scholarly journals PEMODELAN MOLEKUL SENYAWA TURUNAN KOJIC ACID SERTA INTERAKSINYA DENGAN ENZIM TIROSINASE

2020 ◽  
Vol 24 (2) ◽  
pp. 54-58
Author(s):  
Fazrul Permadi
Keyword(s):  
Kojic Acid ◽  
Autodock Vina ◽  
Discovery Studio

Studi HKSA dilakukan pada turunan kojyl thioether sebagai inhibitor tirosinase. Perhitungan prediktotr dilakukan menggunakan aplikasi hyperchem 8.0 dengan metode optimasi geometri semi-empirik PM3. Analisis regresi multilinier menggunakan SPSS 25.0 untuk mencari hubungan antara prediktor dan aktivitas senyawa turunan kojyl thioether sebagai inhibitor tirosinase. Model persamaan HKSA terbaik adalah  :pIC50 = -922.517 + 15.872*ELUMO – 436.654*qC4 – 209.509*qC5 + 1.0008*Eintn = 14; m = 4; r = 0.949; R2 = 0.901; PRESS = 3.0469; q2 = 0.8246Berdasarkan persamaan HKSA diatas didapatkan 4 senyawa baru turunun kojyl thioether yang bisa dijadikan sebagai analog inhibitor tirosinase yang baru. Parameter pemilihan senyawa tersebut karena memiliki aktivitas yang lebih baik sebagai inhibitor tirosinase dibandingkan senyawa penuntun, tidak hepatotoksik, tidak menimbulkan AMES Toxicity, tidak menimbulkan skin sensititasion dan LD50 pada tikus masuk kategori relative tidak membahayakan. Untuk melihat interaksi antara senyawa turunun kojyl thioether dengan enzim tirosinase dilakukan docking menggunakan Autodock vina yang visualisasinya menggunakan discovery studio 2020 client. Hasil docking menunjukkan bahwa semua senyawa setidaknya memiliki satu interaksi pada residu asam amino yang sama dengan native ligan. yaitu Val283.

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 Discovery of Potential Plant-derived Iradoides with COVID-19 Mpro in silico

2021 ◽  
Author(s):  
Mohd Rehan
Keyword(s):  
Natural Products ◽  
Chinese Medicine ◽  
In Silico ◽  
Binding Energies ◽  
Small Class ◽  
Chinese Scientist ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Traditional System ◽  
Potential Target

Abstract Iradoides are a small class of plant derived natural products, which used in traditional system of medicine such as Unani, Tibetan, Ayurveda, Siddha, and Chinese medicine. The several diverse types of iradoides have been isolated from many parts of the plant such as root, leaves, flowers, stem, rhizomes, bark, and seed. Here, we used bioactive iradoides to know the potency against COVID-19 Mpro. The COVID-19 Mpro is a potential target of the drug, which identified by Chinese scientist (published manuscript in Nature on June 2020). From several studies, we found that many natural products such as flavonoids, saponins, steroids, terpenoids, and synthesized compounds have been used on this target (COVID-19 Mpro). We screened a series of iradoides against COVID-19 Mpro (PDB ID: 6LU7) by using many docking software as BIOVIA Discovery Studio 2017 R2, Chimera 1.13.1, Auto Dock Tools-1.5.6, AutoDock Vina to known best inhibitor against COVID-19 Mpro. According to obtained results, 6′-O-trans-feruloylnegundoside, p-hydroxybenzoyl-6′-O-trans-caffeoylgardoside, 2′-O-p-hydroxybenzoyl gardoside, 6-deoxyharpagide, reptoside show binding energies -8.1, -8.3, -8.2, -7.0, and -7.1 Kcal/mol, respectively. From this study, we found that all iradoides show more potency on COVID-19 Mpro when compared with Chloroquine and hydroxychloroquine. The Chloroquine and hydroxychloroquine used as standards for comparison. From the results of this study, we found that iradoides may be useful in the treatment of COVID-19 patients.

scholarly journals Flavonoides das plantas do gênero Lavandula como potenciais inibidores de proteínas-chave do SARS-CoV-2

