scholarly journals Molecular Docking terhadap Senyawa Isoeleutherin dan Isoeleutherol sebagai Penghambat Pertumbuhan SARS-CoV-2

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Nathanael F. Prasetio ◽  
Billy J. Kepel ◽  
Widdhi Bodhi ◽  
. Fatimawali ◽  
Aaltje Manampiring ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Active Compound ◽  
Corona Virus ◽  
Docking Method ◽  
Herbal Plants ◽  
Anti Inflammatory ◽  
Molecular Docking Method

Abstract: Dayak onions are herbal plants used by Indonesians as an anti-inflammatory, anticancer, antimicrobial, antidiabetic, antihypertensive and antiviral. By consuming herbal plants, it can increase immunity which is the main key in preventing the virus, especially COVID-19. This study was aimed to determine the effect of dayak active compound anchoring on the growth of the corona virus. This study used molecular docking method. The results of visualization of molecular docking when compared to the binding affinity of remdesivir obtained a binding affinity of -7.3, while the binding affinity of isoeleutherin and isoeleutherol was -6.9, so the result was lower than remdesivir. isoeleutherin and isoeleutherol compounds have a lower binding affinity value than remdesivir, so isoeleutherin and isoeleutherol compounds have lower yields as inhibitors of COVID-19.Keywords: dayak onions, SARS-CoV-2, molecular docking  Abstrak: Bawang Dayak merupakan tanaman herbal yang digunakan masyarakat Indonesia sebagai antiinflamasi, antikanker, antimikroba, antidiabetes, antihipertensi dan antivirus. Dengan mengkonsumsi tanaman herbal dapat meningkatkan kekebalan tubuh yang menjadi kunci utama dalam mencegah virus terlebih COVID-19. Penelitian ini bertujuan untuk mengetahui pengaruh penambatan senyawa aktif bawang dayak terhadap pertumbuhan dari corona virus. Jenis penelitian ini menggunakan metode penelitian penambatan molekul (molecular docking). Hasil visualisasi molecular docking jika dibandingkan binding affinity dari remdesivir didapatkan binding affinity yaitu -7,3 sedangkan binding affinity dari isoeleutherin dan isoeleutherol adalah -6,9, maka diperoleh hasil yang lebih rendah dari remdesivir. senyawa isoeleutherine dan isoeleutherol memiliki nilai binding affinity yang lebih rendah dari remdesivir, maka senyawa isoeleutherin dan isoeleutherol memiliki hasil yang lebih rendah sebagai penghambat COVID-19.Kata Kunci: bawang dayak, SARS-CoV-2, molecular docking

scholarly journals Penambatan Molekuler α, β, dan γ-mangostin Sebagai Inhibitor α-amilase Pankreas Manusia

2019 ◽  
Vol 6 (2) ◽  
pp. 59-66
Author(s):  
Nelson Gaspersz ◽  
Mario Rowan Sohilait
Keyword(s):  
Molecular Docking ◽  
Hydrogen Bonds ◽  
Binding Affinity ◽  
In Silico ◽  
Van Der Waals ◽  
Affinity Ligand ◽  
Docking Method ◽  
In Silico Studies ◽  
Potential Activity ◽  
Molecular Docking Method

In silico studies on interactions between the human pancreatic α-amylase (HPA) enzyme with α, β, and γ-mangostin ligands has been carried out using the molecular docking method. Ligands α, β, and γ-mangostin interact through the formation of hydrogen and van der waals bonds with residues on the enzyme active side. The α-mangostin ligands form seven hydrogen and six van der waals bonds with residues involved were Trp59, Gln63, Trp96, Thr163, Thr164, Ala198, His201, Glu233, and Asp300; β-mangostin forms five hydrogen and eight van der waals bonds with residues involved were Gln63, Trp96, Thr163, Thr164, Arg195, Asp197, His201, Glu233, Asp300, and His305; while γ-mangostin forms nine hydrogen and five van der waals bonds with residues involved were Trp59, Gln63, Trp96, Thr163, Asp197, Ala198, His201, Glu233, and Asp300. The binding afinity of α, β, and γ-mangostin to the HPA obtained were -7.0; -6.6; and -7.4 kcal/mol with RMSD value were 1,850; 1,956; and 1,811 Å, respectively. The number of hydrogen bonds that can be formed was responsible to the binding affinity. Ligand γ-mangostin has potential activity as an inhibitor of HPA enzyme due to the stable complexes formation with lower binding affinity (validated with RMSD value) when compared to α and β-mangostin.

