In silico study: Potential prediction of Curcuma longa and Cymbopogon citratus essential oil as Lipoxygenase inhibitor

Abstract: Inflammation is the human body response by the injure as a results the inflammation will release LOX. To curve the conditions we use the bioactive from the nature are essential oil from Curcuma longa and Cymbopogon citratus because has a potential has pharmacologist activity. The purpose of this research to investigate the role essential oil from Curcuma longa and Cymbopogon citratus through LOX gene. Several chemical substances, including 3,7-dimethyl-1,3,6-octatriene, camphor, eugenol, curzerene and isoborneol were retrivied from PubChem database. The PyRx 0.8 was used to minimize and convert the sdf file to pdb format file of ligands. Those compounds were predicted their interaction using STITCH online server. Ligands and protein were docked by HEX Cuda 8.0.0 program, 3D and 2D views were evaluated using Discovery studio ver.19.0.0 and LigPlot+ ver 2.2, respectively. We found fourteen amino acid residues from LOX which bound the chemical compounds. Those interaction was supported by hydrogen bond with variety energy binding. To sum up, the essential oil from Curcuma longa and Cymbopogon citratus has a potential function as inhibitor LOX by inhibiting fourteen active side of the LOX gene.

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In silico study: Potential prediction of Curcuma longa and Cymbopogon citratus essential oil as Lipoxygenase inhibitor

JSMARTech ◽

10.21776/ub.jsmartech.2021.002.02.81 ◽

2021 ◽

Vol 2 (2) ◽

pp. 081-086

Author(s):

Yohanes Bare ◽

◽

Lilin Indahsari ◽

Dewi Sari ◽

Theopilus Watuguly ◽

...

Keyword(s):

Essential Oil ◽

Curcuma Longa ◽

Chemical Compounds ◽

Amino Acid Residues ◽

Cymbopogon Citratus ◽

Lipoxygenase Inhibitor ◽

Discovery Studio ◽

Pubchem Database ◽

In Silico Study ◽

Body Response

Inflammation is the human body response by the injure as a results the inflammation will release LOX. To curve the conditions we use the bioactive from the nature are essential oil from Curcuma longa and Cymbopogon citratus because has a potential has pharmacologist activity. The purpose of this research to investigate the role essential oil from Curcuma longa and Cymbopogon citratus through LOX gene. Several chemical substances, including 3,7-dimethyl-1,3,6-octatriene, camphor, eugenol, curzerene and isoborneol were retrivied from PubChem database. The PyRx 0.8 was used to minimize and convert the sdf file to pdb format file of ligands. Those compounds were predicted their interaction using STITCH online server. Ligands and protein were docked by HEX Cuda 8.0.0 program, 3D and 2D views were evaluated using Discovery studio ver.19.0.0 and LigPlot+ ver 2.2, respectively. We found fourteen amino acid residues from LOX which bound the chemical compounds. Those interaction was supported by hydrogen bond with variety energy binding. To sum up, the essential oil from Curcuma longa and Cymbopogon citratus has a potential function as inhibitor LOX by inhibiting fourteen active side of the LOX gene.

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The Potential of Acetylfuran and Furfural from Tamarindus indica as Lipoxygenase Inhibitor: In Silico Study

JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA ◽

10.20473/jfiki.v8i22021.139-142 ◽

2021 ◽

Vol 8 (2) ◽

pp. 139

Author(s):

Apriani Herni Rophi ◽

Yohanes Bare ◽

Dewi Ratih Tirto Sari

Keyword(s):

Arachidonic Acid ◽

Amino Acid ◽

Protein Interactions ◽

Amino Acid Residues ◽

Tamarindus Indica ◽

Lipoxygenase Inhibitor ◽

Discovery Studio ◽

Pubchem Database ◽

In Silico Study ◽

Action Methods

Background: Tamarindus indica is a type of plant sub-family Caesalpinioideae, which is predicted to have anti-inflammatory properties. When inflammation occurs, arachidonic acid will undergo metabolism, the LOX pathway will release 5-lipoxygenase (5-LOX). Objective: This study aimed to analyze the potential of acetylfuran and furfural compounds on LOX action. Methods: The compound Acetylfuran (CID 14505), Furfural (CID 7362) were downloaded from the PubChem database. The 5-LOX protein was obtained from PDB (6N2W), preparation by removing ligands and molecules that bind to Discovery Studio V19.1.0.18287. Compound and protein interactions have interacted with the Vina autodock software integrated into the PyRX software and analyzed by Discovery Studio V19.1.0.18287. Results: The results showed that the content of Acetylfuran and Furfural compounds in Tamarindus indica is predicted to have the potential as an inhibitor of the LOX gene on different amino acid residues, namely 3 amino acid residues and 4 amino acid residues, respectively and produce binding energy. In addition, van der Waals forces, hydrogen and hydrophobic bonds were found, giving the strength of the bonds formed. Conclusion: Bioactive acetylfuran and furfural have the potential as a drug to curve inflammation in the human body.