2021 ◽  
Vol 10 (12) ◽  
pp. e345101220580
Author(s):  
José Gabriel Fontenele Gomes ◽  
Neirigelson Ferreira de Barros Leite
Keyword(s):  
In Silico ◽  
Autodock Vina ◽  
Discovery Studio

Objetivo: avaliar o perfil de interações entre os flavonoides frente às proteínas-chave da infecção pelo SARS-CoV-2, e de modo secundário, objetivou-se analisar as propriedades destes constituintes químicos frente à Regra de Lipinski como potenciais candidatos a fármacos. Metodologia: Este estudo caracteriza-se como do tipo quantitativo descritivo de caráter experimental, através de métodos computacionais, onde foram utilizados os programas AutoDock Tools, AutoDock  Vina, Biovia Discovery Studio e ChimeraX para a realização do acoplamento molecular entre os principais flavonoides presentes nas plantas do gênero Lavandula com a proteína M e o complexo entre a Enzima Conversora de Angiotensina 2 e o domínio de ligação do receptor da proteína S do SARS-CoV-2. Resultados: Analisando-se as interações isoladas de cada flavonoide com as proteínas, nota-se que os compostos apresentaram interações mais favoráveis com a Enzima Conversora de Angiotensina 2 e o domínio de ligação do receptor. Para a regra de Lipinski, a Delfinidina apresentou duas violações, sendo considerada, neste contexto, uma molécula pouco promissora. Conclusão: Conclui-se, portanto, que os flavonoides apresentam in silico um potencial inibitório para as proteínas testadas, sendo mais favorável ao complexo da Enzima Conversora de Angiotensina 2 com o domínio de ligação ao receptor. Frente à regra de Lipinski, apenas a Delfinidina demonstrou baixo potencial para candidata a fármaco, contudo, o uso de nanocarreadores poderia contornar algumas de suas limitações.

scholarly journals Computational analysis of the interaction of limonene with the fat mass and obesity-associated protein

2021 ◽  
Vol 8 (1) ◽  
pp. 154-160
Author(s):  
Muhammad Zeeshan Ahmed ◽  
Shahzeb Hameed ◽  
Mazhar Ali ◽  
Ammad Zaheer
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Fat Mass ◽  
Computational Analysis ◽  
Physical Interaction ◽  
Autodock Vina ◽  
Inhibitory Interaction ◽  
Protein Association ◽  
Discovery Studio ◽  
Bioinformatic Tool

This study aimed to predict the binding affinity, orientation, and physical interaction between limonene and fat mass and obesity-associated protein. The mechanism of limonene and protein association was explored by molecular docking, a bioinformatic tool. The results of association were compared with the reported results of the anti-obesity drug such as orlistat and with the flavonoids. AutoDock Vina tools were used for the molecular docking of limonene with fat mass and obesity-associated protein. PyMol and Discovery Studio Visualizer were used to visualize the results of this docking. The binding affinity of limonene was higher (Least negative G) than the orlistat and flavonoids such as Daidzein, Exemestane, Kaempherol, Letrozole, And Rutin. It is conducted in this study that the Limonene can alleviate obesity by making an interaction with the fat mass and obesity-associated protein. This inhibitory interaction was greater as compared to other reported phytochemicals and drugs.

scholarly journals Prediction of SARS-CoV-2 Main Protease Inhibitors from Several Medicinal Plant Compounds by Drug Repurposing and Molecular Docking Approach.

2020 ◽  
Author(s):  
Sayma Farabi ◽  
Nihar Ranjan Saha ◽  
Noushin Anika Khan ◽  
Md. Hasanuzzaman
Keyword(s):  
Molecular Docking ◽  
Medicinal Plant ◽  
Drug Repurposing ◽  
Effective Vaccine ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Virulent Strains ◽  
Main Protease ◽  
Docking Approach ◽  
Phytochemical Compounds

