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

Al-Kimia ◽  
2019 ◽  
Vol 7 (2) ◽  
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. 

scholarly journals Shogaol, Bisdemethoxycurcumin, and Curcuminoid: Potential Zingiber Compounds Against COVID-19

2021 ◽  
Vol 11 (5) ◽  
pp. 12869-12876
Keyword(s):  
Bioactive Compounds ◽  
Binding Sites ◽  
Active Sites ◽  
Zingiber Officinale ◽  
Amino Acid Residues ◽  
Curcuma Zedoaria ◽  
Rna Dependent Rna Polymerase ◽  
Protein Amino Acid ◽  
Discovery Studio ◽  
Global Pandemic

Coronavirus disease (COVID-19) is a global pandemic in the world. Some treatments, including vaccines and potential drugs, are still developed. This study investigated the bioactive compounds of Zingiber officinale, Kaempferia rotunda, and Curcuma zedoaria as a potential inhibitor for ACE2 and RdRP proteins. Molecular docking was used for screening the bioactive compounds as ACE2 and RdRP inhibitors. Shogaol (CID 5281794), zingerone (CID 31211), chalcone (CID 637760), Ar-turmerone (CID 558221), bisdemothxycurcumin (CID 5315472), and curcuminoid (CID 101341353) interacted with angiotensin-converting enzyme receptor-2/ACE2 (PDB ID 2xd3) and RNA dependent RNA polymerase/RdRP (PDB ID 6xqb), then analyzed using Discovery studio v.19 program. Shogaol, zingerone, chalcone, ar-turmerone, bisdemethoxycurcumin, and curcuminoid bound to ACE2 and RdRP protein in some active sites. Zingerone, chalcone, and ar-turmerone are attached to the ACE-2 and then RdRP protein in similar active sites, suggesting those compounds stabilize the complex ACE-2 and RdRP protein. Shogaol interacted with the RdRP and ACE2 protein amino acid residues in the Shogaol-RdRP+ACE2 complex, indicating shogaol blocks the RdRP-ACE2 interaction. Then, bisdemethoxycurcumin and curcuminoid change the binding sites of ACE2 and RdRP protein when both compounds are bound to RdRP protein. This study suggested that shogaol, bisdemethoxycurcumin, and curcuminoid are potential drugs for COVID-19 prevention.

scholarly journals POTENSI SENYAWA BIOAKTIF TANAMAN GENUS Phyllanthus SEBAGAI INHIBITOR REPLIKASI VIRUS HEPATITIS B

2017 ◽  
Vol 4 (2) ◽  
pp. 85
Author(s):  
. Firdayani ◽  
Susi Kusumaningrum ◽  
Yosephine Ria Miranti
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Hepatitis B ◽  
Protein Data Bank ◽  
Bioactive Compounds ◽  
Core Protein ◽  
Data Bank ◽  
Amino Acid Residues ◽  
Virus Hepatitis ◽  
Molegro Virtual Docker

Potency of Plant Bioactive Compounds from the Genus Phyllanthus as Hepatitis B Virus Replication InhibitorIn this research, simulations of molecular docking of Phyllanthus bioactive compounds were performed into the core protein of HBV. This simulation aimed to predict the interaction between compounds with virus core protein causing disruption of capsid formation and inhibiting its replication. The docking simulation was completed by Molegro Virtual Docker 6.0. The 3D stable conformation of molecule structures were docked into HBV core protein downloaded from Protein Data Bank, then the results were analyzed to view the minimum energy and interactions that occurred. The coordinate docking was done at the same coordinate as the previously docked reference ligand position and was validated. From the results it was known that repandusinic acid formed the most stable affinity bond with amino acid residues of viral core proteins. Interaction of B chain forming hydrogen bonds with the amino acid residues of Thr 33, Trp 102, Phe 23, Leu 140, Tyr 118 and Ser 141, and C chain with Thr 128, Val 124 and Glu 117.These compounds can be used as marker for anti HBV.Keyword: Bioactive compounds, core protein, HBV , molecular docking, Phyllanthus ABSTRAKPada penelitian ini dilakukan simulasi penambatan molekul senyawa-senyawa bioaktif Phyllanthus ke dalam protein inti virus hepatitis B. Simulasi ini bertujuan untuk memprediksi interaksi terbentuk antara senyawa dengan protein yang menyebabkan terganggunya pembentukan kapsid virus dan menghambat replikasinya. Simulasi penambatan molekul dilakukan menggunakan program Molegro Virtual Docker 6.0. Sebagai reseptor target digunakan struktur 3D protein inti yang diunduh dari Protein Data Bank. Posisi penambatan dilakukan pada koordinat yang sama dengan posisi ligan referensi yang sudah tertambat sebelumnya dan tervalidasi. Dari hasil simulasi diketahui bahwa asam repandusinat membentuk komplek dengan energi afinitas ikatan yang paling kecil dengan residu asam amino protein inti virus. Interaksi terjadi dengan rantai B yang membentuk ikatan hidrogen dengan asam amino Thr 33, Trp 102, Phe 23, Leu 140, Tyr 118 dan Ser 141, dan rantai C dengan asam amino Thr 128, Val 124 dan Glu 117. Senyawa ini dapat dijadikan sebagai marka untuk anti VHB.Kata kunci: Penambatan molekul, Phyllanthus, protein inti, senyawa bioaktif, VHBReceived: 11 December 2017                 Accepted: 27 December 2017           Published: 31 December 2017 

scholarly journals Analysis of molecular interactions of 8-gingerol compounds in Ginger (Zingiber officinale) as ACE Inhibitor

