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 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 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 In silico study of lutein as anti-HER-2 receptors in breast cancer treatment

2021 ◽  
Vol 1 (1) ◽  
pp. 17
Author(s):  
Ni Ketut Nitya Cahyani ◽  
Wahyu Nadi Eka Putri ◽  
I Kadek Diva Dwivayana ◽  
Ni Putu Dinda Mirayanti ◽  
Ni Putu Linda Laksmiani
Keyword(s):  
Breast Cancer ◽  
Molecular Docking ◽  
Binding Energy ◽  
Cancer Progression ◽  
In Silico ◽  
Mechanism Of Inhibition ◽  
Docking Protocol ◽  
In Silico Study ◽  
Her 2 ◽  
In Silico Molecular Docking

Human Epidermal Receptor-2 (HER-2) overexpression is implicated in breast cancer progression; thus, HER-2 is widely used as the target of anticancer therapy. Lapatinib is a drug widely used to inhibit the HER-2 receptor and tyrosine kinase; however, it develops drug resistance. Lutein is promising to be developed as breast cancer therapy. This study aims to determine the mechanism of inhibition of HER-2 receptor overexpression by lutein in silico. Molecular docking was carried out by optimizing the lutein and lapatinib, preparing of protein target HER-2 (PDB ID 3PP0), validating of molecular docking protocol, and docking of lutein and lapatinib on HER-2. The study resulted in the binding energy of -12.37 kcal/mol, while the binding energy of the native ligand and lapatinib to HER-2 was -10.43 kcal/mol and -12.25 kcal/mol, respectively. The binding energy showed that lutein has potential as breast anticancer suggested from the stronger affinity to HER2.

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 analysis of some plant derived molecules for anti-inflammatory inhibitory activity

2021 ◽  
pp. 22-27
Author(s):  
L. Thamaraiselvi ◽  
T. Selvankumar ◽  
E.G. Wesely ◽  
N. Vinod Kumar
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
In Silico ◽  
Novel Drugs ◽  
In Silico Study ◽  
Low Toxicity ◽  
Cox 2 ◽  
Anti Inflammatory ◽  
In Silico Molecular Docking ◽  
Oxide Synthase

Herbs are essential resources for drug discovery. However, numerous challenges stand in front of the scientific community to discover novel drugs from herbs. To explore the validation behind the precious knowledge of traditional medicine, we focused on achieving virtual screening to detect the potential medicines from the herbs.  Five bioactive compounds from known anti-inflammatory medicinal plants were examined through molecular docking against  cyclooxygenase-2 (COX-2) and inducible Nitric Oxide Synthase (iNOS), using AutoDock 4.2. The docking of selected ligands with COX-2 showed the binding energy varying from -6.15 Kcal/mol to ‑11.24 Kcal/mol. The docking energies of identified ligands with iNOS were generated ranges from -3.85kcal/mol to -6.99 kcal/mol.  Among the tested ligands, it was noted that 6 urs-12-en-24-oic acid showed the best binding energy than other compounds with the lowest binding energy and highest binding affinity with both anti-inflammatory target proteins COX-2 and iNOS. The in silico study validates the potential phytochemical compound of the medicinal herb that contribute to anti-inflammatory activity with low toxicity and minimal side effects.

scholarly journals Molecular docking of lutein as anti-photoaging agent in silico

2021 ◽  
Vol 1 (1) ◽  
pp. 15
Author(s):  
I Gede Bayu Krisnayana ◽  
Putu Dewi Febyani ◽  
Ida Ayu Yadnyaningtias Permata Sari ◽  
Ni Putu Linda Laksmiani
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Uv Exposure ◽  
Type I ◽  
Fibrillar Collagen ◽  
Matrix Metalloproteinase 1 ◽  
High Antioxidant Activity ◽  
In Silico Molecular Docking ◽  
Native Ligand ◽  
Autodock 4.2

The accumulation of UV exposure resulted in the loss of skin elasticity, and the appearance of wrinkles on the skin is commonly known as photoaging. Matrix metalloproteinase-1 (MMP-1) is an enzyme that degrades type I and III fibrillar collagen. This study aims to determine the mechanism of MMP-1 inhibition by lutein, a carotenoid compound with high antioxidant activity, using in silico molecular docking. This study was conducted by optimization of lutein structure using HyperChem 8, preparation of MMP-1 (PDB ID: 966C) using Chimera 1.10.1, validation of the method, and docking lutein against MMP-1 using Autodock 4.2. The results showed lutein had binding energy of -12.28 kcal/mol, lower than RS2 native ligand (-10.83 kcal/mol). The hydrogen bond formed between lutein and MMP-1 through HIS228 residue. To conclude, lutein may be developed as an anti-photoaging agent by inhibiting the MMP-1.

