Document text
Principal Investigator: Hong Yan Liu
Organization: DOTQUANT, LLC
Fiscal Year: 2023
Award: $275,482
Funding agency: National Center for Immunization and Respiratory Diseases
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.