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

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.

Download Full-text

AKTIVITAS DARI KUERSETIN SEBAGAI AGEN PENCERAH KULIT SECARA IN SILICO

Jurnal Kimia ◽

10.24843/jchem.2019.v13.i02.p14 ◽

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

Download Full-text

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

Jurnal Kimia ◽

10.24843/jchem.2019.v13.i02.p05 ◽

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

Download Full-text

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

International Journal of Applied Pharmaceutics ◽

10.22159/ijap.2021v13i6.42292 ◽

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.

Download Full-text

IN SILICO STUDIES ON DIACYL DERIVATIVES OF PHLOROGLUCINOL TO ENHANCE PHARMACODYNAMIC AND PHARMACOKINETIC PROFILES OF 2,4,6-TRIHYDROXY-3-GERANYL-ACETOPHENONE

International Journal of Applied Pharmaceutics ◽

10.22159/ijap.2021v13i2.40784 ◽

2021 ◽

pp. 173-179

Author(s):

SHEAU WEI CHIONG ◽

CHEAN HUI NG ◽

KHOZIRAH SHAARI

Keyword(s):

Molecular Docking ◽

Amino Acid ◽

Chain Length ◽

In Silico ◽

Van Der Waals ◽

Side Chains ◽

Amino Acid Residues ◽

Pharmacokinetic Profiles ◽

In Silico Studies ◽

Derivatives Of

Objective: The purpose of this study was to evaluate the LOX inhibitory activity, and predict the drug likeness properties of designed diacyl derivatives of phloroglucinol, using in silico method. Methods: The designed derivatives were subjected to molecular docking using AUTODOCK while the receptor used in this study was built from SWISS MODEL. Drug likeness properties of the derivatives were calculated by online programs i.e. MOLINSPIRATION and PreADMET. Results: Molecular docking study revealed that designed tHGA derivative with four-carbon chain length exhibited the best binding affinity with the docking scores of -7.26kcal/mol. Three types of binding interactions were observed between the derivatives and the receptor site i.e H-bonding, hydrophobic and Van der Waals interactions. The important amino acid residues involved in H-bonding were Gln495 and Gln697, while other amino acid residues, such as Leu754 and Ile 553, were involved in the Van der Waals interaction. The designed tHGA derivatives were mainly stabilized through hydrophobic interactions with His499, His504, Ile538, Phe557 and Val750. In silico physicochemical calculations predicted that all the designed derivatives passed the Lipinski’s Rule of 5, and have good human intestinal absorption property (HIA>70%). Further, all the designed derivatives showed moderate central nervous system absorption (0.6<BBB<2.0), except for the derivative with a longer (5-Cs) chain length. Conclusion: The findings of the present study suggested that changing the acyl and geranyl side chains of the natural product molecule, tHGA, into two acyl bearing side chains, will improve its pharmacodynamic and pharmacokinetic profiles.

Download Full-text

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

Jurnal Farmasi Udayana ◽

10.24843/jfu.2019.v08.i01.p07 ◽

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

Download Full-text

Molecular docking studies of natural compounds of naringin on enzymes involved in the urea cycle pathway in hyperammonemia

Tropical Journal of Pharmaceutical Research ◽

10.4314/tjpr.v19i5.19 ◽

2020 ◽

Vol 19 (5) ◽

pp. 1037-1043

Author(s):

Ramakrishnan Arumugam ◽

Renuka Mani ◽

Amalan Venkatesan ◽

Senthilmurugan Sengamalai ◽

Vijayakumar Natesan ◽

...

Keyword(s):

Molecular Docking ◽

Binding Energy ◽

Hydrogen Bonds ◽

Sodium Benzoate ◽

In Silico ◽

Urea Cycle ◽

Molecular Docking Study ◽

Standard Drug ◽

In Silico Studies ◽

Urea Cycle Enzymes

Purpose: To investigate the anti-hyperammonemic activity of naringin by molecular docking via in silico studies.Methods: Urea cycle proteins were docked to the natural compound naringin as well as a standard drug, sodium benzoate. Hydrogen bonds and binding energy were obtained using Catalytic Site Atlas and Cast P Finder Software Tool.Results: There were six urea cycle enzymes, including N-acetyl glutamate synthase, carbamoyl phosphate synthase I, ornithine transcarbamylase, argininosuccinate synthase, argininosuccinate lyase and arginase I. On evaluating protein interactions with naringin, which is dynamically connected to the urea cycle pathway with hyperammonemia, naringin showed more hydrogen bonds and also produced higher binding energy when compared to the standard drug, sodium benzoate.Conclusion: The results of the molecular docking study show that naringin interacts with urea cycle enzymes with more hydrogen bonds and higher bonding energy than the standard drug, sodium benzoate. This supports the hypothesis that naringin can prevent experimental hyperammonemia. Keywords: Naringin, Sodium benzoate, Hyperammonemia, Urea cycle enzymes, In silico studies

Download Full-text

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

Jurnal Kimia ◽

10.24843/jchem.2019.v13.i01.p06 ◽

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.

