A Multifaceted Computational Approach to Understanding the MERS-CoV Main Protease and Brown Algae Compounds’ Interaction
Middle East Respiratory Syndrome (MERS) is a viral respiratory disease caused b a special type of coronavirus called MERS-CoV. In the search for effective substances against the MERS-CoV main protease, we looked into compounds from brown algae, known for their medicinal benefits. From a set of 1212...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-11-01
|
| Series: | Marine Drugs |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1660-3397/21/12/626 |
| _version_ | 1797380205621280768 |
|---|---|
| author | Hattan S. Gattan Maha Mahmoud Alawi Leena H. Bajrai Thamir A. Alandijany Isra M. Alsaady Mai M. El-Daly Vivek Dhar Dwivedi Esam I. Azhar |
| author_facet | Hattan S. Gattan Maha Mahmoud Alawi Leena H. Bajrai Thamir A. Alandijany Isra M. Alsaady Mai M. El-Daly Vivek Dhar Dwivedi Esam I. Azhar |
| author_sort | Hattan S. Gattan |
| collection | DOAJ |
| description | Middle East Respiratory Syndrome (MERS) is a viral respiratory disease caused b a special type of coronavirus called MERS-CoV. In the search for effective substances against the MERS-CoV main protease, we looked into compounds from brown algae, known for their medicinal benefits. From a set of 1212 such compounds, our computer-based screening highlighted four—CMNPD27819, CMNPD1843, CMNPD4184, and CMNPD3156. These showed good potential in how they might attach to the MERS-CoV protease, comparable to a known inhibitor. We confirmed these results with multiple computer tests. Studies on the dynamics and steadiness of these compounds with the MERS-CoV protease were performed using molecular dynamics (MD) simulations. Metrics like RMSD and RMSF showed their stability. We also studied how these compounds and the protease interact in detail. An analysis technique, PCA, showed changes in atomic positions over time. Overall, our computer studies suggest brown algae compounds could be valuable in fighting MERS. However, experimental validation is needed to prove their real-world effectiveness. |
| first_indexed | 2024-03-08T20:34:59Z |
| format | Article |
| id | doaj.art-8c911907ce954895aa447b298274fb52 |
| institution | Directory Open Access Journal |
| issn | 1660-3397 |
| language | English |
| last_indexed | 2024-03-08T20:34:59Z |
| publishDate | 2023-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Marine Drugs |
| spelling | doaj.art-8c911907ce954895aa447b298274fb522023-12-22T14:22:22ZengMDPI AGMarine Drugs1660-33972023-11-01211262610.3390/md21120626A Multifaceted Computational Approach to Understanding the MERS-CoV Main Protease and Brown Algae Compounds’ InteractionHattan S. Gattan0Maha Mahmoud Alawi1Leena H. Bajrai2Thamir A. Alandijany3Isra M. Alsaady4Mai M. El-Daly5Vivek Dhar Dwivedi6Esam I. Azhar7Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi ArabiaSpecial Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi ArabiaSpecial Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi ArabiaSpecial Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi ArabiaSpecial Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi ArabiaSpecial Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi ArabiaCenter for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College and Hospitals, Saveetha University, Chennai 605102, IndiaSpecial Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi ArabiaMiddle East Respiratory Syndrome (MERS) is a viral respiratory disease caused b a special type of coronavirus called MERS-CoV. In the search for effective substances against the MERS-CoV main protease, we looked into compounds from brown algae, known for their medicinal benefits. From a set of 1212 such compounds, our computer-based screening highlighted four—CMNPD27819, CMNPD1843, CMNPD4184, and CMNPD3156. These showed good potential in how they might attach to the MERS-CoV protease, comparable to a known inhibitor. We confirmed these results with multiple computer tests. Studies on the dynamics and steadiness of these compounds with the MERS-CoV protease were performed using molecular dynamics (MD) simulations. Metrics like RMSD and RMSF showed their stability. We also studied how these compounds and the protease interact in detail. An analysis technique, PCA, showed changes in atomic positions over time. Overall, our computer studies suggest brown algae compounds could be valuable in fighting MERS. However, experimental validation is needed to prove their real-world effectiveness.https://www.mdpi.com/1660-3397/21/12/626MERS-CoVbrown algaemain proteasemolecular dynamics |
| spellingShingle | Hattan S. Gattan Maha Mahmoud Alawi Leena H. Bajrai Thamir A. Alandijany Isra M. Alsaady Mai M. El-Daly Vivek Dhar Dwivedi Esam I. Azhar A Multifaceted Computational Approach to Understanding the MERS-CoV Main Protease and Brown Algae Compounds’ Interaction Marine Drugs MERS-CoV brown algae main protease molecular dynamics |
| title | A Multifaceted Computational Approach to Understanding the MERS-CoV Main Protease and Brown Algae Compounds’ Interaction |
| title_full | A Multifaceted Computational Approach to Understanding the MERS-CoV Main Protease and Brown Algae Compounds’ Interaction |
| title_fullStr | A Multifaceted Computational Approach to Understanding the MERS-CoV Main Protease and Brown Algae Compounds’ Interaction |
| title_full_unstemmed | A Multifaceted Computational Approach to Understanding the MERS-CoV Main Protease and Brown Algae Compounds’ Interaction |
| title_short | A Multifaceted Computational Approach to Understanding the MERS-CoV Main Protease and Brown Algae Compounds’ Interaction |
| title_sort | multifaceted computational approach to understanding the mers cov main protease and brown algae compounds interaction |
| topic | MERS-CoV brown algae main protease molecular dynamics |
| url | https://www.mdpi.com/1660-3397/21/12/626 |
| work_keys_str_mv | AT hattansgattan amultifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT mahamahmoudalawi amultifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT leenahbajrai amultifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT thamiraalandijany amultifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT isramalsaady amultifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT maimeldaly amultifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT vivekdhardwivedi amultifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT esamiazhar amultifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT hattansgattan multifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT mahamahmoudalawi multifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT leenahbajrai multifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT thamiraalandijany multifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT isramalsaady multifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT maimeldaly multifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT vivekdhardwivedi multifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction AT esamiazhar multifacetedcomputationalapproachtounderstandingthemerscovmainproteaseandbrownalgaecompoundsinteraction |