Aptamers as Insights for Targeting SARS-CoV-2
Abstract
:1. Introduction
2. Aptamers
2.1. Artificial Intelligence: An Emerging Approach to Aptamer Selection
2.2. Aptamers against the Virus: Therapeutic and Diagnostic Applications
Aptamer Type | Aptamer Name | Molecular Target | Organism | Effect | Reference |
---|---|---|---|---|---|
Phosphorothioate guanosine-quartets oligonucleotide | T2G4T2 | V3 region of the gp120 protein | HIV | Blocking the virus–cell membrane fusion | [44] |
6-mer sequence d(TGGGAG) | R-95288 | V3 and CD4-binding site of gp120 | HIV | Anti-virus activity in the range of micromolar and low toxicity | [45,46,47,48,49,50] |
RNA | RNA-Tat | TAT | HIV | Even in the presence of a significant abundance of HIV TAR in cell culture, exhibits strong binding to Tat | [41] |
RNA | B40 | Gp120 | HIV | Blockage of the interaction between gp120 and C-C chemokine receptor type 5 | [43] |
DNA | T30695 | Integrase | HIV | HIV-1 integrase inhibition | [61] |
2′-DEOXY-2′-FLUOROARABINONUCLEOTIDE (FANA) | FA1 | RT | HIV RT inhibition | [62] | |
RNA | G6-16 | N53 protein | HCV | N53 inhibition | [63] |
DNA | ZE2 | E2 | HCV | Inhibition of HCV in vitro | [51] |
DNA | C4 | Core protein | HCV | Inhibition of HCV | [64] |
DNA | E10 | HA | Influenza A virus (H5N1) | Receptor-binding inhibition | [54] |
DNA | HA12-16 | Glycosylated HA | Influenza A virus (H5N2) | Prevention of influenza virus infection | [55] |
RNA | S9 | Truncated P protein | HBV | Inhibition of P protein binding | [65] |
DNA | S15 | Envelope protein domain III | DENV-2 | Inhibition of proliferation | [58] |
DNA | GE54 | Glycoprotein | RABV | Inhibition of viral replication | [59] |
RNA | G5 α3N.4 | E7 protein | Human papillomavirus 16 | E7 Inhibition | [66] |
3. Severe Acute Respiratory Syndrome Coronavirus SARS-CoV-2
3.1. Spike Receptor: Its Structure and Mechanism of Binding
3.2. Aptamers against Spike Receptors
Aptamer Type | Aptamer Name | Molecular Target | SELEX Method | Reference |
---|---|---|---|---|
DNA | CoV2-RBD-1C CoV2-RBD-4C | RBD | Bead-based | [89] |
DNA | CoV2-6C3 cb-CoV2-6C3 | RBD | Bead-based | [90] |
DNA | Aptamer-1 Aptamer-2 | RBD | Bead-based | [92] |
DNA | nCoV-S1-Apt1 | RBD, S1 protein | Capillary electrophoresis-based | [8] |
DNA | MSA1 MSA5 | RBD, S1 protein, trimeric S protein | EMSA (electrophoretic mobility shift assay and magnetic bead-based) | [95] |
RNA | RBD-PB6 | RBD | Bead-based | [91] |
DNA | XN-268s | S1 protein | Magnetic bead-based | [96] |
DNA | ST-6 ST-6-1 ST-6-2 | Trimeric S protein | Bead-based | [93] |
DNA | S2A2C1 S1B6C3 | S2 protein, RBD | Bead-based | [97] |
DNA | MSA52 | S1 protein | Electrophoretic mobility shift assay, EMSA-based | [94] |
3.3. Aptamers as Diagnostics for SARS-CoV-2
4. Novel Receptors Promote SARS-CoV-2 Entry into Host Cells
4.1. Alternative Receptors That Mediate SARS-CoV-2 Entry
4.2. Aptamers against Those Receptors
5. Single-Cell Transcriptomics Analysis as a Potential Tool to Define Novel Targets of SARS-CoV-2
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
SARS-CoV-2 | Severe Acute Respiratory Syndrome coronavirus |
COVID-19 | Coronavirus disease 2019 |
MERS-CoV | Middle East Respiratory Syndrome coronavirus |
WHO | World Health Organization |
S | Spike |
ACE 2 | Angiotensin-converting enzyme 2 |
AXL | Anexelekto |
AI | Artificial Intelligence |
SELEX | System evolution of ligand by exponential enrichment |
CoVs | Coronaviruses |
KREMEN1 | Kringle Containing Transmembrane Protein 1 |
HCV | Hepatitis C Virus |
HIV | Human Immunodeficiency Virus |
TMPRSS2 | Type 2 TM serine protease TM protease serine 2 |
S-RBD | Receptor-binding domain |