scholarly journals Molecular Docking Senyawa Gingerol dan Zingiberol pada Tanaman Jahe sebagai Penanganan COVID-19

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Belinda D. P. M. Ratu ◽  
Widdhi Bodhi ◽  
Fona Budiarso ◽  
Billy J. Kepel ◽  
. Fatimawali ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Amino Acid Residues ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Main Protease ◽  
Docking Method ◽  
Pubmed Database ◽  
Almost All ◽  
The Impact

Abstract: COVID-19 is a new disease. Many people feel the impact of this disease. There is no definite cure for COVID-19, so many people use traditional medicine to ward off COVID-19, including ginger. This study aims to determine whether there is an interaction between compounds in ginger (gingerol and zingiberol) and the COVID-19’s main protease (6LU7). This study uses a molecular docking method using 4 main applications, namely Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, and Open Babel GUI. The samples used were gingerol and zingiberol compounds in ginger plants downloaded from Pubchem. The data used in this study used Mendeley, Clinical Key, and PubMed database. The study showed that almost all of the amino acid residues in the gingerol compound acted on the 6LU7 active site, whereas the zingiberol did not. The results of the binding affinity of ginger compounds, both gingerol and zingiberol, do not exceed the binding affinity of remdesivir, a drug that is widely researched as a COVID-19 handling drug. In conclusion, gingerol and zingiberol compounds in ginger can’t be considered as COVID-19’s treatment.Keywords: molecular docking, gingerol, zingiberol Abstrak: COVID-19 merupakan sebuah penyakit yang baru. Banyak masyarakat yang merasakan dampak dari penyakit ini. Belum ada pengobatan pasti untuk menyembuhkan COVID-19, sehingga banyak masyarakat yang menggunakan pengobatan tradisional untuk menangkal COVID-19, termasuk jahe. Penelitian ini bertujuan untuk mengetahui apakah ada interaksi antara senyawa pada jahe (gingerol dan zingiberol) dengan main protease COVID-19 (6LU7). Penelitian ini menggunakan metode molecular docking dengan menggunakan 4 aplikasi utama, yaitu Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, dan Open Babel GUI. Sampel yang digunakan yaitu senyawa gingerol dan zingiberol pada tanaman jahe yang diunduh di Pubchem. Data yang digunakan dalam penelitian ini menggunakan database Mendeley, Clinical Key, dan PubMed. Penelitian menunjukkan bahwa hampir semua residu asam amino pada senyawa gingerol bekerja pada sisi aktif 6LU7, sedangkan tidak demikian pada zingiberol. Hasil binding affinity senyawa jahe, baik gingerol maupun zingiberol tidak  melebihi binding affinity remdesivir, obat yang banyak diteliti sebagai obat penanganan COVID-19. Sebagai simpulan, senyawa gingerol dan zingiberol pada tanaman jahe tidak dapat dipertimbangkan sebagai penanganan COVID-19Kata Kunci: molecular docking, gingerol, zingiberol

scholarly journals Bhringraj Derived Phytochemicals against Pneumonia

2020 ◽  
pp. 93-96
Author(s):  
Debajani Tripathy ◽  
Chandana Adhikari ◽  
Mukundjee Pandey ◽  
Dipankar Bhattacharayay
Keyword(s):  
Molecular Docking ◽  
Life Cycle ◽  
Glutamic Acid ◽  
Interaction Energy ◽  
Plant Extract ◽  
Klebsiella Pneumonia ◽  
Discovery Studio ◽  
Docking Method ◽  
Dehydrogenase Enzyme ◽  
Molecular Docking Method

