RNA aptamers for rapid response to COVID-19 variants

ABSTRACT The COVID-19 pandemic caused by SARS-CoV-2 viruses has had an unprecedented disruptive global impact. Although vaccination has been expected to end the spread, the fast mutations have increased the breakthrough infection rates in the fully vaccinated population. RNA viruses are known to have very high rates of mutation and evolution. The high rate of mutation is correlated with virulence modulation and the ability to escape host immunity posting an urgent need for treatments that can keep up with the virus mutations. On the molecular level, spike (S) protein receptor binding domain (RBD) and angiotensin-converting enzyme 2 (ACE2) are key mediators for viral entry, therefore pharmacological disruption of S1 RBD binding to ACE2 could be an effective treatment against SARS-CoV-2. Indeed, neutralization antibodies against the S protein have been developed and are used in clinics. Unfortunately, it is difficult for antibody engineering to keep up with the virus evolution. The Delta variant is twice as contagious as the previous variants, whereas the Omicron variant exhibits more mutations in the spike protein than other variants. These variants have raised CDC's concerns due to the risks of immune escape and increased transmissibility. The need for effective drugs against the fast mutating variants can not be met by antibodies because the production of therapeutic antibodies is time-consuming and costly. In this context, nucleic acid-based aptamers, also known as `chemical antibodies' have the potential to address this challenge. Aptamers are selected using an in vitro chemical combinatorial approach, systematic evolution of ligands by exponential enrichment (SELEX), and offer advantages over antibodies to address the problem of mutating viruses because of the fast selection and chemical production, easy chemical modification, high thermostability, and low immunogenicity. Although RNA aptamer is sensitive to nucleases and renal clearance, 2'-fluoro-pyrimidine modification has significantly increased the resistance nucleases, while multivalent aptamers or conjugation to PEGs can increase aptamer sizes and consequently the circulation time. In our preliminary studies, we have selected a series of RNA aptamers targeting the wild-type SARS-CoV-2 S1RBD protein and invented a proprietary approach to generate chemical-modified serum-stable RNAs at high yield and low cost. The selected aptamers show the universal inhibitory effect to RBD-ACE2 binding for WT and variants (Alpha, Beta, Gamma, and Omicron) but not the Delta variant yet. In this project, we will address the Delta variant and optimize our current aptamers and the new anti-Delta aptamer into a bispecific format (avoid rapid renal clearance). We will reach our goals through the following specific aims:1) Screening and characterization of aptamers against the Delta variant and optimization of aptamers by forming bivalent structures, and 2) Evaluation of the antiviral activity. The antiviral capability will be assessed in pseudovirus as well as live infectious viruses through our established agreement with NIAID. Beyond the specific aptamers, we will establish a platform and our ability for quick responses to virus mutations. In terms of responding to fast-mutating infectious diseases, developing aptamer-based therapeutics as an alternative to antibodies is similar to developing mRNA vaccines over conventional inactivated virus vaccines because both aptamers and mRNAs can be screened/designed quickly.