A Molecular Docking and Dynamics Simulation Study on Prevention of Merozoite Red Blood Cell Invasion by Targeting Plasmodium vivax Duffy Binding Protein with Zingiberaceae Bioactive Compounds
| Autores principales: | , , , , , |
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| Formato: | Online |
| Idioma: | eng |
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Universidad Nacional, Costa Rica
2024
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| Acceso en línea: | https://www.revistas.una.ac.cr/index.php/uniciencia/article/view/18995 |
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UNICIENCIA18995 |
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ojs |
| institution |
Universidad Nacional de Costa Rica |
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Uniciencia |
| language |
eng |
| format |
Online |
| author |
Fikri Heikal, Muhammad Putra, Wira Eka Sustiprijatno Hidayatullah, Arief Widiastuti, Diana Lelitawati, Mardiana |
| spellingShingle |
Fikri Heikal, Muhammad Putra, Wira Eka Sustiprijatno Hidayatullah, Arief Widiastuti, Diana Lelitawati, Mardiana A Molecular Docking and Dynamics Simulation Study on Prevention of Merozoite Red Blood Cell Invasion by Targeting Plasmodium vivax Duffy Binding Protein with Zingiberaceae Bioactive Compounds |
| author_facet |
Fikri Heikal, Muhammad Putra, Wira Eka Sustiprijatno Hidayatullah, Arief Widiastuti, Diana Lelitawati, Mardiana |
| author_sort |
Fikri Heikal, Muhammad |
| title |
A Molecular Docking and Dynamics Simulation Study on Prevention of Merozoite Red Blood Cell Invasion by Targeting Plasmodium vivax Duffy Binding Protein with Zingiberaceae Bioactive Compounds |
| title_short |
A Molecular Docking and Dynamics Simulation Study on Prevention of Merozoite Red Blood Cell Invasion by Targeting Plasmodium vivax Duffy Binding Protein with Zingiberaceae Bioactive Compounds |
| title_full |
A Molecular Docking and Dynamics Simulation Study on Prevention of Merozoite Red Blood Cell Invasion by Targeting Plasmodium vivax Duffy Binding Protein with Zingiberaceae Bioactive Compounds |
| title_fullStr |
A Molecular Docking and Dynamics Simulation Study on Prevention of Merozoite Red Blood Cell Invasion by Targeting Plasmodium vivax Duffy Binding Protein with Zingiberaceae Bioactive Compounds |
| title_full_unstemmed |
A Molecular Docking and Dynamics Simulation Study on Prevention of Merozoite Red Blood Cell Invasion by Targeting Plasmodium vivax Duffy Binding Protein with Zingiberaceae Bioactive Compounds |
| title_sort |
molecular docking and dynamics simulation study on prevention of merozoite red blood cell invasion by targeting plasmodium vivax duffy binding protein with zingiberaceae bioactive compounds |
| title_alt |
Estudio de simulación dinámica y de acoplamiento molecular sobre la prevención de la invasión de glóbulos rojos de merozoitos atacando la proteína de unión al antígeno Duffy de Plasmodium vivax con compuestos bioactivos de Zingiberáceas Estudo de simulação dinâmica e de acoplamento molecular na prevenção da invasão de glóbulos vermelhos por merozoítos, visando a proteína de ligação Duffy do Plasmodium vivax com compostos bioativos de Zingiberaceae |
| publisher |
Universidad Nacional, Costa Rica |
| publishDate |
2024 |
| url |
https://www.revistas.una.ac.cr/index.php/uniciencia/article/view/18995 |
| work_keys_str_mv |
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UNICIENCIA189952024-10-24T00:06:37Z A Molecular Docking and Dynamics Simulation Study on Prevention of Merozoite Red Blood Cell Invasion by Targeting Plasmodium vivax Duffy Binding Protein with Zingiberaceae Bioactive Compounds Estudio de simulación dinámica y de acoplamiento molecular sobre la prevención de la invasión de glóbulos rojos de merozoitos atacando la proteína de unión al antígeno Duffy de Plasmodium vivax con compuestos bioactivos de Zingiberáceas Estudo de simulação dinâmica e de acoplamento molecular na prevenção da invasão de glóbulos vermelhos por merozoítos, visando a proteína de ligação Duffy do Plasmodium vivax com compostos bioativos de Zingiberaceae Fikri Heikal, Muhammad Putra, Wira Eka Sustiprijatno Hidayatullah, Arief Widiastuti, Diana Lelitawati, Mardiana anti-malaria drug in silico Plasmodium vivax PvDBP Zingiberaceae Medicamento contra la malaria en silicio Plasmodium vivax PvDBP Zingiberáceas Medicamentos antimalária em silício Plasmodium vivax PvDBP Zingiberáceas [Objective] Plasmodium vivax predominantly infects many people in numerous tropical areas, including Southeast Asia, the Western Pacific, the Americas, and the Eastern Mediterranean. The uniqueness of forming dormant stages can lead to relapse in vivax malaria upon further infection. This study used molecular docking and dynamic simulation to predict potential bioactive compounds from the Zingiberaceae plant family as inhibitors by targeting Plasmodium vivax Duffy Binding Protein (PvDBP). PvDBP-DARC molecular interaction is required to mediate the merozoite invasion process into red blood cells. Inhibiting this process can possibly control parasite growth and