Phytochemicals from Bhringaraj plant extract are traditionally used to cure Pneumonia. It is caused by Klebsiella pneumonia. Molecular docking method applied using “Biovia Discovery Studio”. “High positive values of -CDOCKER energy and -CDOCKER interaction energy” suggested that glutamic acid can effectively deactivate the dehydrogenase enzyme, thereby interrupting the life cycle of the organism.

scholarly journals Trigonella foenum-graecum Derived Phytochemicals against Tuberculosis

2020 ◽  
pp. 121-124
Author(s):  
Bidyashree Tripathy ◽  
Elina Sahoo ◽  
Sidhartha Ray ◽  
Soumya Jal ◽  
Dipankar Bhattacharyay
Keyword(s):  
Molecular Docking ◽  
Life Cycle ◽  
Interaction Energy ◽  
Dihydrofolate Reductase ◽  
Plant Extract ◽  
Discovery Studio ◽  
Trigonella Foenum Graecum ◽  
Docking Method ◽  
Molecular Docking Method

Phytochemicals from Trigonella foenum-graecum plant extract are traditionally used to cure Tuberculosis. Molecular docking method applied using “Biovia Discovery Studio”. “High positive values of -CDOCKER energy and -CDOCKER interaction energy” suggested that this plant extract can effectively deactivate the dihydrofolate reductase enzyme thereby interrupting the life cycle of the organism.

scholarly journals Michelia champaca L. Derived Phytochemicals against Peptidase Do of Bordetella pertussis Causing Cough

2020 ◽  
pp. 133-135
Author(s):  
Sanjeeb Kumar Dash ◽  
Sidhartha Ray ◽  
Smruti Ranjan Behera ◽  
Soumya Jal ◽  
Dipankar Bhattacharyay
Keyword(s):  
Molecular Docking ◽  
Life Cycle ◽  
Interaction Energy ◽  
Plant Extract ◽  
Bordetella Pertussis ◽  
Discovery Studio ◽  
Docking Method ◽  
Michelia Champaca ◽  
Molecular Docking Method

Phytochemicals from Michelia champaca L. plant extract are traditionally used to cure cough.  Cough can be caused by many reasons. Caugh can be caused by the infection of Bordetella pertussis. The objective of the study is to identify the phytochemical of Michelia champaca capable of curing cough. Molecular docking method applied using “Biovia Discovery Studio”. “High positive values of -CDOCKER energy and -CDOCKER interaction energy” suggested that magnoflorine can effectively deactivate the peptidase Do enzyme which will interrupt the life cycle of the microorganism and inhibit the multiplication.

scholarly journals Capsicum anum L. Derived Phytochemicals against Haemophilus influenzae Causing Bronchitis

2020 ◽  
pp. 100-103
Author(s):  
Debadatta Nayak ◽  
Debesh Kumar Hota ◽  
Tophani Sahu ◽  
Soumya Jal ◽  
Dipankar Bhattacharyay
Keyword(s):  
Molecular Docking ◽  
Life Cycle ◽  
Haemophilus Influenzae ◽  
Interaction Energy ◽  
Plant Extract ◽  
Haemophilus Influenza ◽  
Discovery Studio ◽  
Docking Method ◽  
Coa Hydrolase ◽  
Molecular Docking Method

Phytochemicals from Capsicum anum L. plant extract are traditionally used to cure bronchitis. Bronchitis is caused by Haemophilus influenzae. Molecular docking method applied using “Biovia Discovery Studio”. “High positive values of -CDOCKER energy and -CDOCKER interaction energy” suggested that myrcetin and quercetin can effectively deactivate the Palmitoyl-CoA hydrolase enzyme thereby interrupting the life cycle of Haemophilus influenza.

scholarly journals 2D-QSAR and docking study of a series of coumarin derivatives as inhibitors of CDK (anticancer activity) with an application of the molecular docking method

Heliyon ◽  
2020 ◽  
Vol 6 (8) ◽  
pp. e04514
Author(s):  
Rania Kasmi ◽  
Elghalia Hadaji ◽  
Oussama Chedadi ◽  
Abdellah El Aissouq ◽  
Mohammed Bouachrine ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Anticancer Activity ◽  
Docking Study ◽  
Coumarin Derivatives ◽  
2D Qsar ◽  
Docking Method ◽  
Molecular Docking Method
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