<div> <sup>Coronaviruses are endemic in humans and infections normally mild, such as the common cold but cross-species transmission has produced some unusually virulent strains which now causing viral pneumonia and in serious cases even acute respiratory distress syndrome and death. SARS-CoV-2 is the most threatening issue which leads the world to an uncertainty alongside thousands of regular death scenes. For this virus, death toll is increasing in. An effective vaccine to cure this virus is not yet available, thus requires concerted efforts at various scales. The viral Main Protease controls Coronavirus replication and is a proven drug discovery target for SARS-CoV-2. Here, comprehensive computational approaches including drug repurposing and molecular docking were employed to predict the efficacy of medicinal plant-based bioactive compounds against SARS-CoV-2 Mpro. Molecular docking was performed using PyRx-autodock vina to analyze the inhibition probability. MPP (6LU7) was docked with 90 phytochemical compounds and docking was analysed by PyRx-autodock vina, Pymol version 1.7.4.5 Edu, and Biovia Discovery Studio 4.5. Furthermore, ADME analysis along with analysis of toxicity was also investigated to check the pharmacokinetics and drug-likeness properties of the antiviral phytochemicals. Remdesivir and lopinavir were used as standards for comparison. Our analyses revealed that the top ten (Azadirachtin, -12.5kcal/mol; Rutin, -9 kcal/mol; Theaflavin, -9 kcal/mol; Astragalin, -8.8 kcal/mol; Isoquercitrin, -8.7 kcal/mol; Hyperoside, -8.6 kcal/mol; Baicalin, -8.4 kcal/mol; Saponin, -8.3 kcal/mol; Sennoside A, -8.3 kcal/mol; Aloin, -8.2 kcal/mol, while Remdesivir and Lopinavir showed -8.2 and -7.9 kcal/mol) hits might serve as potential anti- SARS-CoV-2 lead molecules for further optimization and drug development process to combat COVID-19. <br></sup></div><div><sup><br></sup></div>

scholarly journals Prediction of SARS-CoV-2 Main Protease Inhibitors from Several Medicinal Plant Compounds by Drug Repurposing and Molecular Docking Approach.

2020 ◽  
Author(s):  
Sayma Farabi ◽  
Nihar Ranjan Saha ◽  
Noushin Anika Khan ◽  
Md. Hasanuzzaman
Keyword(s):  
Molecular Docking ◽  
Medicinal Plant ◽  
Drug Repurposing ◽  
Effective Vaccine ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Virulent Strains ◽  
Main Protease ◽  
Docking Approach ◽  
Phytochemical Compounds

<div> <sup>Coronaviruses are endemic in humans and infections normally mild, such as the common cold but cross-species transmission has produced some unusually virulent strains which now causing viral pneumonia and in serious cases even acute respiratory distress syndrome and death. SARS-CoV-2 is the most threatening issue which leads the world to an uncertainty alongside thousands of regular death scenes. For this virus, death toll is increasing in. An effective vaccine to cure this virus is not yet available, thus requires concerted efforts at various scales. The viral Main Protease controls Coronavirus replication and is a proven drug discovery target for SARS-CoV-2. Here, comprehensive computational approaches including drug repurposing and molecular docking were employed to predict the efficacy of medicinal plant-based bioactive compounds against SARS-CoV-2 Mpro. Molecular docking was performed using PyRx-autodock vina to analyze the inhibition probability. MPP (6LU7) was docked with 90 phytochemical compounds and docking was analysed by PyRx-autodock vina, Pymol version 1.7.4.5 Edu, and Biovia Discovery Studio 4.5. Furthermore, ADME analysis along with analysis of toxicity was also investigated to check the pharmacokinetics and drug-likeness properties of the antiviral phytochemicals. Remdesivir and lopinavir were used as standards for comparison. Our analyses revealed that the top ten (Azadirachtin, -12.5kcal/mol; Rutin, -9 kcal/mol; Theaflavin, -9 kcal/mol; Astragalin, -8.8 kcal/mol; Isoquercitrin, -8.7 kcal/mol; Hyperoside, -8.6 kcal/mol; Baicalin, -8.4 kcal/mol; Saponin, -8.3 kcal/mol; Sennoside A, -8.3 kcal/mol; Aloin, -8.2 kcal/mol, while Remdesivir and Lopinavir showed -8.2 and -7.9 kcal/mol) hits might serve as potential anti- SARS-CoV-2 lead molecules for further optimization and drug development process to combat COVID-19. <br></sup></div><div><sup><br></sup></div>

scholarly journals DOCKING MOLEKULER SENYAWA B-KAROTEN DALAM TANAMAN KELOR (Moringa Oleifera L.) SEBAGAI PENGHAMBAT ENZIM TIROSINASE DENGAN AUTODOCK – VINA

