High-Affinity Neutralizing DNA Aptamers against SARS-CoV-2 Spike Protein Variants
The continuous emergence of new variants of concern for SARS-CoV-2 has created a challenge for existing therapies. To address this, we developed a series of single-stranded DNA aptamers that not only bind specifically to the trimer S protein of SARS-CoV-2 but also block the interaction between the t...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-04-01
|
| Series: | COVID |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2673-8112/3/4/38 |
| _version_ | 1797605859525656576 |
|---|---|
| author | Mohamad Ammar Ayass Natalya Griko Victor Pashkov Trivendra Tripathi Wanying Cao Nazanin Javan Jun Dai Jin Zhang Kevin Zhu Lina Abi-Mosleh |
| author_facet | Mohamad Ammar Ayass Natalya Griko Victor Pashkov Trivendra Tripathi Wanying Cao Nazanin Javan Jun Dai Jin Zhang Kevin Zhu Lina Abi-Mosleh |
| author_sort | Mohamad Ammar Ayass |
| collection | DOAJ |
| description | The continuous emergence of new variants of concern for SARS-CoV-2 has created a challenge for existing therapies. To address this, we developed a series of single-stranded DNA aptamers that not only bind specifically to the trimer S protein of SARS-CoV-2 but also block the interaction between the trimer S protein and ACE2 receptors. The systematic evolution of ligands by exponential enrichment (SELEX) was performed to select the aptamers for SARS-CoV-2 trimer S protein. ELISA-based assay and flow cytometry were performed to test the apatmers’ binding and inhibition of trimer S protein in vitro. Binding affinity was measured using surface plasmon resonance. Significance was determined in Prism 9.0 using the one-way ANOVA test (Dunnett’s multiple comparisons test) or two-way ANOVA test (Tukey’s multiple comparisons test) for comparisons. The <i>p</i> values < 0.05 were considered statistically significant. After 12 rounds of SELEX, eight highly enriched aptamers were able to bind to the trimer S protein of the SARS-CoV-2 Wuhan original strain as well as the trimer S proteins of the Delta, Delta plus, Alpha, Lambda, Mu, and Omicron variants, with affinities in the nM range, while also inhibiting their interaction with ACE2 receptors in Vero E6 cells. Modifications to our best aptamer were made by adding forward and reverse primer sequences and truncation. The modified aptamers AYA2012004_L and AYA2012004_L-M1 showed up to 70% inhibition of the binding of virus-like particles (VLPs) expressing S protein to the ACE2 receptor expressed in HEK293T cells. Our findings imply that the selected aptamers can prevent SARS-CoV-2 from entering host cells and hence suppress the viral infection. In addition, the findings suggest that the selected aptamers might be an innovative therapy for the treatment of COVID-19. |
| first_indexed | 2024-03-11T05:07:03Z |
| format | Article |
| id | doaj.art-7afe7e1e30884c60ac7b39bbe12b8b5e |
| institution | Directory Open Access Journal |
| issn | 2673-8112 |
| language | English |
| last_indexed | 2024-03-11T05:07:03Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | COVID |
| spelling | doaj.art-7afe7e1e30884c60ac7b39bbe12b8b5e2023-11-17T18:50:02ZengMDPI AGCOVID2673-81122023-04-013452054210.3390/covid3040038High-Affinity Neutralizing DNA Aptamers against SARS-CoV-2 Spike Protein VariantsMohamad Ammar Ayass0Natalya Griko1Victor Pashkov2Trivendra Tripathi3Wanying Cao4Nazanin Javan5Jun Dai6Jin Zhang7Kevin Zhu8Lina Abi-Mosleh9Ayass Bioscience LLC, Frisco, TX 75034, USAAyass Bioscience LLC, Frisco, TX 75034, USAAyass Bioscience LLC, Frisco, TX 75034, USAAyass Bioscience LLC, Frisco, TX 75034, USAAyass Bioscience LLC, Frisco, TX 75034, USAAyass Bioscience LLC, Frisco, TX 75034, USAAyass Bioscience LLC, Frisco, TX 75034, USAAyass Bioscience LLC, Frisco, TX 75034, USAAyass Bioscience LLC, Frisco, TX 75034, USAAyass Bioscience LLC, Frisco, TX 75034, USAThe continuous emergence