In Silico Approach to Inhibition of Tyrosinase by Ascorbic Acid Using Molecular Docking Simulations

2014 ◽  
Vol 14 (12) ◽  
pp. 1469-1472 ◽  
Author(s):  
F. Senol ◽  
M. Khan ◽  
Gurdal Orhan ◽  
Erdem Gurkas ◽  
Ilkay Orhan ◽  
...  
Keyword(s):  
Ascorbic Acid ◽  
Molecular Docking ◽  
In Silico ◽  
Docking Simulations

scholarly journals Interaction of ZnO Nanostructures with Proteins: In Vitro Fibrillation/Antifibrillation Studies and in Silico Molecular Docking Simulations

2020 ◽  
Vol 11 (3) ◽  
pp. 436-444 ◽  
Author(s):  
Kleoniki Giannousi ◽  
George Geromichalos ◽  
Dionysia Kakolyri ◽  
Stefanos Mourdikoudis ◽  
Catherine Dendrinou-Samara
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Zno Nanostructures ◽  
Docking Simulations ◽  
In Silico Molecular Docking

scholarly journals Molecular Docking Senyawa Asam Askorbat dan Kuersetin pada Tumbuhan Jambu Biji Merah (Psidium guajava L.) Sebagai Pencegah COVID-19

2021 ◽  
Vol 9 (2) ◽  
Author(s):  
Inggrid V. Gandu ◽  
Fona D. H. Budiarso ◽  
Billy J. Kepel ◽  
. Fatimawali ◽  
Aaltje Manampiring ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Ascorbic Acid ◽  
Molecular Docking ◽  
Immune System ◽  
Binding Affinity ◽  
In Silico ◽  
Preventive Measure ◽  
Psidium Guajava ◽  
Positive Control ◽  
Important Thing

Abstract: Coronavirus Disease 2019 or COVID-19 is an infectious disease first identified in Wuhan, China in December 2019. Prevention of COVID-19 infection is an important thing to do in reducing the spread of this virus. Boosting the body's immune system can be done as a preventive measure, one of which is by consuming natural plants such as red guava. This study aims to determine the molecular docking of red guava (Psidium guajava L.) as a plant to prevent COVID-19. This was an in silico with computerized methods. The samples in this study were ascorbic acid and quercetin compounds in red guava plants obtained from the PubChem website. The results showed that the binding affinity of ascorbic acid is -5.4 and the binding affinity of quercetin is -7.6. Remdesivir which was used as a positive control had a binding affinity of -7.3. In conclusion, quercetin compounds have better results than ascorbic acid compounds and remdesivir.Keywords: COVID-19, red guava, molecular docking  Abstrak: Coronavirus Disease 2019 atau COVID-19 merupakan suatu penyakit menular yang pertama kali ditemukan di Wuhan, Tiongkok pada Desember 2019. Pencegahan infeksi COVID-19 merupakan hal yang penting untuk dilakukan dalam mengurangi penyebaran dari virus ini. Meningkatkan sistem imun tubuh dapat dilakukan sebagai tindakan pencegahan salah satunya dengan mengonsumsi tumbuhan-tumbuhan alami seperti jambu biji merah. Penelitian ini bertujuan untuk mengetahui molecular docking jambu biji merah (Psidium guajava L.) sebagai tanaman pencegah COVID-19. Jenis penelitian ialah in silico dengan metode komputerisasi. Sampel penelitian yaitu senyawa asam askorbat dan kuersetin pada tumbuhan jambu biji merah yang diperoleh dari website pubchem. Hasil penelitian mendapatkan binding affinity dari senyawa asam askorbat yaitu -5.4 dan binding affinity dari senyawa kuersetin yaitu -7.6. Remdesivir yang dijadikan sebagai kontrol positif mendapatkan hasil binding affinity yaitu -7.3. Simpulan penelitian ini ialah senyawa kuersetin memiliki hasil yang lebih baik daripada senyawa asam askorbat dan juga obat remdesivir.Kata kunci: COVID-19, jambu biji merah, molecular docking

scholarly journals Interacting Cubane Assisted Bi-Cytidine with COVID-19 Main Protease: In Silico Study

2021 ◽  
Vol 11 (6) ◽  
pp. 13962-13967
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
In Silico ◽  
Quantum Chemical ◽  
Imaginary Frequency ◽  
Docking Simulations ◽  
Patients With Cancer ◽  
Main Protease ◽  
In Silico Study ◽  
Quantum Chemical Computations