2020 ◽  
Vol 3 (2) ◽  
pp. 230-240
Author(s):  
Bayu Herdi Al Huda ◽  
◽  
Nining Sugihartini ◽  
Hari susanti ◽  
Dwi Utami
Keyword(s):  
Binding Affinity ◽  
Interaction Mechanism ◽  
Ligand Docking ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Amino Acid Receptors ◽  
Know How ◽  
Tyrosinase Enzyme ◽  
Whitening Activity ◽  
Autodock 4.2

Hydroquinone has been used in cosmetics because of its whitening activity. In previous studies, B-carotene in Moringa plants was also known as an inhibitor of the tyrosinase enzyme. It is necessary to know how the interaction mechanism of B-carotene with tyrosinase (5M8N) and which compounds between hydroquinone and B-carotene provide computationally better activity as whitening. Tyrosinase was prepared using Discovery Studio Visualizer. Ligands were prepared using Autodock 4.2. Autodock-Vina is used for ligand docking between proteins. The result is the binding affinity (kcal/mol) of the ligand to protein. Visualization of docking between ligands and proteins using the Ligplot + Program with a 1 year license. Media used for the docking process is a computer with an Intel Core i7-3770 CPU with a speed of 3.40 GHz 8 cores, 1920x1080p resolution, VGA NVIDIA GeForce GTX 750, 8 GB RAM, Windows 8 64-bit. The docking results showed that the binding affinity of B-carotene to tyrosinase was -11.2 while hydroquinone with tyrosinase was -5.4 with RMSD 0. The results of visualization showed that B-carotene binds more amino acid receptors than hydroquinone. B-carotene in moringa has been shown to be active not only in wet laboratories, but also in dry laboratories.

scholarly journals Molecular Docking Studies on Phenolic Constituents of Anethum graveolens L. Seed Extracts

2021 ◽  
pp. 119-128
Author(s):  
Paul Andrei Negru ◽  
Sanda Rodica Bota ◽  
Oana Delia Stanasel ◽  
Cristian Felix Blidar ◽  
Georgeta Serban
Keyword(s):  
Antioxidant Activity ◽  
Molecular Docking ◽  
Docking Studies ◽  
Autodock Vina ◽  
Anethum Graveolens ◽  
Inhibitory Potency ◽  
Molecular Docking Studies ◽  
Discovery Studio ◽  
Phenolic Constituents ◽  
Seed Extracts

Background: There are studies indicating that aqueous or hydroalcoholic dill extracts showed higher antioxidant activity compared to other fractions. Molecular docking studies would be relevant to get information on the mechanism of action of the phenolic constituents of Anethum graveolens seed extracts as bioactive compounds. Methodology: In order to perform the docking studies of antioxidant activity of phenolic constituents of Anethum graveolens seed extracts, BIOVIA Discovery Studio and AutoDock Vina software were used. Results: The orientation of flavonoids within Hck and CYP2C9 binding sites has been shown to be the main reason for their inhibitory potency. Conclusion: Molecular docking studies indicate that the compounds identified interact with the target enzymes Hck and CYP2C9 at molecular level through their condensed ring systems and hydroxyl substituents and therefore support the antioxidant capacity of the studied phenolic compounds.

scholarly journals Molekuler Docking tehadap Senyawa Eugenol dan Myricetin pada Tanaman Cengkeh (Syzygium aromaticum) sebagai Penghambat Pertumbuhan SARS-CoV-2

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Yizreel Y. Gerungan ◽  
Billy J. Kepel ◽  
. Fatimawali ◽  
Aaltje Manampiring ◽  
Fona D. Budiarso ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Growth Inhibitor ◽  
Syzygium Aromaticum ◽  
Amino Acid Residues ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Main Protease ◽  
Almost All ◽  
The Impact

