Molecular Docking and Interaction Analysis of Propolis Compounds Against SARS-CoV-2 Receptor

Syaban, Mokhamad Fahmi Rizki; Faratisha, Icha Farihah Deniyati; Yunita, Khadijah Cahya; Erwan, Nabila Erina; Kurniawan, Dedy Budi; Putra, Gumilar Fardhani Ami

doi:10.11594/jtls.12.02.08

Cited by 6 publications

(3 citation statements)

References 31 publications

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“…The different types of bonds found between chanoclavine, nootkatone and the target protein were analyzed. The type of interaction between the ligand and protein target is a critical parameter in predicting the effect of interactions (25,26). Chanoclavine attaches to JNK via six hydrophobic bond interactions, (ILE70, VAL78, ALA91, MET146, VAL196 and LEU206).…”

Section: Resultsmentioning

confidence: 99%

Integrated molecular docking, dynamic simulations and in vivo analysis of ethanol extract Citrus sinensis peel as an antioxidant and neurotrophic agent for ameliorating motor and cognitive functions in traumatic brain injury

Santoso,

Putra,

Syaban

et al. 2023

World Acad Sci J

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Traumatic brain injury (TBI) is the primary injury to the brain caused by mechanical forces. It is one of the leading causes of mortality in mid-life. Increased levels of inflammation and oxidation, and decreased levels of neurotrophic factor lead to a worsening of the condition. In previous studies, the authors demonstrated that the ethanol extract of Citrus sinensis peel (CSPE) functioned as an antioxidant using molecular docking and dynamic simulations. In the present study, in order to confirm these findings, a Marmarou weight drop model which included rats with TBI. Molecular docking against c-Jun N-terminal kinase 3 (JNK3) was also performed. The rats were divided into the sham-operated, control and treatment groups. The treatment groups received CSPE at 50, 250 and 500 mg/kg body weight (groups 1, 2 and 3, respectively) orally once a day for 7 days following the induction of TBI. Superoxide dismutase (SOD)1, SOD2, and brain-derived neurotrophic factor (BDNF) expression levels were analyzed using immunohistochemistry. Surviving neurons were analyzed using hematoxylin and eosin staining. Barnes' maze and wire grip tests were performed on the 1st, 3rd and 7th days following TBI. The results revealed a significant increase in the numbers of surviving neurons and in BDNF expression in groups 2 and 3, a higher expression of SOD1 in group 3, and a higher expression of SOD2 in all the treatment groups. Wire grip duration was significantly longer on the 7th day following TBI in group 3, and Barnes maze latency was significantly shorter on the 3rd and 7th days following TBI compared to the previous time in all treatment groups. Molecular docking analysis also revealed that CSPE compounds, particularly chanoclavine and nootkatone, interacted with JNK3 in the same binding pocket. On the whole, the present study demonstrates that CSPE helps protect the brain from damage by functioning as an antioxidant, increasing neurotrophic activities and inhibiting apoptosis. This reduces the overall neurological issues that are associated with TBI. However, further studies on the efficacy and safety of CSPE are required in order to determine its full potential in improving motor and cognitive functions following TBI.

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Section: Resultsmentioning

confidence: 99%

Integrated molecular docking, dynamic simulations and in vivo analysis of ethanol extract Citrus sinensis peel as an antioxidant and neurotrophic agent for ameliorating motor and cognitive functions in traumatic brain injury

Santoso,

Putra,

Syaban

et al. 2023

World Acad Sci J

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“…It covers a wide range of >4,000 biological activities and achieves an average accuracy rate of >95%. The predictions are obtained by studying structure-activity relationships in a training set consisting of structure and biological activity data for >300,000 organic molecules (26,27). Briefly, a canonical molecule from PubChem was entered into the PASS online web server.…”

Section: Biological Activity and Molecular Potential Predictionmentioning

confidence: 99%

7,8‑Dihydroxyflavone functions as an antioxidant through the inhibition of Kelch‑like ECH‑associated protein 1: Molecular docking and an in vivo approach in a rat model of ischemia‑reperfusion brain injury

