Computational Exploration of Licorice for Lead Compounds against <i>Plasmodium vivax</i> Duffy Binding Protein Utilizing Molecular Docking and Molecular Dynamic Simulation
<i>Plasmodium vivax</i> (<i>P. vivax</i>) is one of the human’s most common malaria parasites. <i>P. vivax</i> is exceedingly difficult to control and eliminate due to the existence of extravascular reservoirs and recurring infections from latent liver stages. Tra...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-04-01
|
| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/28/8/3358 |
| _version_ | 1797604127421759488 |
|---|---|
| author | Muhammad Yasir Jinyoung Park Eun-Taek Han Won Sun Park Jin-Hee Han Yong-Soo Kwon Hee-Jae Lee Wanjoo Chun |
| author_facet | Muhammad Yasir Jinyoung Park Eun-Taek Han Won Sun Park Jin-Hee Han Yong-Soo Kwon Hee-Jae Lee Wanjoo Chun |
| author_sort | Muhammad Yasir |
| collection | DOAJ |
| description | <i>Plasmodium vivax</i> (<i>P. vivax</i>) is one of the human’s most common malaria parasites. <i>P. vivax</i> is exceedingly difficult to control and eliminate due to the existence of extravascular reservoirs and recurring infections from latent liver stages. Traditionally, licorice compounds have been widely investigated against viral and infectious diseases and exhibit some promising results to combat these diseases. In the present study, computational approaches are utilized to study the effect of licorice compounds against <i>P. vivax</i> Duffy binding protein (DBP) to inhibit the malarial invasion to human red blood cells (RBCs). The main focus is to block the DBP binding site to Duffy antigen receptor chemokines (DARC) of RBC to restrict the formation of the DBP–DARC complex. A molecular docking study was performed to analyze the interaction of licorice compounds with the DARC binding site of DBP. Furthermore, the triplicates of molecular dynamic simulation studies for 100 ns were carried out to study the stability of representative docked complexes. The leading compounds such as licochalcone A, echinatin, and licochalcone B manifest competitive results against DBP. The blockage of the active region of DBP resulting from these compounds was maintained throughout the triplicates of 100 ns molecular dynamic (MD) simulation, maintaining stable hydrogen bond formation with the active site residues of DBP. Therefore, the present study suggests that licorice compounds might be good candidates for novel agents against DBP-mediated RBC invasion of <i>P. vivax</i>. |
| first_indexed | 2024-03-11T04:42:58Z |
| format | Article |
| id | doaj.art-e0ba13d5c0da4bfc8b0b275ef6b7cf1d |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-11T04:42:58Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-e0ba13d5c0da4bfc8b0b275ef6b7cf1d2023-11-17T20:37:49ZengMDPI AGMolecules1420-30492023-04-01288335810.3390/molecules28083358Computational Exploration of Licorice for Lead Compounds against <i>Plasmodium vivax</i> Duffy Binding Protein Utilizing Molecular Docking and Molecular Dynamic SimulationMuhammad Yasir0Jinyoung Park1Eun-Taek Han2Won Sun Park3Jin-Hee Han4Yong-Soo Kwon5Hee-Jae Lee6Wanjoo Chun7Department of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of KoreaDepartment of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of KoreaDepartment of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon 24341, Republic of KoreaDepartment of Physiology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of KoreaDepartment of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon 24341, Republic of KoreaCollege of Pharmacy, Kangwon National University School of Medicine, Chuncheon 24341, Republic of KoreaDepartment of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of KoreaDepartment of Pharmacology, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea<i>Plasmodium vivax</i> (<i>P. vivax</i>) is one of the human’s most common malaria parasites. <i>P. vivax</i> is exceedingly difficult to control and eliminate due to the existence of extravascular reservoirs and recurring infections from latent liver stages. Traditionally, licorice compounds have been widely investigated against viral and infectious diseases and exhibit some promising results to combat these diseases. In the present