of new variants of concern for SARS-CoV-2 has created a challenge for existing therapies. To address this, we developed a series of single-stranded DNA aptamers that not only bind specifically to the trimer S protein of SARS-CoV-2 but also block the interaction between the trimer S protein and ACE2 receptors. The systematic evolution of ligands by exponential enrichment (SELEX) was performed to select the aptamers for SARS-CoV-2 trimer S protein. ELISA-based assay and flow cytometry were performed to test the apatmers’ binding and inhibition of trimer S protein in vitro. Binding affinity was measured using surface plasmon resonance. Significance was determined in Prism 9.0 using the one-way ANOVA test (Dunnett’s multiple comparisons test) or two-way ANOVA test (Tukey’s multiple comparisons test) for comparisons. The <i>p</i> values < 0.05 were considered statistically significant. After 12 rounds of SELEX, eight highly enriched aptamers were able to bind to the trimer S protein of the SARS-CoV-2 Wuhan original strain as well as the trimer S proteins of the Delta, Delta plus, Alpha, Lambda, Mu, and Omicron variants, with affinities in the nM range, while also inhibiting their interaction with ACE2 receptors in Vero E6 cells. Modifications to our best aptamer were made by adding forward and reverse primer sequences and truncation. The modified aptamers AYA2012004_L and AYA2012004_L-M1 showed up to 70% inhibition of the binding of virus-like particles (VLPs) expressing S protein to the ACE2 receptor expressed in HEK293T cells. Our findings imply that the selected aptamers can prevent SARS-CoV-2 from entering host cells and hence suppress the viral infection. In addition, the findings suggest that the selected aptamers might be an innovative therapy for the treatment of COVID-19.https://www.mdpi.com/2673-8112/3/4/38DNA apatmerCOVID-19SARS-CoV-2 virusspike proteinSARS-CoV-2 variantsinnovative therapy |
| spellingShingle | Mohamad Ammar Ayass Natalya Griko Victor Pashkov Trivendra Tripathi Wanying Cao Nazanin Javan Jun Dai Jin Zhang Kevin Zhu Lina Abi-Mosleh High-Affinity Neutralizing DNA Aptamers against SARS-CoV-2 Spike Protein Variants COVID DNA apatmer COVID-19 SARS-CoV-2 virus spike protein SARS-CoV-2 variants innovative therapy |
| title | High-Affinity Neutralizing DNA Aptamers against SARS-CoV-2 Spike Protein Variants |
| title_full | High-Affinity Neutralizing DNA Aptamers against SARS-CoV-2 Spike Protein Variants |
| title_fullStr | High-Affinity Neutralizing DNA Aptamers against SARS-CoV-2 Spike Protein Variants |
| title_full_unstemmed | High-Affinity Neutralizing DNA Aptamers against SARS-CoV-2 Spike Protein Variants |
| title_short | High-Affinity Neutralizing DNA Aptamers against SARS-CoV-2 Spike Protein Variants |
| title_sort | high affinity neutralizing dna aptamers against sars cov 2 spike protein variants |
| topic | DNA apatmer COVID-19 SARS-CoV-2 virus spike protein SARS-CoV-2 variants innovative therapy |
| url | https://www.mdpi.com/2673-8112/3/4/38 |
| work_keys_str_mv | AT mohamadammarayass highaffinityneutralizingdnaaptamersagainstsarscov2spikeproteinvariants AT natalyagriko highaffinityneutralizingdnaaptamersagainstsarscov2spikeproteinvariants AT victorpashkov highaffinityneutralizingdnaaptamersagainstsarscov2spikeproteinvariants AT trivendratripathi highaffinityneutralizingdnaaptamersagainstsarscov2spikeproteinvariants AT wanyingcao highaffinityneutralizingdnaaptamersagainstsarscov2spikeproteinvariants AT nazaninjavan highaffinityneutralizingdnaaptamersagainstsarscov2spikeproteinvariants AT jundai highaffinityneutralizingdnaaptamersagainstsarscov2spikeproteinvariants AT jinzhang highaffinityneutralizingdnaaptamersagainstsarscov2spikeproteinvariants AT kevinzhu highaffinityneutralizingdnaaptamersagainstsarscov2spikeproteinvariants AT linaabimosleh highaffinityneutralizingdnaaptamersagainstsarscov2spikeproteinvariants |