TM | Transmembrane |
FS | Fusion Peptide |
HR1 | Heptapeptide repeat sequence 1 |
HR2 | Heptapeptide repeat sequence 2 |
RTK | Receptor Tyrosine Kinase |
Gas6 | Growth Arrest Protein 6 |
TAM | TYRO3, AXL, and MERTK Family |
EGFR | Epidermal Growth Factor Receptor |
LDLR | Low-Density Lipoprotein Receptor |
CD147 | Cluster of Differentiation 147 |
ASGR1 | Asialoglycoprotein receptor 1 |
LDLRAD3 | Low-Density Lipoprotein Receptor Class A Domain Containing 3 |
TMEM30A | Transmembrane Protein 30A |
CD209 | Cluster of Differentiation 209 |
CD209L | Cluster of Differentiation 209 Ligand |
L-SIGN | Liver/lymph node-specific intercellular adhesion molecule-3-grabbing integrin |
DC-SIGN | Dendritic Cell-Specific Intercellular Adhesion molecule-3-Grabbing Non-integrin |
CCR5 | C–C chemokine receptor type 5 |
SCAP | Spherical cocktail aptamers–gold nanoparticles |
SERS | Surface-enhanced Raman Spectroscopy |
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Assay | Mechanism | Specificity and Sensitivity | Advantages | Disadvantages | References |
---|---|---|---|---|---|
RT-PCR | Based on the polymerase chain reaction | Sensitivity: 92.7% (4–5 days after infection), 88% (5–14 days after infection), and specificity ~100% | The best available diagnostic test enables the qualitative and quantitative determination of the COVID-19 virus in the downloaded material | -Expensive -Risk of false negative or false positive results -Requires special equipment -Not fast as antigen tests | [102,103] |
Antibody | Monoclonal antibodies detect the host’s antibodies (usually directed against two virus proteins, S and N) | Depends on the detected antibody; average specificity: 75–90% and sensitivity: 77–90% | Helps to detect who previously had COVID-19 or evaluate how the vaccine affected the immune response | -Gives information only about the number of antibodies in the patient’s blood -Does not provide information about how strong the infection is -Does not detect antibodies in early stages of the disease -The level of antibodies does not correspond to the stage of the disease -Risk of cross-reactions and similarity to the SARS-CoV-2 virus sequence to other viruses | [101,104,105] |
Antigen | Detect SARS-CoV-2 proteins | Specificity: 55–100% Sensitivity: 30–100% | Fast time to obtain results, does not require expensive equipment, and is cheap | -False-positive results in patients without symptoms -Accuracy of tests is unknown -These tests are not approved by the WHO for diagnosis | [106] |
Aptamers | Recognize S and N proteins of SARS-CoV-2 | Depending on the aptamer, sensitivity, and specificity are comparable with RT-PCR | Cheaper than RT_PCR, detects virus in early stages, detects small amounts of the virus in the sample, does not require extraction and amplification of the virus’s genetic material, and low cost of tests | -Expensive cost of synthesis aptamers on a big scale (kilograms) | [107,108,109] |
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Karadeniz Saygılı, S.; Szymanowska, A.; Lopez-Berestein, G.; Rodriguez-Aguayo, C.; Amero, P. Aptamers as Insights for Targeting SARS-CoV-2. Biologics 2023, 3, 116-137. https://doi.org/10.3390/biologics3020007
Karadeniz Saygılı S, Szymanowska A, Lopez-Berestein G, Rodriguez-Aguayo C, Amero P. Aptamers as Insights for Targeting SARS-CoV-2. Biologics. 2023; 3(2):116-137. https://doi.org/10.3390/biologics3020007
Chicago/Turabian StyleKaradeniz Saygılı, Suna, Anna Szymanowska, Gabriel Lopez-Berestein, Cristian Rodriguez-Aguayo, and Paola Amero. 2023. "Aptamers as Insights for Targeting SARS-CoV-2" Biologics 3, no. 2: 116-137. https://doi.org/10.3390/biologics3020007