (HRVs) and Coronaviruses (CoVs) are notable for their ability to exploit conserved host protein receptors to mediate cellular entry—a feature that presents an attractive target for therapeutic intervention. This thesis focuses on the preclinical development of Aptamer 6 (Apt6), a nucleic acid ligand previously identified in our laboratory for its ability to inhibit coronavirus infection by binding to the human angiotensin-converting enzyme 2 (ACE2) receptor (Villa et al., 2022). To translate Apt6 into a viable therapeutic candidate, we implemented a comprehensive optimization strategy, including metabolic stabilization through chemical modifications and PEGylation, as well as sequence minimization guided by structural modelling. Functional evaluation was carried out using advanced in vitro systems, particularly air–liquid interface (ALI) cultures of human airway epithelium, to assess antiviral efficacy under physiologically relevant conditions. A second aim of the thesis is to validate the aptamer selection pipeline and demonstrate its broader applicability to other conserved viral entry mechanisms. To this end, we initiated a de novo aptamer selection procedure targeting the intercellular adhesion molecule 1 (ICAM1)—the primary receptor for the major group of HRV serotypes. Since ICAM-1 is a conserved entry receptor utilized by a large number of HRVs, its blockade offers a strategic point of intervention. Using an optimized in-house SELEX (Systematic Evolution of Ligands by EXponential enrichment) protocol, we selected and characterized novel aptamers capable of binding ICAM-1 and interfering with HRV entry. Together, these efforts advance the development of aptamer-based antivirals targeting host-virus interactions and highlight the potential of this platform for broader therapeutic applications.