Highly efficacious and safe neutralizing DNA aptamer of SARS-CoV-2 as an emerging therapy for COVID-19 disease

Abstract

Background The paucity of SARS-CoV-2-specific virulence factors has greatly hampered the therapeutic management of patients with COVID-19 disease. Although available vaccines and approved therapies have shown tremendous benefits, the continuous emergence of new variants of SARS-CoV-2 and side effects of existing treatments continue to challenge therapy, necessitating the development of a novel effective therapy. We have previously shown that our developed novel single-stranded DNA aptamers not only target the trimer S protein of SARS-CoV-2, but also block the interaction between ACE2 receptors and trimer S protein of Wuhan origin, Delta, Delta plus, Alpha, Lambda, Mu, and Omicron variants of SARS-CoV-2. We herein performed in vivo experiments that administer the aptamer to the lungs by intubation as well as in vitro studies utilizing PBMCs to prove the efficacy and safety of our most effective aptamer, AYA2012004_L. Methods In vivo studies were conducted in transgenic mice expressing human ACE2 (K18hACE2), C57BL/6J, and Balb/cJ. Flow cytometry was used to check S-protein expressing pseudo-virus-like particles (VLP) uptake by the lung cells and test the immuogenicity of AYA2012004_L. Ames test was used to assess mutagenicity of AYA2012004_L. RT-PCR and histopathology were used to determine the biodistribution and toxicity of AYA2012004_L in vital organs of mice. Results We measured the in vivo uptake of VLPs by lung cells by detecting GFP signal using flow cytometry. AYA2012004_L specifically neutralized VLP uptake and also showed no inflammatory response in mice lungs. In addition, AYA2012004_L did not induce inflammatory response in the lungs of Th1 and Th2 mouse models as well as human PBMCs. AYA2012004_L was detectable in mice lungs and noticeable in insignificant amounts in other vital organs. Accumulation of AYA2012004_L in organs decreased over time. AYA2012004_L did not induce degenerative signs in tissues as seen by histopathology and did not cause changes in the body weight of mice. Ames test also certified that AYA2012004_L is non-mutagenic and proved it to be safe for in vivo studies. Conclusions Our aptamer is safe, effective, and can neutralize the uptake of VLPs by lung cells when administered locally suggesting that it can be used as a potential therapeutic agent for COVID-19 management.

Inhibition of SARS-CoV-2 infection in human airway epithelium with a xeno-nucleic acid aptamer

“…Recently, several aptamers to the spike protein of SARS-CoV-2 have been characterized ([ 6 – 16 ]; Reviewed in: [ 17 , 18 ]). The majority are composed of DNA with the exceptions being a coupled peptide/DNA aptamer [ 42 ], an RNA/2′-fluoro RNA (F-RNA) mixed aptamer [ 9 ], and the FANA R8-9 aptamer used in this research [ 15 ].…”

“…Importantly, beyond potential XNA-mediated effects, SARS-CoV-2 spike aptamers have been shown to block pseudovirus or live virus [ 9 ] infections in cell culture and the respiratory tract of ACE2 transgenic mice [ 16 ]. However, there is a clear need to examine aptamers in models that more closely mimic human physiology, an approach already being used to test other potential SARS-CoV-2 inhibitors [ 46 ].…”

“…Aptamers have the potential to block virus entry into cells or detect specific viruses in diagnostic assays (reviewed in [ 4 , 5 ]). Several groups have produced DNA aptamers that bind to the SARS-CoV-2 S1 protein (a subunit of the viral spike protein found on the outer surface of the virus envelope) and block the interaction between the receptor binding domain (RBD) of S1 and the host cell receptor, angiotensin-converting enzyme 2 (ACE2) [ 6 – 16 ]; (Reviewed in: [ 17 , 18 ]). Blocking this interaction prevents virus entry into cells, similar to how current neutralizing antibody therapies block SARS-CoV-2 infection (Reviewed in [ 19 ]).…”

Inhibition of SARS-CoV-2 Infection in Human Airway Epithelium with a Xeno-Nucleic Acid Aptamer

“…Recently, several aptamers to the spike protein of SARS-CoV-2 have been characterized [6][7][8][9][10][11][12][13][14][15][16]Reviewed in: 17,18].…”

New High-Affinity Thrombin Aptamers for Advancing Coagulation Therapy: Balancing Thrombin Inhibition for Clot Prevention and Effective Bleeding Management with Antidote

“…The mutagenic potential of AYA1809002 and AYA1809004 was evaluated using the Ames test with the Xenometrix Ames MPF PENTA I kit, including S9 and Positive Controls (Aniara Diagnostica, code: AC01-512-S2-P; manufacturer’s part number: C01-512-S2-P, West Chester Township, OH). The assay procedure followed the protocol outlined in our previous publication [ 34 ].…”