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Chemotypes of turmeric (Curcuma longa L.) essential oil from four different states of Brazil

Australian Journal of Crop Science ◽

10.21475/ajcs.21.15.07.p3146 ◽

2021 ◽

pp. 1035-1042

Author(s):

Franciele da Silva Quemel ◽

Andira Pricila Dantas ◽

Lincon Sanches ◽

Ana Cláudia Graças Alves Viana ◽

Eloísa Schneider Silva ◽

...

Keyword(s):

Essential Oil ◽

Chemical Constituents ◽

Curcuma Longa ◽

Principal Component ◽

Chemical Compounds ◽

Hierarchical Cluster ◽

Main Compound ◽

Group Iii ◽

Group I ◽

Chemical Class

Turmeric or curcuma (Curcuma longa L.) is a Zingiberaceae whose essential oil and coloring pigments obtained from the rhizome have been widely used in the food industry and medicine. This study aimed to extract and identify the chemical compounds found in C. longa essential oil from rhizomes collected in six different locations of Brazil. The oil extraction was carried out by hydrodistillation technique, using a Clevenger- type apparatus. The chemical constituents were identified by Gas Chromatography coupled to Mass Spectrometry (GC-MS). The principal component analysis (PCA) and the hierarchical cluster analysis (cluster)were done for the obtained data; and the composition of the studied accesses was verified. Three groups of chemotypes were obtained: group I was formed by the accesses of Campo Grande / Indígena-MS, Mara Rosa-GO, Campo Grande-MS and Perobal-PR, and had Ar-turmerone as its main compound; group II, formed by the access of Santa Tereza do Oeste-PR, presented α-costol and α-Phellandrene as the predominant compounds; and group III, the access of Holambra-SP, differed from the others regarding its essential oil chemical composition whose main agents were Curlone, Zingiberene, β-sesquiphellandrene, Humulene epoxide II, cis-α-trans-Bergamotol. The predominant chemical class in all accesses was hydrocarbon sesquiterpenes (Santa Tereza do Oeste-PR and Holambra-SP) and oxygenated sesquiterpenes (the others). This study evidenced the formation of three chemotypes

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In-silico Approach for The Prediction of Chlorogenic Acid as PPAR-γ Activator

Biota ◽

10.20414/jb.v13i1.197 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Yohanes Bare ◽

Mansur S ◽

Sukarman Hadi Jaya Putra ◽

Margaretha Rika W G L ◽

Dewi Ratih Tirto Sari

Keyword(s):

Physicochemical Properties ◽

Chlorogenic Acid ◽

Peroxisome Proliferator ◽

Amino Acid Residues ◽

Peroxisome Proliferator Activated Receptor ◽

Discovery Studio ◽

Ppar Γ ◽

Pubchem Database

Coffee is one of the essential crops commonly cultivated in Indonesia. Coffee contains diverse bioactive compounds, which are associated with human health benefits. One of the compounds is Chlorogenic acid, which able to decrease the risk of type 2 diabetes mellitus (T2DM). However, the mechanism of chlorogenic acid toward anti-diabetes still unclear. This study aimed to analyze and investigate the potential role of chlorogenic acid as anti-diabetes through their interaction with Peroxisome proliferator-activated receptor gamma (PPAR-γ) as an enzyme to phosphorylate and regulate the mechanism of T2DM. The physicochemical properties of chlorogenic acid also performed in this study. The PPAR-γ was downloaded from the PDB database, and the chlorogenic acid was retrieved from the PubChem database. The protein and ligand were prepared using the PyRx program and were docked using Hex 8.0.0 software. Discovery Studio client 4.1 software was used to analyze the interaction between chlorogenic acid and PPAR-γ protein. Based on the physicochemical properties, chlorogenic acid is highly permeable to the cell and easily absorbed. Thirteen amino acid residues of PPAR-γ (GLN410, SER394, ASP396, GLY395, GLU407, LEUA401, LEU400, VAL403, LYS373, LYS438, LEU377, LYS434, and GLY437) were identified on the chlorogenic acid-PPAR-γ interaction. Interestingly, the kind of interactions, including hydrophobic interaction, hydrogen bond, and van der Waals, which are supported by the tight interaction. Our study indicated that chlorogenic acid might have anti-diabetes activity through PPAR-γ interaction.