study, computational approaches are utilized to study the effect of licorice compounds against <i>P. vivax</i> Duffy binding protein (DBP) to inhibit the malarial invasion to human red blood cells (RBCs). The main focus is to block the DBP binding site to Duffy antigen receptor chemokines (DARC) of RBC to restrict the formation of the DBP–DARC complex. A molecular docking study was performed to analyze the interaction of licorice compounds with the DARC binding site of DBP. Furthermore, the triplicates of molecular dynamic simulation studies for 100 ns were carried out to study the stability of representative docked complexes. The leading compounds such as licochalcone A, echinatin, and licochalcone B manifest competitive results against DBP. The blockage of the active region of DBP resulting from these compounds was maintained throughout the triplicates of 100 ns molecular dynamic (MD) simulation, maintaining stable hydrogen bond formation with the active site residues of DBP. Therefore, the present study suggests that licorice compounds might be good candidates for novel agents against DBP-mediated RBC invasion of <i>P. vivax</i>.https://www.mdpi.com/1420-3049/28/8/3358<i>Plasmodium vivax</i>molecular dockingmolecular dynamic simulationDBP inhibition |
| spellingShingle | Muhammad Yasir Jinyoung Park Eun-Taek Han Won Sun Park Jin-Hee Han Yong-Soo Kwon Hee-Jae Lee Wanjoo Chun Computational Exploration of Licorice for Lead Compounds against <i>Plasmodium vivax</i> Duffy Binding Protein Utilizing Molecular Docking and Molecular Dynamic Simulation Molecules <i>Plasmodium vivax</i> molecular docking molecular dynamic simulation DBP inhibition |
| title | Computational Exploration of Licorice for Lead Compounds against <i>Plasmodium vivax</i> Duffy Binding Protein Utilizing Molecular Docking and Molecular Dynamic Simulation |
| title_full | Computational Exploration of Licorice for Lead Compounds against <i>Plasmodium vivax</i> Duffy Binding Protein Utilizing Molecular Docking and Molecular Dynamic Simulation |
| title_fullStr | Computational Exploration of Licorice for Lead Compounds against <i>Plasmodium vivax</i> Duffy Binding Protein Utilizing Molecular Docking and Molecular Dynamic Simulation |
| title_full_unstemmed | Computational Exploration of Licorice for Lead Compounds against <i>Plasmodium vivax</i> Duffy Binding Protein Utilizing Molecular Docking and Molecular Dynamic Simulation |
| title_short | Computational Exploration of Licorice for Lead Compounds against <i>Plasmodium vivax</i> Duffy Binding Protein Utilizing Molecular Docking and Molecular Dynamic Simulation |
| title_sort | computational exploration of licorice for lead compounds against i plasmodium vivax i duffy binding protein utilizing molecular docking and molecular dynamic simulation |
| topic | <i>Plasmodium vivax</i> molecular docking molecular dynamic simulation DBP inhibition |
| url | https://www.mdpi.com/1420-3049/28/8/3358 |
| work_keys_str_mv | AT muhammadyasir computationalexplorationoflicoriceforleadcompoundsagainstiplasmodiumvivaxiduffybindingproteinutilizingmoleculardockingandmoleculardynamicsimulation AT jinyoungpark computationalexplorationoflicoriceforleadcompoundsagainstiplasmodiumvivaxiduffybindingproteinutilizingmoleculardockingandmoleculardynamicsimulation AT euntaekhan computationalexplorationoflicoriceforleadcompoundsagainstiplasmodiumvivaxiduffybindingproteinutilizingmoleculardockingandmoleculardynamicsimulation AT wonsunpark computationalexplorationoflicoriceforleadcompoundsagainstiplasmodiumvivaxiduffybindingproteinutilizingmoleculardockingandmoleculardynamicsimulation AT jinheehan computationalexplorationoflicoriceforleadcompoundsagainstiplasmodiumvivaxiduffybindingproteinutilizingmoleculardockingandmoleculardynamicsimulation AT yongsookwon computationalexplorationoflicoriceforleadcompoundsagainstiplasmodiumvivaxiduffybindingproteinutilizingmoleculardockingandmoleculardynamicsimulation AT heejaelee computationalexplorationoflicoriceforleadcompoundsagainstiplasmodiumvivaxiduffybindingproteinutilizingmoleculardockingandmoleculardynamicsimulation AT wanjoochun computationalexplorationoflicoriceforleadcompoundsagainstiplasmodiumvivaxiduffybindingproteinutilizingmoleculardockingandmoleculardynamicsimulation |