Computational Study of the Phytochemical Constituents from Uncaria tomentosa Stem Bark against SARS-CoV-2 Omicron Spike Protein
The SARS-CoV-2 Omicron variant has spread rapidly and is considered the predominant variant in the world, and its main characteristic is related to evade immunity from natural infection or vaccines, due to its multiple mutations in the spike protein. On the other hand, medicinal plants have been use...
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Wiley
2022-01-01
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| Series: | Journal of Chemistry |
| Online Access: | http://dx.doi.org/10.1155/2022/8539918 |
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| author | Oscar Herrera-Calderon Abdulrahman M. Saleh Andres F. Yepes-Perez Nada H. Aljarba Saad Alkahtani Gaber El-Saber Batiha Renan Dilton Hañari-Quispe Haydee Chavez Josefa Bertha Pari-Olarte Eddie Loyola-Gonzales José Santiago Almeida-Galindo José Francisco Kong-Chirinos Taoufiq Benali |
| author_facet | Oscar Herrera-Calderon Abdulrahman M. Saleh Andres F. Yepes-Perez Nada H. Aljarba Saad Alkahtani Gaber El-Saber Batiha Renan Dilton Hañari-Quispe Haydee Chavez Josefa Bertha Pari-Olarte Eddie Loyola-Gonzales José Santiago Almeida-Galindo José Francisco Kong-Chirinos Taoufiq Benali |
| author_sort | Oscar Herrera-Calderon |
| collection | DOAJ |
| description | The SARS-CoV-2 Omicron variant has spread rapidly and is considered the predominant variant in the world, and its main characteristic is related to evade immunity from natural infection or vaccines, due to its multiple mutations in the spike protein. On the other hand, medicinal plants have been used as alternatives therapies to ameliorate some signs and symptoms in COVID-19, and in our previous work, the cat’s claw (Uncaria tomentosa) stem bark has been studied in vitro and showed antiviral activity on SARS-CoV-2 as well as in silico studies on the 3CLpro protein and as disruptor between the ACE-2 human receptor and the spike protein. The aim in this computational study was to determine the main phytochemical constituents from U. tomentosa stem bark against the SARS-CoV-2 Omicron spike protein based on molecular modeling. A molecular docking was carried out on the isolated phytochemicals in a previous work against the SARS-CoV-2 Omicron spike protein-binding domain (PDB ID: 7T9K). Next, a molecular dynamic study was carried out to monitor the stability during the MD simulations. As results proanthocyanidin-C1 (-10.76 kcal/mol), quinovic acid-type 2 (-9.86 kcal/mol), and proanthocyanidin-B2 (-9.82 kcal/mol) were the constituents with the best binding free energy on the SARS-CoV-2 Omicron spike protein, and the best compound was stable during the dynamic simulation under physiological conditions. It is concluded that the anthocyanidin-based compounds determined in the stem bark ethanol extract could be responsible for the potential antiviral activity on SARS-CoV-2 Omicron variant, and the proanthocyanidin-C1 emerged as a powerful candidate to combat new variants. |
| format | Article |
| id | doaj-art-6f8ce169fbd242238cae1636dc68d99d |
| institution | Kabale University |
| issn | 2090-9071 |
| language | English |
| publishDate | 2022-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Chemistry |
| spelling | doaj-art-6f8ce169fbd242238cae1636dc68d99d2025-02-03T01:06:39ZengWileyJournal of Chemistry2090-90712022-01-01202210.1155/2022/8539918Computational Study of the Phytochemical Constituents from Uncaria tomentosa Stem Bark against SARS-CoV-2 Omicron Spike ProteinOscar Herrera-Calderon0Abdulrahman M. Saleh1Andres F. Yepes-Perez2Nada H. Aljarba3Saad Alkahtani4Gaber El-Saber Batiha5Renan Dilton Hañari-Quispe6Haydee Chavez7Josefa Bertha Pari-Olarte8Eddie Loyola-Gonzales9José Santiago Almeida-Galindo10José Francisco Kong-Chirinos11Taoufiq Benali12Department of PharmacologyPharmaceutical Medicinal Chemistry & Drug Design DepartmentChemistry of Colombian PlantsDepartment of BiologyDepartment of ZoologyDepartment of Pharmacology and TherapeuticsClinical Pathology LaboratoryDepartment of Pharmaceutical ChemistryDepartment of Pharmaceutical ChemistryDepartment of Pharmaceutical SciencesDepartment of Basic SciencesDepartment of Surgical Clinical SciencesEnvironment and Health TeamThe SARS-CoV-2 Omicron variant has spread rapidly and is considered the predominant variant in the world, and its main characteristic is related to evade immunity from natural infection or vaccines, due to its multiple mutations in the spike protein. On the other hand, medicinal plants have been used as alternatives therapies to ameliorate some signs and symptoms in COVID-19, and in our previous work, the cat’s claw (Uncaria tomentosa) stem bark has been studied in vitro and showed antiviral activity on SARS-CoV-2 as well as in silico studies on the 3CLpro protein and as disruptor between the ACE-2 human receptor and the spike protein. The aim in this computational study was to determine the main phytochemical constituents from U. tomentosa stem bark against the SARS-CoV-2 Omicron spike protein based on molecular modeling. A molecular docking was carried out on the isolated phytochemicals in a previous work against the SARS-CoV-2 Omicron spike protein-binding domain (PDB ID: 7T9K). Next, a molecular dynamic study was carried out to monitor the stability during the MD simulations. As results proanthocyanidin-C1 (-10.76 kcal/mol), quinovic acid-type 2 (-9.86 kcal/mol), and proanthocyanidin-B2 (-9.82 kcal/mol) were the constituents with the best binding free energy on the SARS-CoV-2 Omicron spike protein, and the best compound was stable during the dynamic simulation under physiological conditions. It is concluded that the anthocyanidin-based compounds determined in the stem bark ethanol extract could be responsible for the potential antiviral activity on SARS-CoV-2 Omicron variant, and the proanthocyanidin-C1 emerged as a powerful candidate to combat new variants.http://dx.doi.org/10.1155/2022/8539918 |
| spellingShingle | Oscar Herrera-Calderon Abdulrahman M. Saleh Andres F. Yepes-Perez Nada H. Aljarba Saad Alkahtani Gaber El-Saber Batiha Renan Dilton Hañari-Quispe Haydee Chavez Josefa Bertha Pari-Olarte Eddie Loyola-Gonzales José Santiago Almeida-Galindo José Francisco Kong-Chirinos Taoufiq Benali Computational Study of the Phytochemical Constituents from Uncaria tomentosa Stem Bark against SARS-CoV-2 Omicron Spike Protein Journal of Chemistry |
| title | Computational Study of the Phytochemical Constituents from Uncaria tomentosa Stem Bark against SARS-CoV-2 Omicron Spike Protein |
| title_full | Computational Study of the Phytochemical Constituents from Uncaria tomentosa Stem Bark against SARS-CoV-2 Omicron Spike Protein |
| title_fullStr | Computational Study of the Phytochemical Constituents from Uncaria tomentosa Stem Bark against SARS-CoV-2 Omicron Spike Protein |
| title_full_unstemmed | Computational Study of the Phytochemical Constituents from Uncaria tomentosa Stem Bark against SARS-CoV-2 Omicron Spike Protein |
| title_short | Computational Study of the Phytochemical Constituents from Uncaria tomentosa Stem Bark against SARS-CoV-2 Omicron Spike Protein |
| title_sort | computational study of the phytochemical constituents from uncaria tomentosa stem bark against sars cov 2 omicron spike protein |
| url | http://dx.doi.org/10.1155/2022/8539918 |
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