scholarly journals AKTIVITAS ANTI-RHEUMATOID ARTHRITIS DARI BRAZILIN DAN BRAZILEIN SECARA IN SILICO

Jurnal Kimia ◽  
2019 ◽  
pp. 153
Author(s):  
G. A. K. Amarawati ◽  
N. M. P. Susanti ◽  
N. P. L. Laksmiani
Keyword(s):  
Rheumatoid Arthritis ◽  
Molecular Docking ◽  
Binding Energy ◽  
In Silico ◽  
Inflammatory Process ◽  
Joint Destruction ◽  
Protein Preparation ◽  
3D Structures ◽  
Docking Method ◽  
Molecular Docking Method

Rheumatoid arthritis is an autoimmune disease that occur by inflammation chronic which persist as a permanent symptom. That inflammatory process caused joint destruction. Production of pro-inflammatory sytokin such as Tumor Necrosis Factor Alpha (TNF-?) stimulate an autoimmunity. Active TNF-? plays a role in the occurrence of chronic inflammation, in which the formation of active TNF-? is regulated by TNF-? Converting Enzyme (TACE). Brazilin and brazilein are known to have anti-inflammatory activity and immunommodulator potentially as anti-rheumatoid arthritis. The purpose of this study were to determine the affinity and mechanisms of brazilin and brazilein against TACE proteins as anti-rheumatoid arthritis perfomed using molecular docking method. The study was conducted exploratively with several steps such as databases preparation of 3D structures brazilin, brazilein, TACE protein, optimization of brazilin and brazilein 3D structures, protein preparation, molecular docking method validation, and docking brazilin and brazilein in these proteins. The docking results are assessed from the binding energy and hydrogen bonds formed between brazilin and brazilein in proteins. The smaller value to the binding energy, will made the bond between brazilin and brazilein with proteins will be stronger and more stable. The results showed that brazilin and brazilein have activities as anti-rheumatoid arthritis because they are able to inhibit TACE proteins with respective bond energy values -7,24 for brazilin and – 7,59 kcal/mol for brazilein. These results show that brazilin and brazilein have the potential to inhibit inflammatory process and joint destruction in rheumatoid arthritis. Keywords : brazilin, brazilein, in silico, rheumatoid arthritis

scholarly journals AKTIVITAS DARI KUERSETIN SEBAGAI AGEN PENCERAH KULIT SECARA IN SILICO

Jurnal Kimia ◽  
2019 ◽  
pp. 207
Author(s):  
K. D. Adnyani ◽  
L. W. E. Lestari ◽  
H. Prabowo ◽  
P. A. I. A. Siaka ◽  
N. P. L. Laksmiani
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
In Silico ◽  
Target Protein ◽  
Related Protein ◽  
Skin Whitening ◽  
Whitening Agent ◽  
Docking Method ◽  
Tyrosinase Related Protein ◽  
Molecular Docking Method

Increasing melanogenesis process causes excessive melanin synthesis resulting in darkening of the skin color. The melanogenesis process requires mealnogenesis enzymes, one of which is tyrosinase-related protein 1. One of the flavonoid compounds that has the potential as a skin lightening agent is quercetin. The antioxidant activity of quercetin plays a very important role in antimelanogenesis. This study aims to determine the affinity and molecular mechanism of quercetin on the target protein tyrosinase-related protein 1 using in silico molecular docking method. Molecular docking is carried out through stages including optimization of the structure of quercetin compounds, preparation of the target protein tyrosinase-related protein 1, validation of the molecular docking method, and docking of quercetin on the tyrosinase-related protein 1. Docking of quercetin with tyrosinase-related protein 1 produces binding energy values of -7.81 kcal/mol, while docking of native ligand with tyrosinase-related protein 1 produces binding energy values of -5.39 kcal/mol. Quercetin has a strong affinity for tyrosinase-related protein 1 which is indicated by the binding energy from the docking results. Quercetin has activity as a skin whitening agent with in silico test with molecular mechanisms through inhibition of the activity of tyrosinase-related protein 1 enzyme.  Keywords: skin whitening agent, in silico, quercetin, tyrosinase-related protein 1

scholarly journals Molecular Docking Sianidin dan Peonidin sebagai Antiinflamasi pada Aterosklerosis Secara In Silico