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 Molecular docking of gallic acid as anti-photoaging in silico

2021 ◽  
Vol 1 (2) ◽  
pp. 18
Author(s):  
Ni Kadek Diah Parwati Dewi ◽  
Kadek Dinda Suryadewi ◽  
Diah Mawarni Fitriari ◽  
Kadek Lia Andini ◽  
Ni Putu Linda Laksmiani
Keyword(s):  
Molecular Docking ◽  
Gallic Acid ◽  
In Silico ◽  
Potential Effect ◽  
Skin Aging ◽  
Amino Acid Residues ◽  
Docking Protocol ◽  
Skin Photoaging ◽  
In Silico Molecular Docking ◽  
Native Ligand

Skin aging caused by excessive exposure to ultraviolet is known as photoaging. The mechanism underlying skin photoaging relates to collagen degradation in the extracellular matrix (ECM) by overexpression of matrix metalloproteinases-1 (MMP-1). Gallic acid is a phenolic antioxidant found in many types of plants and can be used as an anti-photoaging agent due to its antioxidant activity. This study aims to determine the potential effect of gallic acid as an anti-photoaging against MMP-1 using in silico molecular docking. The stages included gallic acid structure optimization using the HyperChem 8, preparation of protein target MMP-1 (PDB ID: 966C) using the Chimera1.10.1, validation the molecular docking protocol, and docking gallic acid on MMP-1 with the Autodock 1.5.6. The results showed that gallic acid had an affinity for MMP-1 with a binding energy of -6.0 kcal/mol. There are similar amino acid residues in hydrogen bonds between the native ligand RS2 with MMP-1 and gallic acid with MMP-1, namely ALA 182, LEU 181, and HIS 218. The results suggest that gallic acid has the potential as the anti-photoaging agent through the inhibition of the MMP-1 enzyme.

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

scholarly journals MOLECULAR DOCKING AKTIVITAS ANTIKANKER DARI KUERSETIN TERHADAP KANKER PAYUDARA SECARA IN SILICO

Jurnal Kimia ◽  
2019 ◽  
pp. 180
Author(s):  
M. B. O. Rastini ◽  
N. K. M. Giantari ◽  
K. D. Adnyani ◽  
N. P. L. Laksmiani
Keyword(s):  
Breast Cancer ◽  
Molecular Docking ◽  
Bond Energy ◽  
In Silico ◽  
Flavonoid Compound ◽  
Molecular Formula ◽  
Mechanism Of Inhibition ◽  
Her 2 ◽  
In Silico Molecular Docking ◽  
Native Ligand

Breast cancer can be initiated by either overexpression of HER-2 protein which can induce dimerization and autophosphorylation so that it triggers the activation of Focal Adhesion Kinase (FAK) resulting in migration and metastasis in breast cancer cells. Quercetin which has another name 3,5,7,3 ', 4'-pentahydroxyflavon with the molecular formula of (C15H10O7) is a flavonoid compound which is very widely found in nature. The purpose of this study was to determine the mechanism of inhibition of overexpression of HER-2 proteins by quercetin compounds by in silico molecular docking. In silico molecular docking was carried out in several stages namely method validation, optimization of 3D quercetin compound structure, docking between quercetin compounds optimized with HER-2 protein based on bond energy parameters the lower the bond energy the stronger and the more stable the bond is. The results of docking expressed by the binding energy of quercetin compounds with HER-2 protein are -8.24 kcal / mol, while the energy of the native ligand bond with HER-2 protein is -10.45 kcal / mol. The bonding energy shows that quercetin compounds have the potential as breast anticancer because they can modulate the overexpression of HER-2 proteins.   Keywords: quercetin, breast cancer, HER-2, in silico

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