Evaluation of Predicted siRNA as an Antiviral against MERS-CoV Targeting the Membrane Gene in the Vero Cell Line
The Middle East respiratory syndrome coronavirus (MERS-CoV) was first isolated from a patient with acute pneumonia and renal failure in Saudi Arabia in 2012. By July 2023, MERS-CoV had resulted in 2605 human cases worldwide, causing a fatality rate of 36%, with 90.2% of cases being located in the Ar...
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MDPI AG
2023-10-01
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| Series: | Microbiology Research |
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| Online Access: | https://www.mdpi.com/2036-7481/14/4/116 |
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| author | Amany Y. El-Sayed Mahmoud Shehata Sara H. Mahmoud Mahmoud ElHefnawi Dina M. Seoudi Mohamed A. Ali |
| author_facet | Amany Y. El-Sayed Mahmoud Shehata Sara H. Mahmoud Mahmoud ElHefnawi Dina M. Seoudi Mohamed A. Ali |
| author_sort | Amany Y. El-Sayed |
| collection | DOAJ |
| description | The Middle East respiratory syndrome coronavirus (MERS-CoV) was first isolated from a patient with acute pneumonia and renal failure in Saudi Arabia in 2012. By July 2023, MERS-CoV had resulted in 2605 human cases worldwide, causing a fatality rate of 36%, with 90.2% of cases being located in the Arabian Peninsula. The dromedary camel (<i>Camelus dromedarius</i>) is presumed to be an intermediate host for viral transmission to humans. So far, no prophylactic vaccines or effective antiviral treatments have been approved for MERS-CoV. RNA silencing is a novel approach for treating several diseases. A web-based bioinformatics tool (i-Score Designer) with integrative computational methods was used to predict and evaluate the designed siRNAs. This approach enabled the targeting of a highly conserved region of the MERS-CoV membrane (M) gene to inhibit virus replication. siRNA-M1, -M2, and -M3 were selected as the best of 559 designed siRNA candidates for an in vitro validation based on 2nd generation algorithm scoring, thermodynamic properties, off-target filtration, position-specific nucleotide preferences, and a free immune-stimulatory motifs. siRNAs were evaluated in Vero cells for their cytotoxicity and antiviral efficacy in vitro. Our results showed that the predicted siRNAs had no apparent cytotoxicity observed in Vero cells. The obtained results from the plaque reduction assay and RT-qPCR indicated that siRNA-M3 was the best candidate to inhibit MERS-CoV replication with a defined concentration of 400 picoMolar (pM). The computational methods used, and the in vitro evaluation, may provide an insight for a new antiviral strategy against MERS-CoV, a further in vivo study will nevertheless be required. |
| first_indexed | 2024-03-08T20:31:58Z |
| format | Article |
| id | doaj.art-7691ca0ff8f24c51b43a2fd621632012 |
| institution | Directory Open Access Journal |
| issn | 2036-7481 |
| language | English |
| last_indexed | 2024-03-08T20:31:58Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microbiology Research |
| spelling | doaj.art-7691ca0ff8f24c51b43a2fd6216320122023-12-22T14:25:05ZengMDPI AGMicrobiology Research2036-74812023-10-011441687170110.3390/microbiolres14040116Evaluation of Predicted siRNA as an Antiviral against MERS-CoV Targeting the Membrane Gene in the Vero Cell LineAmany Y. El-Sayed0Mahmoud Shehata1Sara H. Mahmoud2Mahmoud ElHefnawi3Dina M. Seoudi4Mohamed A. Ali5Center of Scientific Excellence for Influenza Viruses, National Research Centre, Cairo 12622, EgyptCenter of Scientific Excellence for Influenza Viruses, National Research Centre, Cairo 12622, EgyptCenter of Scientific Excellence for Influenza Viruses, National Research Centre, Cairo 12622, EgyptBiomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo 12622, EgyptBiochemistry Department, Faculty of Science, Ain Shams University, Cairo 11566, EgyptCenter of Scientific Excellence for Influenza Viruses, National Research Centre, Cairo 12622, EgyptThe Middle East respiratory syndrome coronavirus (MERS-CoV) was first isolated from a patient with acute pneumonia and renal failure in Saudi Arabia in 2012. By July 2023, MERS-CoV had resulted in 2605 human cases worldwide, causing a fatality rate of 36%, with 90.2% of cases being located in the Arabian Peninsula. The dromedary camel (<i>Camelus dromedarius</i>) is presumed to be an intermediate host for viral transmission to humans. So far, no prophylactic vaccines or effective antiviral treatments have been approved for MERS-CoV. RNA silencing is a novel approach for treating several diseases. A web-based bioinformatics tool (i-Score Designer) with integrative computational methods was used to predict and evaluate the designed siRNAs. This approach enabled the targeting of a highly conserved region of the MERS-CoV membrane (M) gene to inhibit virus replication. siRNA-M1, -M2, and -M3 were selected as the best of 559 designed siRNA candidates for an in vitro validation based on 2nd generation algorithm scoring, thermodynamic properties, off-target filtration, position-specific nucleotide preferences, and a free immune-stimulatory motifs. siRNAs were evaluated in Vero cells for their cytotoxicity and antiviral efficacy in vitro. Our results showed that the predicted siRNAs had no apparent cytotoxicity observed in Vero cells. The obtained results from the plaque reduction assay and RT-qPCR indicated that siRNA-M3 was the best candidate to inhibit MERS-CoV replication with a defined concentration of 400 picoMolar (pM). The computational methods used, and the in vitro evaluation, may provide an insight for a new antiviral strategy against MERS-CoV, a further in vivo study will nevertheless be required.https://www.mdpi.com/2036-7481/14/4/116siRNAMERS-CoVin silicoin vitroantiviral |
| spellingShingle | Amany Y. El-Sayed Mahmoud Shehata Sara H. Mahmoud Mahmoud ElHefnawi Dina M. Seoudi Mohamed A. Ali Evaluation of Predicted siRNA as an Antiviral against MERS-CoV Targeting the Membrane Gene in the Vero Cell Line Microbiology Research siRNA MERS-CoV in silico in vitro antiviral |
| title | Evaluation of Predicted siRNA as an Antiviral against MERS-CoV Targeting the Membrane Gene in the Vero Cell Line |
| title_full | Evaluation of Predicted siRNA as an Antiviral against MERS-CoV Targeting the Membrane Gene in the Vero Cell Line |
| title_fullStr | Evaluation of Predicted siRNA as an Antiviral against MERS-CoV Targeting the Membrane Gene in the Vero Cell Line |
| title_full_unstemmed | Evaluation of Predicted siRNA as an Antiviral against MERS-CoV Targeting the Membrane Gene in the Vero Cell Line |
| title_short | Evaluation of Predicted siRNA as an Antiviral against MERS-CoV Targeting the Membrane Gene in the Vero Cell Line |
| title_sort | evaluation of predicted sirna as an antiviral against mers cov targeting the membrane gene in the vero cell line |
| topic | siRNA MERS-CoV in silico in vitro antiviral |
| url | https://www.mdpi.com/2036-7481/14/4/116 |
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