2018 ◽  
pp. 28
Author(s):  
Diajeng Putri Dwinda Saputra
Keyword(s):  
Hydrogen Bond ◽  
Molecular Docking ◽  
Endothelial Dysfunction ◽  
Atherosclerotic Plaque ◽  
In Silico ◽  
Inflammatory Process ◽  
3D Structure ◽  
Chronic Inflammatory Disease ◽  
Protein Preparation ◽  
Docking Method

Atherosclerosis is a chronic inflammatory disease that begins with endothelial dysfunction resulting in plaque growth in the inner walls of the arteries. Endothelial dysfunction causes endothelial activates NF-?B resulting in a transcription of proinflammatory gene supporting the growth of atherosclerotic plaque. The purple sweet potato anthocyanin is a compound known to have activity inhibiting the inflammatory process. The major anthocyanins contained in purple sweetpotato are cyanidine and peonidine. The cyanidine and peonidin activity test was performed as antiinflammatory at atherosclerosis based on their interaction on NF-?B protein using molecular docking method in silico. The stages of this research are preparation of protein structure database of NF-?B, protein preparation using Chimera1.10.1 application, preparation and optimization of cyanidin and peonidin 3D structure using HyperChem8 application, and validation of molecular docking and docking method of cyanidin and peonidin on NF-?B protein using application Autodock4.2. The results showed that cyanidine and peonidine had affinity and formed a hydrogen bond with the NF-?B protein. The bond energy between cyanidine and peonidine with the NF-?B protein is -7.92 kcal/mol and -7.86 kcal/mol which together form the hydrogen bond with the LEU472 amino acid on the binding site equal to the native ligand. Cyanidin and peonidine have the potential of activity as antiatherosklerosis because it has an affinity with the NF-?B protein so that it prevents the inflammatory process in the formation of atherosclerotic plaque.

scholarly journals MOLECULAR DOCKING TERPINEN-4-OL SEBAGAI ANTIINFLAMASI PADA ATEROSKLEROSIS SECARA IN SILICO

Jurnal Kimia ◽  
2019 ◽  
pp. 221
Author(s):  
N. M. P. Susanti ◽  
N. P. L. Laksmiani ◽  
N. K. M. Noviyanti ◽  
K. M. Arianti ◽  
I K. Duantara
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Endothelial Dysfunction ◽  
Hydrogen Bonds ◽  
In Silico ◽  
Inflammatory Process ◽  
Mapk Pathway ◽  
Chronic Inflammatory Disease ◽  
Mitogen Activated Protein Kinase ◽  
Mitogen Activated Protein

Atherosclerosis is a chronic inflammatory disease that begins with endothelial dysfunction, it caused fat accumulation and plaque growth in the inner arteries walls. Endothelial dysfunction will activate the Mitogen Activated Protein Kinase (MAPK) pathway involving ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins, as well as the Nuclear Factor Kappa B (NF-kB) pathway involving IKK proteins. Terpinen-4-ol is constituent found in the bangle rhizome. The purpose of this study were to determine the affinity and mechanisms of terpinen-4-ol against ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins as anti-inflammatory in atherosclerosis performed using molecular docking method. The study was conducted exploratively with several steps such as preparation and optimization of terpinen-4-ol structure, preparation of 3D ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins, validation method of molecular docking, and docking terpinen-4-ol in these proteins. The docking result are assessed from the binding energy and hydrogen bonds formed between terpinen-4-ol and proteins. The smaller value of binding energy terpinen-4-ol with target proteins showed the complex that form more stable. The result showed that terpinen-4-ol and has activity in inhibiting the inflammatory process because it is able to disturb ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins with respective bond energy values -5,12; -5,24; -5,08; -5,88; and -4,99 Kcal/mol. The molecular mechanism in inhibiting the activity of ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins is through the formation of hydrogen bonds in these proteins. These results show that terpinen-4-ol have the potential to inhibit inflammatory process and the formation of atherosclerotic plaque can be obstructed. Keywords : atherosclerosis, terpinen-4-ol, molecular docking, in silico

scholarly journals NATURAL ISOTHIOCYANATE ANTI-MALARIA: MOLECULAR DOCKING, PHYSICOCHEMICAL, ADME, TOXICITY AND SYNTHETIC ACCESSIBILITY STUDY OF EUGENOL AND CINNAMALDEHYDE

