Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking
The novel Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is currently one of the most contagious viruses in existence and the cause of the worst pandemic in this century, COVID-19. SARS-CoV-2 infection begins with the recognition of the cellular receptor angiotensin converting enzyme-2...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Beilstein-Institut
2022-07-01
|
| Series: | Beilstein Journal of Nanotechnology |
| Subjects: | |
| Online Access: | https://doi.org/10.3762/bjnano.13.62 |
| _version_ | 1818010690037743616 |
|---|---|
| author | Kendra Ramirez-Acosta Ivan A. Rosales-Fuerte J. Eduardo Perez-Sanchez Alfredo Nuñez-Rivera Josue Juarez Ruben D. Cadena-Nava |
| author_facet | Kendra Ramirez-Acosta Ivan A. Rosales-Fuerte J. Eduardo Perez-Sanchez Alfredo Nuñez-Rivera Josue Juarez Ruben D. Cadena-Nava |
| author_sort | Kendra Ramirez-Acosta |
| collection | DOAJ |
| description | The novel Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is currently one of the most contagious viruses in existence and the cause of the worst pandemic in this century, COVID-19. SARS-CoV-2 infection begins with the recognition of the cellular receptor angiotensin converting enzyme-2 by its spike glycoprotein receptor-binding domain (RBD). Thus, the use of small peptides to neutralize the infective mechanism of SARS-CoV-2 through the RBD is an interesting strategy. The binding ability of 104 peptides (University of Nebraska Medical Center’s Antimicrobial Peptide Database) to the RBD was assessed using molecular docking. Based on the molecular docking results, peptides with great affinity to the RBD were selected. The most common amino acids involved in the recognition of the RBD were identified to design novel peptides based on the number of hydrogen bonds that were formed. At physiological pH, these peptides are almost neutral and soluble in aqueous media. Interestingly, several peptides showed the capability to bind to the active surface area of the RBD of the Wuhan strain, as well as to the RBD of the Delta variant and other SARS-Cov-2 variants. Therefore, these peptides have promising potential in the treatment of the COVID-19 disease caused by different variants of SARS-CoV-2. This research work will be focused on the molecular docking of peptides by molecular dynamics, in addition to an analysis of the possible interaction of these peptides with physiological proteins. This methodology could be extended to design peptides that are active against other viruses. |
| first_indexed | 2024-04-14T05:58:43Z |
| format | Article |
| id | doaj.art-447e2c605f0843cebc353ca685f730b7 |
| institution | Directory Open Access Journal |
| issn | 2190-4286 |
| language | English |
| last_indexed | 2024-04-14T05:58:43Z |
| publishDate | 2022-07-01 |
| publisher | Beilstein-Institut |
| record_format | Article |
| series | Beilstein Journal of Nanotechnology |
| spelling | doaj.art-447e2c605f0843cebc353ca685f730b72022-12-22T02:08:51ZengBeilstein-InstitutBeilstein Journal of Nanotechnology2190-42862022-07-0113169971110.3762/bjnano.13.622190-4286-13-62Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular dockingKendra Ramirez-Acosta0Ivan A. Rosales-Fuerte1J. Eduardo Perez-Sanchez2Alfredo Nuñez-Rivera3Josue Juarez4Ruben D. Cadena-Nava5Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México Departamento de Física, Universidad de Sonora, Blvd. Luis Encinas y Rosales, Hermosillo, Sonora, México Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México The novel Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is currently one of the most contagious viruses in existence and the cause of the worst pandemic in this century, COVID-19. SARS-CoV-2 infection begins with the recognition of the cellular receptor angiotensin converting enzyme-2 by its spike glycoprotein receptor-binding domain (RBD). Thus, the use of small peptides to neutralize the infective mechanism of SARS-CoV-2 through the RBD is an interesting strategy. The binding ability of 104 peptides (University of Nebraska Medical Center’s Antimicrobial Peptide Database) to the RBD was assessed using molecular docking. Based on the molecular docking results, peptides with great affinity to the RBD were selected. The most common amino acids involved in the recognition of the RBD were identified to design novel peptides based on the number of hydrogen bonds that were formed. At physiological pH, these peptides are almost neutral and soluble in aqueous media. Interestingly, several peptides showed the capability to bind to the active surface area of the RBD of the Wuhan strain, as well as to the RBD of the Delta variant and other SARS-Cov-2 variants. Therefore, these peptides have promising potential in the treatment of the COVID-19 disease caused by different variants of SARS-CoV-2. This research work will be focused on the molecular docking of peptides by molecular dynamics, in addition to an analysis of the possible interaction of these peptides with physiological proteins. This methodology could be extended to design peptides that are active against other viruses.https://doi.org/10.3762/bjnano.13.62angiotensin converting enzyme-2 (ace2)antiviral peptideshydrogen bondsmolecular dockingsars-cov-2 rbd |
| spellingShingle | Kendra Ramirez-Acosta Ivan A. Rosales-Fuerte J. Eduardo Perez-Sanchez Alfredo Nuñez-Rivera Josue Juarez Ruben D. Cadena-Nava Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking Beilstein Journal of Nanotechnology angiotensin converting enzyme-2 (ace2) antiviral peptides hydrogen bonds molecular docking sars-cov-2 rbd |
| title | Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking |
| title_full | Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking |
| title_fullStr | Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking |
| title_full_unstemmed | Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking |
| title_short | Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking |
| title_sort | design and selection of peptides to block the sars cov 2 receptor binding domain by molecular docking |
| topic | angiotensin converting enzyme-2 (ace2) antiviral peptides hydrogen bonds molecular docking sars-cov-2 rbd |
| url | https://doi.org/10.3762/bjnano.13.62 |
| work_keys_str_mv | AT kendraramirezacosta designandselectionofpeptidestoblockthesarscov2receptorbindingdomainbymoleculardocking AT ivanarosalesfuerte designandselectionofpeptidestoblockthesarscov2receptorbindingdomainbymoleculardocking AT jeduardoperezsanchez designandselectionofpeptidestoblockthesarscov2receptorbindingdomainbymoleculardocking AT alfredonunezrivera designandselectionofpeptidestoblockthesarscov2receptorbindingdomainbymoleculardocking AT josuejuarez designandselectionofpeptidestoblockthesarscov2receptorbindingdomainbymoleculardocking AT rubendcadenanava designandselectionofpeptidestoblockthesarscov2receptorbindingdomainbymoleculardocking |