development. [Methodology] Molecular docking screening was conducted by using 138 natural compounds from the Zingiberaceae plant family targeting Plasmodium vivax Duffy binding protein (PvDBP). The top two compounds with the lowest binding energy were selected to be analyzed by pharmacokinetics prediction and molecular dynamic (MD) simulation. [Results] Molecular docking screening resulted in the top two compounds with the lowest binding energy value, including 5,7-dihydroxyflavanone (-9.3 kcal/mol) and pinostrobin (-9.2 kcal/mol). These compounds are predicted to have stronger interaction than chloroquine as a control. Furthermore, the potential compounds also interact with DARC binding site residues and maintain them during the molecular dynamic simulation process. Otherwise, chloroquine as a control cannot retain 75% binding residues towards PvDBP. A molecular dynamic study revealed that all three complexes have relatively similar stability. [Conclusions] We predicted that the two bioactive compounds (5,7-dihydroxyflavanone and pinostrobin) have the potential as merozoite invasion inhibitors. Objetivo] Plasmodium vivax infecta ampliamente a muchas personas en algunas regiones. La singularidad de formar una etapa latente hace que la malaria vivax pueda ser inducida por una recaída por una infección adicional. En el presente estudio, utilizamos un enfoque de simulación dinámica y acoplamiento molecular para predecir la posibilidad de que compuestos bioactivos de la familia de plantas Zingiberaceae sean candidatos a fármaco contra la malaria dirigiéndose a la proteína de unión a Duffy de Plasmodium vivax (PvDBP). Se requiere la interacción molecular PvDBP-DARC para mediar el proceso de invasión de merozoitos en los glóbulos rojos. La inhibición de este proceso posiblemente pueda controlar el crecimiento y desarrollo del parásito. [Metodología] El análisis de acoplamiento molecular dio como resultado los dos compuestos principales con el valor de energía de unión más bajo, incluida la 5,7-dihidroxiflavanona (-9,3 kcal/mol) y la pinostrobina (-9,2 kcal/mol). [Resultados] Estos compuestos previstos tienen una interacción más fuerte que la cloroquina como control. Además, los compuestos potenciales también interactúan con los residuos del sitio de unión de DARC y lo mantienen durante el proceso de simulación de dinámica molecular. De lo contrario, la cloroquina como control no puede retener el 75% de los residuos de unión hacia PvDBP. El estudio de dinámica molecular reveló que los tres complejos tienen una estabilidad relativamente similar. [Conclusiones] Predijimos que los dos compuestos bioactivos tienen potencial como inhibidores de la invasión de merozoitos. [Objetivo] O Plasmodium vivax infecta amplamente muitas pessoas em algumas regiões. A singularidade de formar um estágio latente significa que a malária vivax pode ser induzida por recaída devido à infecção adicional. No presente estudo, utilizamos uma abordagem de simulação dinâmica e de acoplamento molecular para prever a possibilidade de compostos bioativos da família de plantas Zingiberaceae como candidatos a medicamentos antimaláricos, visando a proteína de ligação Duffy do Plasmodium vivax (PvDBP). A interação molecular PvDBP-DARC é necessária para mediar o processo de invasão de merozoítos nos glóbulos vermelhos. A inibição deste processo pode possivelmente controlar o crescimento e desenvolvimento do parasita. [Metodologia] A análise de acoplamento molecular resultou nos dois principais compostos com o menor valor de energia de ligação, incluindo 5,7-dihidroxiflavanona (-9,3 kcal/mol) e pinostrobina (-9,2 kcal/mol). [Resultados] Esses compostos previstos têm uma interação mais forte do que a cloroquina como controle. Além disso, os compostos potenciais também interagem e mantêm resíduos do sítio de ligação do DARC durante o processo de simulação de dinâmica molecular. Caso contrário, a cloroquina como controle não pode reter 75% dos resíduos de ligação ao PvDBP. O estudo de dinâmica molecular revelou que os três complexos apresentam estabilidade relativamente semelhante. [Conclusões] Previmos que os dois compostos bioativos têm potencial como inibidores da invasão de merozoítos. Universidad Nacional, Costa Rica 2024-07-31 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Papers evaluated by academic peers Artículos evaluados por pares académicos application/pdf text/html application/epub+zip https://www.revistas.una.ac.cr/index.php/uniciencia/article/view/18995 10.15359/ru.38-1.18 Uniciencia; Vol. 38 No. 1 (2024): Uniciencia. January-December, 2024; 1-15 Uniciencia; Vol. 38 Núm. 1 (2024): Uniciencia. January-December, 2024; 1-15 Uniciencia; v. 38 n. 1 (2024): Uniciencia. January-December, 2024; 1-15 2215-3470 eng https://www.revistas.una.ac.cr/index.php/uniciencia/article/view/18995/30962 https://www.revistas.una.ac.cr/index.php/uniciencia/article/view/18995/30963 https://www.revistas.una.ac.cr/index.php/uniciencia/article/view/18995/30964 Copyright (c) 2024 Shared by Journal and Authors (CC-BY-NC-ND) https://creativecommons.org/licenses/by-nc-nd/4.0 |