2021 ◽  
pp. 82-88
Author(s):  
LUCY ARIANIE ◽  
WIDODO ◽  
ELVINA DHIAUL IFTITAH ◽  
WARSITO
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Docking Study ◽  
Drug Candidate ◽  
Molecular Docking Study ◽  
Docking Method ◽  
Synthetic Accessibility ◽  
Medium Risk ◽  
Moringa Oleifera Leaves ◽  
Molecular Docking Method

Objective: This study aims to evaluate novel compounds of isothiocyanate (ITC) based on eugenol and cinnamaldehyde derivatives as the drug candidate of Plasmodium falciparum anti-malaria using in silico method, physicochemical, pharmacokinetics, toxicity, and synthetic accessibility prediction. This present study also describes molecular docking and pharmacoinformatics of natural ITC in Moringa oleifera leaves. Methods: A series of novel ITC compounds (3, 5, and 6) were designed and analyzed with a series of natural ITC compounds (7, 8, 9, 10) for P. falciparum anti-malaria. This research is descriptive qualitative and uses the reverse molecular docking method, proving the biological activity of compounds theoretically using software and database information. Results: Molecular docking study showed that compound 6 exhibits binding affinity (-5.3 Kcal/mol) on Van der Waals interaction with the residual active site (His159, Cys25) of cysteine protease. All designed ITC compounds are obeyed the Lipinski and Veber Rule, have a well-brain penetrant character and have a medium risk for mutagenic, tumorigenic, and reproductive prediction. They are also in the simple rate of synthetic accessibility (SA) estimation. In regards to natural ITCs, they all have better assay characteristics except the SA. Conclusion: Molecular docking, physicochemical, pharmacokinetic, and toxicity studies show that methyl eugenol isothiocyanate and cinnamaldehyde isothiocyanate are promising anti-malaria compounds. Substituents of hydroxy, acetate and tetrahydropyran groups in the building block ring are suggested for better in silico profiles enhancement.

scholarly journals The potency of alpha-humulene as HER-2 inhibitor by molecular docking

2022 ◽  
Vol 2 (1) ◽  
pp. 19
Author(s):  
I Made Harimbawa Putra ◽  
I Putu Ari Anggara Catur Pratama ◽  
Komang Dian Aditya Putra ◽  
G. A. Desya Pradnyaswari ◽  
Ni Putu Linda Laksmiani
Keyword(s):  
Breast Cancer ◽  
Molecular Docking ◽  
Binding Energy ◽  
In Silico ◽  
Van Der Waals ◽  
Electrostatic Energy ◽  
Protein Preparation ◽  
Her 2 ◽  
In Silico Molecular Docking

HER-2 overexpression is present in approximately 20% of breast cancer. This research aims to study the interactions of α-humulene to HER-2 protein by using in silico molecular docking. The experiment was carried out by HER-2 protein preparation (PDB ID 3PP0), docking validation, α-humulene optimization, and α-humulene docking. The results showed that α-humulene had binding energy of -7.50 kcal/mol, Van der Waals binding energy of -7.48 kcal/mol, and electrostatic energy of -0.02 kcal/mol. α-Humulene is potential as anti-breast cancer towards HER-2 in silico.

scholarly journals In silico molecular docking of quercetin as anti-colorectal cancer agents by inhibiting LT4AH

2021 ◽  
Vol 1 (2) ◽  
pp. 16
Author(s):  
Made Agus Widiana Saputra ◽  
Anak Agung Istri Rani Mahaswari ◽  
Ni Ketut Sri Anggreni ◽  
Wahyu Nadi Eka Putri ◽  
Ni Putu Linda Laksmiani
Keyword(s):  
Colorectal Cancer ◽  
Molecular Docking ◽  
Binding Energy ◽  
In Silico ◽  
Malignant Neoplasm ◽  
Docking Method ◽  
Leukotriene A4 Hydrolase ◽  
Leukotriene A4 ◽  
In Silico Molecular Docking ◽  
Native Ligand