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Studi In Silico: Prediksi Potensi 6-shogaol dalam Zingiber officinale sebagai Inhibitor JNK

Al-Kimia ◽

10.24252/al-kimia.v7i2.10638 ◽

2019 ◽

Vol 7 (2) ◽

Cited By ~ 1

Author(s):

Sri Sulystyaningsih Natalia Daeng Tiring ◽

Yohanes Bare ◽

Andri Maulidi ◽

Mansur S ◽

Fitra Arya Dwi Nugraha

Keyword(s):

Bioactive Compounds ◽

Antioxidant Properties ◽

Zingiber Officinale ◽

Data Bank ◽

Protein Docking ◽

Amino Acid Residues ◽

Discovery Studio ◽

Cell Dysfunction ◽

Pubchem Database ◽

Docking Protein

Type 2 Diabetes Mellitus (T2DM) is a metabolic disease characterized by hyperglycemia and insulin resistance. T2DM therapy against c-Jun N-terminal kinase (JNK) is one of the recovery solutions using bioactive compounds from ginger. 6-shogaol is bioactive compounds of ginger that has antioxidant properties. The purpose of this study is to analyze the potential of 6-shogaol as a JNK inhibitor. JNK protein (ID: 464Y) was obtained from Protein Data Bank (PDB) through 6-shogaol ligand (CID: 5281794) obtained from the PubChem database. Protein docking protein and ligand use Hex 8.0.0 software while visualization and analysis using Discovery Studio client 4.0. The results showed that 6-shogaol was predicted to have potential as a JNK inhibitor. Proving this by finding five amino acid residues (TRY223, LEU210, THR103 ALA214, ARG107) with an energy of -236.29cal/mol. We found the type of hydrogen bonds and the van der waals forces formed. The interaction of ligand and protein successfully inactivates JNK and stops pancreatic β cell dysfunction. 6-shogaol has pharmacological properties as a JNK,T2DM.

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In Silico Study of Vacuolin-1 as an Inhibitor of HSP27 for Precancerous Treatment of Breast Cancer

JSMARTech ◽

10.21776/ub.jsmartech.2021.002.03.107 ◽

2021 ◽

Vol 2 (3) ◽

pp. 107-112

Author(s):

Diah Agustin ◽

◽

Mumtaz Nabila Ulfah ◽

Siti Nur Aisyah ◽

Pamuji Lestari Arumsari ◽

...

Keyword(s):

Breast Cancer ◽

Early Stage ◽

Web Server ◽

Great Chance ◽

Lipinski’S Rule ◽

Discovery Studio ◽

Pubchem Database ◽

In Silico Study ◽

Low Toxicity ◽

Drug Compound

Breast cancer has a great chance of being cured if it is diagnosed and treated properly in its early stage. The pre-cancer stage is an early stage of cancer development characterized by the overexpression of HSP27. Therefore, HSP27 can be a therapeutic target of cancer. This study aims to analyze whether vacuolin-1, a small drug compound known for its ability to inhibit metastasis, can inhibit HSP27 to prevent precancerous development in breast cancer, as well as its ADME and biosafety aspects. Protein & ligand structures were obtained from RCSB PDB and PubChem database. Preparation was performed with Discovery Studio and PyRx. Drug-likeness/ADME analysis was performed in Swiss-ADME web server. Biosafety analysis was performed in MetaTox web server. Molecular docking was performed using PyRx. The visualization of docking results was performed using Discovery Studio. The docking result between vacuolin-1 and HSP27 showed that vacuolin-1 can act as an HSP27 inhibitor by interacting with S78 residue of HSP27 and blocking its phosphorylation as well as depolymerization process. The drug-likeness characterization result of this compound showed that vacuolin-1 violates one of the four Lipinski's Rule of Five. Biosafety analysis showed that vacuolin-1 has a low toxicity level with an estimated LD50 around 13,016.65 mg/kg.

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