BIOEDUSCIENCE ◽  
2020 ◽  
Vol 4 (2) ◽  
pp. 183-187
Author(s):  
Yohanes Bare ◽  
Mansur S ◽  
Aprianus Pani Pili ◽  
Maria Helvina
Keyword(s):  
Amino Acid ◽  
Hydrogen Bonds ◽  
Ace Inhibitor ◽  
Van Der Waals ◽  
Zingiber Officinale ◽  
Van Der Waals Forces ◽  
Amino Acid Residues ◽  
Protein Database ◽  
Discovery Studio ◽  
Software Analysis

Background: Hypertension is a disease with increasing characteristics of blood pressure. The ACE gene has a role in the conversion of ATI to ATII in hypertensive conditions. Healing is done by using the 8-gingerol content contained in ginger. The purpose of this study is to analyze the molecular interaction that occurs between 8-gingerol and ACE. Method: ACE model proteins (ID: 3bkk) were obtained from the Bank Data Protein database (PDB) through 8-gingerol ligands (CID: 168114) obtained from the PubChem database. ACE and 8-gingerol were docked by Discovery Study Client 4.1 software. Analysis of amino acid residues, binding energy, Van der Waals forces, and hydrogen bonds formed using Discovery Studio Client 4.1. Results: The interaction between 8-gingerol and ACE showed that there were seven amino acid residues that interacted with 8-gingerol, also found hydrogen bonds, hydrophobic and Van der Waals forces that strengthen and stabilize these bonds. Conclusion: the interaction of 8-ginger with the active side of ACE is determined as an ACE inhibitor, the inhibition is a significant effect on the obstruction of ACE conversion.

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

JSMARTech ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 075-080
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

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.

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

Biota ◽  
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.  

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

JSMARTech ◽  
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.

scholarly journals Virtual Screening: Prediksi potensi 8-shogaol terhadap c-Jun N-Terminal Kinase (JNK)

2020 ◽  
Vol 4 (1) ◽  
pp. 1 ◽  
Author(s):  
Yohanes Bare ◽  
Mansur S ◽  
Sri Sulystyaningsih Natalia Daeng Tiring ◽  
Dewi Ratih Tirto Sari ◽  
Andri Maulidi
Keyword(s):  
Hydrogen Bond ◽  
Amino Acid ◽  
Virtual Screening ◽  
Protein Data Bank ◽  
Van Der Waals ◽  
Data Bank ◽  
Software Visualization ◽  
Amino Acid Residues ◽  
Discovery Studio ◽  
Protein Model

JNK adalah gen yang berperan dalam metabolisme DMT2. Dalam pengobatan T2DM digunakan JNK sebagai potensi terapi dengan menggunakan bahan alam. 8-shogaol adalah komponen kimia yang terkandung dalam jahe yang memiliki aktivitas antioksidan. Tujuan dari penelitina ini adalah menginversitagasi dan menganalisis peran 8-shogaol terhadap JNK. Protein JNK (ID: 464Y) diperoleh dari Protein Data Bank dan ligan 8-shogaol (CID:6442560 ) didapat dari pubchem. Ligan dan protein didocking menggunakan Hex 8.0.0. File dalam bentuk pdb divisualtisasi dan analisis menggunakan Discovery Studio Client 4.1 software. Interaksi ligan-protein menunjukan ikatan hidrogen pada residu asam amino LYS93 dan van der Waals pada 18 residu asam amino dengan energi ikatan-289.68cal/mol. Interkasi ini berpotensi sebagai penghambat kerja JNK dan dapat digunakan dalam terapi DMT2.Virtual screening: potential prediction of 8-shogaol againts c-Jun N-Terminal Kinase (JNK)AbstractJNK is one of gene that has a role in T2DM condition. To curve T2DM use JNK as potential healing using natural compounds. Eight-shogaol which found in ginger has function as a antioxidant.. The aim of the research is to investigate and analyze role 8-shogaol againts JNK. Protein JNK (ID: 464Y) was taken from Protein Data Bank and ligand 8-shogaol (CID:6442560 ) acquired from pubchem. Ligand and protein model were docked using Hex 8.0.0 software. Visualization and analysis molecular interactions by the Discovery Studio Client 4.1 software. Interaction ligand-protein showed one hydrogen bond in amino acid residue LYS93 and formed van der Waals in eighteen amino acid residues which energy binding -289.68cal/mol. This interaction has a potential to inhibit JNK role and lead to therapy T2DM.

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

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.

Flavones and Their Analogues as Bioactive Compounds – An Overview

2019 ◽  
Vol 16 (4) ◽  
pp. 377-391 ◽  
Author(s):  
B.S. Jayashree ◽  
H. Venkatachalam ◽  
Sanchari Basu Mallik
Keyword(s):  
Biological Activity ◽  
Free Radical ◽  
Bioactive Compounds ◽  
Antioxidant Properties ◽  
Radical Scavenging ◽  
Cost Effective ◽  
Free Radical Scavenging ◽  
Polyphenolic Compounds ◽  
Pharmacological Activities ◽  
Poor Solubility

Flavonoids constitute a large group of polyphenolic compounds that are known to have antioxidant properties, through their free radical scavenging abilities. They possess a chromone (γ- benzopyrone) moiety, responsible for eliciting many pharmacological activities. Even though, natural flavonoids are highly potent, owing to their poor solubility, they are less used. Therefore, attempts have been made to improve their stability, solubility, efficacy and kinetics by introducing various substituents on the flavone ring. For nearly the last two decades, flavones were synthesized in our laboratory by simple, convenient and cost-effective methods, with the knowledge of both synthetic and semi-synthetic chemistry. In this direction, it was considered worthwhile to present an overview on the synthesized flavonoids. This review creates a platform for highlighting various modifications done on the flavone system along with their biological activity.

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