Colorectal cancer is a malignant neoplasm originating from the colon or rectum. Overexpression of leukotriene A4 hydrolase (LTA4H) increases the growth of HCT116 colon cancer cells, therefore, this enzyme becomes an attractive target for commercial drug bestatin. Meanwhile, quercetin is a member of flavonoids possessing a wide variety of anticancer. This study aimed to determine the potential of quercetin as anti-colorectal cancer by inhibiting LTA4H through in silico molecular docking. The docking process involved optimizing quercetin structure, preparing LTA4H protein (PDB ID: 3U9W), validating the molecular docking method, and docking quercetin and bestatin on LTA4H. The binding energy of quercetin to LTA4H was -9.57 kcal/mol, while 28P native ligand and bestatin yielded -10.22 kcal/mol and -9.10 kcal/mol, respectively. Based on the binding energy value, quercetin has a potential inhibitory against the LTA4H.

scholarly journals Molecular Docking Terpinen-4-ol pada Protein IKK sebagai Antiinflamasi pada Aterosklerosis secara In Silico

2019 ◽  
pp. 44
Author(s):  
Putu Pradnya Pramita Dewi
Keyword(s):  
Molecular Docking ◽  
Endothelial Dysfunction ◽  
Hydrogen Bonds ◽  
In Silico ◽  
Inflammatory Process ◽  
Chronic Inflammatory Disease ◽  
Docking Method ◽  
Result Show ◽  
Keywords Atherosclerosis ◽  
Zingiber Cassumunar

ABSTRACT   Atherosclerosis is a chronic inflammatory disease that begins with endothelial dysfunction, it caused fat accumulation and plaque growth in the inner arteries walls. Endothelial dysfunction will activate the Nuclear Factor Kappa B (NF-kB) pathway involving IKK proteins. Terpinen4-ol is constituent found in the bangle (Zingiber cassumunar) rhizome. The purpose of this study were to determine the affinity and mechanisms of terpinen-4-ol against IKK protein as anti-inflammatory in atherosclerosis performed using molecular docking method. The docking result are assessed from the binding energy and hydrogen bonds formed between terpinen-4-ol and protein. The result showed that terpinen-4-ol has activity in inhibiting the inflammatory process because it is able to disturb IKK protein with bond energy values -4.89 kcal/mol. The molecular mechanism in inhibiting the activity of IKK protein through the formation of hydrogen bonds in these proteins. These result show that terpinen-4-ol has the potential to inhibiting inflammatory process and it caused the formation of atherosclerotic plaque can be obstructed.   Keywords: Atherosclerosis, Terpinen-4-ol, Molecular Docking, In Silico

scholarly journals STUDI POTENSI SIANIDIN DAN PEONIDIN DARI UBI JALAR UNGU (ipomoea batatas L.) SEBAGAI AGEN DEPIGMENTASI SECARA IN SILICO

Jurnal Kimia ◽  
2019 ◽  
Vol 13 (1) ◽  
pp. 34
Author(s):  
N. P.L. Laksmiani ◽  
I G.P. Putra ◽  
I P.W. I P. W. Nugraha ◽  
I W. Suwartawan ◽  
N. K.S. Ani
Keyword(s):  
Molecular Docking ◽  
Sweet Potato ◽  
In Silico ◽  
Target Protein ◽  
Program Optimization ◽  
Test Compound ◽  
Docking Method ◽  
Purple Sweet Potato ◽  
Native Ligand ◽  
Molecular Docking Method

Hyperpigmentation is caused by enhancement of melanin production that causes skin darkening. Purple sweet potato is one of the plants that is potentially developed as skin depigmentation agent because it contains anthocyanin. The most common types of anthocyanins in purple sweet potato are cyanidin and peonidin which are in vitro proven to be used as skin lightening. The objective of this study is to determine the potential of cyanidin and peonidin as skin depigmentation agent against target protein D-Dopachrome taumerase  through in silico molecular docking method. The research steps include the preparation of target protein using Chimera 1.10.1 program, optimization of cyanidine and peonidin 3D structures using Hyperchem 8 program, validation of molecular docking method, and docking of cyanidine and peonidine on target protein using Autodock 4.2 program. The bond energy between cyanidin and peonidin with the target protein D-Dopachrome taumerase are -7.75 kcal / mol and -8.38 kcal / mol. The cyanidin and peonidin bond values ??are smaller than the native ligand, suggesting that the bond between the test compound (cyanidin and peonidin) with the target protein are stronger and more stable than the native ligand, so that the affinity of the test compound was greater than the native ligand. This suggests that the cyanidin and peonidin compounds in purple sweet potato have potential as a depigmentation agent by inhibiting D-Dopachrome taumerase protein.