Yueniwati,

Syaban,

Kurniawan

et al. 2024

World Acad Sci J

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Stroke is a medical condition characterized by a sudden, localized neurological impairment caused by damage to the central nervous system due to either a blockage or bleeding in the blood vessels. This process leads to increased oxidation, which can exacerbate brain damage. Flavonoids are compounds that are widely found in nature and are considered to have numerous health benefits. 7,8-dihydroxyflavone (7,8-DHF) is a flavonoid that has tropomyosin receptor kinase B agonist activity. However, the other beneficial activities of 7,8-DHF remain to be explored, particularly in neuron-related diseases. The present study aimed to explore 7,8-DHF as an antioxidant agent using in vivo and in silico analyses. An in vivo experiment was conducted using Rattus novergicus, in which ischemia-reperfusion brain injury was induced. A total of 30 rats were divided into the sham-operated, control and treatment groups. The treatment groups were administered doses of 10, 20 and 50 mg/kg body weight of 7,8-DHF orally, once daily for a duration of 14 days following the induction of ischemia-reperfusion brain injury. Subsequently, blood and brain tissues were collected for the examination of nuclear factor E2-related factor 2 (Nrf2) expression, glutathione peroxidase-1 (GPX-1) expression and the malondialdehyde (MDA) level. Molecular docking analysis and dynamic simulations of 7,8-DHF and Kelch like ECH-associated protein 1 (Keap1) protein interactions were performed using AutoDock Vina and AMBER. The visualization of the interaction was performed using ChimeraX and Discovery Studio. The drug-like properties of 7,8-DHF were predicted using the SwissADME web server, and the bioactivity of the compounds was evaluated using the PASS online server. The results revealed that 7,8-DHF exhibits antioxidant activity through the inhibition of Keap1, thereby increasing Nrf2 and GPX-1 expression and decreasing the levels of MDA. In silico analysis revealed that 7,8-DHF can bind Keap1 protein, thereby disrupting the interaction between Nrf2 and Keap1. Molecular dynamics also demonstrated that 7,8-DHF has good stability compared to the control. On the whole, as demonstrated in the present study

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“…The compound database in propolis was obtained from several previously reported literature [28][29][30][31][32][33][34][35][36], compounds not in the PubChem database will be visualized using the Marvin JS plug-in on the SwissADME Web server (http://www.swissadme.ch/index.php) [37].…”

Section: Acquisition Of Compounds Database For Propolis Compoundsmentioning

confidence: 99%

Exploring Therapeutic Potential of Nutraceutical Compounds from Propolis on MAPK1 Protein Using Bioinformatics Approaches as Anti-Coronavirus Disease 2019 (COVID-19)

Siregar,

Kustiawan,

Sari

et al. 2024

BIO Web Conf.

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This study explores the potential of propolis, a natural substance, as a gene therapy for treating COVID-19. Despite the advent of COVID-19 vaccines, their side effects pose new health challenges. Utilizing network pharmacology, this research identifies propolis compounds through various databases and assesses their ability to target proteins associated with COVID-19. MAPK1 emerges as a potential therapeutic target, and molecular docking reveals Broussoflavonol F, Glyasperin A, and Sulabiroins as promising compounds with strong binding affinities, i.e.,- 9.0, -9.0, and -8.8 kcal/mol, respectively, exceeding the native ligand (-7.2 kcal/mol). Molecular Dynamics displays stable complex behavior, with backbone RMSD values consistently below 4 Angstroms and RMSF simulations showing minimal fluctuations within ±2 Angstroms error. Moreover, MM-PBSA analysis further supports the strong binding of Broussoflavonol F, Glyasperin A, and Sulabiroins A, with relative binding energies of -122.82±89.65, 131.48±95.39, and -155.97±111,37 kJ/mol, respectively. These results indicate that propolis has potential as an anti-COVID-19 agent, primarily through inhibiting the MAPK1 pathway. However, further research is needed to validate these results and develop practical applications for COVID-19 therapy. This study underscores the significance of network pharmacology and computational models in understanding propolis mechanisms, offering potential directions for future research and treatment strategies against COVID-19.

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Molecular Docking and Interaction Analysis of Propolis Compounds Against SARS-CoV-2 Receptor

Cited by 6 publications

References 31 publications

Integrated molecular docking, dynamic simulations and in vivo analysis of ethanol extract Citrus sinensis peel as an antioxidant and neurotrophic agent for ameliorating motor and cognitive functions in traumatic brain injury

Integrated molecular docking, dynamic simulations and in vivo analysis of ethanol extract Citrus sinensis peel as an antioxidant and neurotrophic agent for ameliorating motor and cognitive functions in traumatic brain injury

7,8‑Dihydroxyflavone functions as an antioxidant through the inhibition of Kelch‑like ECH‑associated protein 1: Molecular docking and an in vivo approach in a rat model of ischemia‑reperfusion brain injury

Exploring Therapeutic Potential of Nutraceutical Compounds from Propolis on MAPK1 Protein Using Bioinformatics Approaches as Anti-Coronavirus Disease 2019 (COVID-19)

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