Abstract: Cloves contain many chemical compounds that can be used for health. COVID-19 is a disease that is shaking the world today. Many people feel the impact of this disease. Until now, there is no definite cure and vaccine for the handling of COVID-19.  Objective to determine the interaction between compounds in cloves (eugenol and myricetin) and the main protease COVID-19 (6LU7). This study use a molecular docking, method using 4 main applications: autodock tools, autodock vina, biovia discovery studio and open babel. This study showed that almost all amino acid residues in the eugenol and myricetin compounds worked on the 6LU7 active site. The binding affinity of eugenol compounds in clove plants does not exceed the binding affinity of remdesivir, a drug studied as a drug for handling COVID-19, while the binding affinity of myricetin compounds in cloves plant exceeds the binding affinity of remdesivir. In conclusion, myricetin compounds have better results for use as a growth inhibitor for COVID-19 than eugenol.Key words: Cloves, COVID-19, molecular docking.  Abstrak: Cengkeh memiliki banyak kandungan senyawa kimia yang dapat dimanfaatkan bagi kesehatan. COVID-19 merupakan penyakit yang mengguncang dunia saat ini. Banyak masyarakat yang merasakan dampak dari penyakit ini. Hingga saat ini belum ada obat dan vaksin yang pasti untuk penanganan COVID-19. Penelitian ini bertujuan untuk mengetahui interaksi antara senyawa pada cengkeh (eugenol dan myricetin) dengan main protease COVID-19 (6LU7). Jenis penelitian ini menggunakan metode molekuler docking dengan menggunakan 4 aplikasi utama: autodock tools, autodock vina, biovia discovery studio dan open babel. Hasil penelitian ini menunjukkan bahwa hampir semua residu asam amino pada senyawa eugenol dan myricetin bekerja pada sisi aktif 6LU7. Hasil binding affinity senyawa eugenol pada tumbuhan cengkeh tidak melebihi binding affinity dari remdesivir, obat yang diteliti sebagai obat penanganan COVID-19, sedangkan hasil binding affinity senyawa myricetin pada tumbuhan cengkeh melebihi binding affinity dari remdesivir. Simpulan penelitian ini ialah senyawa myricetin memiliki hasil yang lebih baik untuk digunakan sebagai penghambat pertumbuhan COVID-19 dari pada eugenol.Kata kunci: Cengkeh, COVID-19, molekuler docking.

scholarly journals Ácido Valerênico e seu potencial ansiolítico por meio da interação com receptores do tipo GABAA: um estudo in silico

2021 ◽  
Vol 10 (13) ◽  
pp. e07101320677
Author(s):  
José Gabriel Fontenele Gomes ◽  
Liliam With Monalisa Araujo Silva ◽  
Weslley Tiago Bitencourt de Andrade ◽  
Anne Karolinne Melo de Andrade Gomes ◽  
Clara Rita de Sousa Magalhães ◽  
...  
Keyword(s):  
In Silico ◽  
Autodock Vina ◽  
Discovery Studio ◽  
De Se

Objetivo: Analisar o potencial ansiolítico do Ácido Valerênico mediante o acoplamento molecular in silico em receptores do tipo GABAA. Metodologia: Realizou-se um estudo do tipo quantitativo descritivo, com caráter experimental. A fim de se confirmar a validade da metodologia durante o acoplamento molecular, realizou-se um redocking utilizando a molécula de Diazepam nativa cristalografada com o receptor GABAA. As interações já apresentadas pelo Diazepam com o receptor, foram utilizadas para fins comparativos com as interações do Ácido Valerênico. As estruturas dos compostos foram obtidas por meio da plataforma PubChem. Para a representação tridimensional das estruturas foi utilizado o programa ChimeraX. Para a realização de todo o procedimento de docking foram utilizados os programas Biovia Discovery Studio, Avogadro, AutoDock Tools e AutoDock Vina. Resultados: Constatou-se que dentre todos os valores de afinidade demonstrados, levando-se em conta sua eletronegatividade, o Ácido Valerênico foi quem apresentou menor gasto energético. Nota-se também que o composto em questão viola apenas o parâmetro do LogP, o que o configura como um bom candidato a possível novo fármaco. Conclusão: Através do estudo in silico, foi possível a análise do potencial ansiolítico do Ácido Valerênico. Por meio da utilização do Diazepam e suas interações com o receptor GABAA como parâmetro, foi possível identificar que o Ácido Valerênico apresenta interações com gasto energético mínimo, e consequentemente valores aceitáveis de afinidade.

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