Download Full-text

In Silico Analysis of Antiviral Activity of Analog Curcumin Compounds

Jurnal Jamu Indonesia ◽

10.29244/jji.v5i3.173 ◽

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).

Download Full-text

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

Jurnal e-Biomedik ◽

10.35790/ebm.v9i1.31809 ◽

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

Download Full-text

Molecular Docking Senyawa Vitexin, Ursolic Acid dan Flavonol dalam Tumbuhan Binahong (Andredera Cordifolia (Ten.) Steenis) yang Berpotensi sebagai Penghambat Pertumbuhan COVID-19

Jurnal e-Biomedik ◽

10.35790/ebm.v9i2.31825 ◽

2021 ◽

Vol 9 (2) ◽

Author(s):

Sensea R. Rambitan ◽

Aaltje Manampiring ◽

. Fatimawali ◽

Billy J. Kepel ◽

Fona Budiarso ◽

...

Keyword(s):

Molecular Docking ◽

Binding Affinity ◽

Ursolic Acid ◽

In Silico ◽

Van Der Waals ◽

Specific Treatment ◽

Amino Acid Residues ◽

The People ◽

The World ◽

Affinity Score

Abstract: Currently, there is no specific treatment for all the COVID-19 patients the procedures that can be done are just a symptomatic and oxygen therapy, Therefore all the people around the world have try to avoid this infection by consuming the potensial plants that can boost our body immunity like Binahong. This study was an in silico experimental. The finale result is the binding affinity score from each compound, for vitexin’s binding affinity score is – 8.0 kcal/mol, ursolic acid – 7.6 kcal/mol and flavonol – 7.8 kcal/mol. The finale result of this procedure also obtained all the amino acid residues that works on the active site of receptor 6LU7 as a main protase of COVID-19, namely THR24, LEU27, HIS41, THR45, SER46, MET49, PHE140, LEU141, ASN142, GLY143, SER144, CYS145, HIS163, MET165, GLU166 and HIS172. In conclusion, the binding affinity of vitexin, ursolic acid and flavonol are higher than remdesivir. Vitexin, ursolic acid and flavonol have a several similar bonds, particularly the van der waals bond and hydrogen bond.Keywords: Molecular docking, COVID-19, binahong, flavonoid Abstrak: Saat ini belum tersedia rekomendasi tatalaksana khusus bagi pasien COVID-19, termasuk antivirus atau vaksin dan tata laksana yang dapat dilakukan adalah terapi simtomatik dan karena itulah, masyarakat dunia mencoba banyak cara agar menghindari infeksi virus ini dengan mengolah dan mengonsumsi tumbuhan yang dinilai berpotensi dalam meningkatkan imunitas tubuh seperti tumbuhan Binahong. Penelitian ini menggunakan metode penelitian in silico. Pada hasil akhir penelitian diperoleh nilai binding affinity dari ketiga senyawa yaitu senyawa vitexin - 8.0 kcal/mol, Ursolic Acid -7.6 kcal/mol dan Flavonol -7.8 kcal/mol. Diperoleh data mengenai residu asam amino yang bekerja pada sisi aktif reseptor 6LU7 sebagai main protase COVID-19 yaitu THR24, LEU27, HIS41, THR45, SER46, MET49, PHE140, LEU141, ASN142, GLY143, SER144, CYS145, HIS163, MET165, GLU166, dan HIS172. Sebagai simpulan, binding affinity dari senyawa vitexin, ursolic acid dari flavonol lebih tinggi dari nilai binding affinity remdesivir. Senyawa vitexin, ursolic acid dan flavonol memiliki beberapa jenis ikatan yang sama termasuk ikatan van der Waals dan ikatan hydrogen.Kata Kunci: Molecular docking, COVID-19, binahong, flavonoid

Download Full-text