scholarly journals In Silico Analysis of Antiviral Activity of Analog Curcumin Compounds

2020 ◽  
Vol 5 (3) ◽  
pp. 114-121
Author(s):  
Esti Mulatsari ◽  
Titiek Martati ◽  
Esti Mumpuni ◽  
Nidya Luciana Dewi
Keyword(s):  
Biological Activity ◽  
Molecular Docking ◽  
Antiviral Activity ◽  
In Silico ◽  
In Silico Analysis ◽  
Curcumin Analog ◽  
Compound Control ◽  
Docking Method ◽  
Silico Analysis ◽  
Molecular Docking Method

Some studies state that curcumin analog compounds can improve the bioavailability and biological activity of curcumin. One of the methods to predict the bioactivity of curcumin was computational using molecular docking method. This study has done bioactivity tests of curcumin analog compounds as antiviral using the molecular docking method with the software used are PLANTS, YASARA, MarvinSketch, and Pymol for visualization. This study used analog curcumin compounds derived from previous research. This study used five different viral reseptor types. The maraviroc, docosanol, ribavirin, and zanamivir were used as compound control in this research. The validated target protein consists of 5 (five) receptors with PDB codes 1V2I, 4WEG, 2HWI, 2QAD, and 3ALP. Based on this research, compounds that are predicted active as antiviral on each receptors that are: 2,5-bis(3,5-ditertbutyl-4-hydroxy benzyl)cyclopentanone (1V2I), 1,7- diphenyl-1,6-heptadiene-3,5-dione (4WEG), 1,7-bis(3,4-dibenzyloxiphenyl)-1,6-heptadiene-3,5-dione (2HWI), and 2,5-bis(3,5-ditertbutyl-4-hydroxybenzyl)cyclopentanone (3ALP). 

scholarly journals SENYAWA KUERSETIN SEBAGAI AGEN ANTIKANKER KOLOREKTAL SECARA IN SILICO

Jurnal Kimia ◽  
2019 ◽  
pp. 166
Author(s):  
P. V. P. Putri ◽  
N. M. P. Susanti ◽  
N. P. L. Laksmiani
Keyword(s):  
Colorectal Cancer ◽  
Molecular Docking ◽  
Binding Energy ◽  
Cancer Cells ◽  
In Silico ◽  
Caspase 3 ◽  
Protein Preparation ◽  
Keywords Colorectal Cancer ◽  
Cox 2

Colorectal cancer is a third rank malignant cancer in Indonesia, generally caused by the diet of the Indonesian people who have change with the consumption of food with high fat and low in fiber, also due to the production of carcinogenic substances from the breakdown of fat. In the condition of colorectal cancer there is overexpression of COX-2 and inhibition of Caspase-3 which causes the increase of cancer cells survival and causes inhibition of apoptosis mechanism. Quercetin is one of flavonoid which known have activity as an antitumor and tested in vitro can induce apoptosis on WiDr colorectal cancer cells . The purpose of this study was to determine the affinity and mechanism of quercetin compounds on COX-2 and Caspase-3 target proteins as colorectal anticancer by in silico with molecular docking. The study was conducted exploratively with the stages of preparing a database of 3D quercetin structures, as well as COX-2 and Caspase-3 proteins, optimization of 3D quercetin structure, protein preparation, molecular docking method validation, and quercetin docking on these proteins. Docking results were assessed from the binding energy and hydrogen bonds that formed between quercetin with proteins. The smaller binding energy value, the stronger the bond between quercetin and proteins is. The results showed that quercetin had an activity as a colorectal anticancer because it was able to inhibit COX-2 and induce Caspase-3 with binding energy values of -9.54 and -4.59. These results showed that quercetin has the potential to induce apoptosis in colorectal cancer.   Keywords: colorectal cancer, quercetin, caspase-3, in silico

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