In silico approach, the quantum chemical computations and molecular docking simulations have been used to investigate the formation of cubane assisted cytidine (B-Cyt) derivative for examining its interactions with the COVID-19 main protease. The obtained results indicated that the new B-Cyt derivative could be stabilized without any imaginary frequency. Its orbital orbital-based electronic properties indicated that the structure could have a better interaction with the target than the singular Cyt ligand. The docking process results approved the trend, in which the value of binding energy was very much favorable regarding the singular models, and the number of interaction amino acids was increased. The idea of forming a Cyt derivative with efficient activity against COVID-19 main protease was approved here, which is very much important for protecting the patients with cancer or HIV against the COVID-19 pandemic.

scholarly journals Chemical Composition, Antioxidant and Enzyme Inhibitory Activities of Onosma bourgaei and Onosma trachytricha and in Silico Molecular Docking Analysis of Dominant Compounds

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 2981
Author(s):  
Erman Salih Istifli
Keyword(s):  
Molecular Docking ◽  
Chemical Composition ◽  
In Silico ◽  
Digestive Enzymes ◽  
Binding Affinities ◽  
Docking Analysis ◽  
Docking Simulations ◽  
Inhibitory Activities ◽  
In Silico Molecular Docking ◽  
Molecular Docking Analysis

The aim of this study was to investigate the chemical composition, antioxidant and enzyme inhibitory activities of methanol (MeOH) extracts from Onosma bourgaei (Boiss.) and O. trachytricha (Boiss.). In addition, the interactions between phytochemicals found in extracts in high amounts and the target enzymes in question were revealed at the molecular scale by performing in silico molecular docking simulations. While the total amount of flavonoid compounds was higher in O. bourgaei, O. trachytricha was richer in phenolics. Chromatographic analysis showed that the major compounds of the extracts were luteolin 7-glucoside, apigenin 7-glucoside and rosmarinic acid. With the exception of the ferrous ion chelating assay, O. trachytricha exhibited higher antioxidant activity than O. bourgaei. O. bourgaei exhibited also slightly higher activity on digestive enzymes. The inhibitory activities of the Onosma species on tyrosinase were almost equal. In addition, the inhibitory activities of the extracts on acetylcholinesterase (AChE) were stronger than the activity on butyrylcholinesterase (BChE). Molecular docking simulations revealed that luteolin 7-glucoside and apigenin 7-glucoside have particularly strong binding affinities against ChEs, tyrosinase, α-amylase and α-glucosidase when compared with co-crystallized inhibitors. Therefore, it was concluded that the compounds in question could act as effective inhibitors on cholinesterases, tyrosinase and digestive enzymes.

EVALUATION OF IN-SILICO ANTICANCER POTENTIAL OF PYRETHROIDS: A COMPARATIVE MOLECULAR DOCKING STUDY

2015 ◽  
Author(s):  
Manik Ghosh ◽  
Kamal Kant ◽  
Anoop Kumar ◽  
Padma Behera ◽  
Naresh Rangra ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Docking Study ◽  
Molecular Docking Study

In Silico Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of 3C-like Main Proteinase (3CLpro) from Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Using Selected African Medicinal Plants

2020 ◽  
Author(s):  
Sahar Qazi ◽  
Mustafa Alhaji Isa ◽  
Adam Mustapha ◽  
Khalid Raza ◽  
Ibrahim Alkali Allamin ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Severe Acute Respiratory Syndrome ◽  
In Silico ◽  
Md Simulation ◽  
Binding Energies ◽  
Anacardium Occidentale ◽  
Upper Respiratory Tract ◽  
Ligand Complex ◽  
In Silico Docking ◽  
Main Protease

<p>The Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) is an infectious virus that causes mild to severe life-threatening upper respiratory tract infection. The virus emerged in Wuhan, China in 2019, and later spread across the globe. Its genome has been completely sequenced and based on the genomic information, the virus possessed 3C-Like Main Protease (3CLpro), an essential multifunctional enzyme that plays a vital role in the replication and transcription of the virus by cleaving polyprotein at eleven various sites to produce different non-structural proteins. This makes the protein an important target for drug design and discovery. Herein, we analyzed the interaction between the 3CLpro and potential inhibitory compounds identified from the extracts of <i>Zingiber offinale</i> and <i>Anacardium occidentale</i> using in silico docking and Molecular Dynamics (MD) Simulation. The crystal structure of SARS-CoV-2 main protease in complex with 02J (5-Methylisoxazole-3-carboxylic acid) and PEJ (composite ligand) (PDB Code: 6LU7,2.16Å) retrieved from Protein Data Bank (PDB) and subject to structure optimization and energy minimization. A total of twenty-nine compounds were obtained from the extracts of <i>Zingiber offinale </i>and the leaves of <i>Anacardium occidentale. </i>These compounds were screened for physicochemical (Lipinski rule of five, Veber rule, and Egan filter), <i>Pan</i>-Assay Interference Structure (PAINS), and pharmacokinetic properties to determine the Pharmaceutical Active Ingredients (PAIs). Of the 29 compounds, only nineteen (19) possessed drug-likeness properties with efficient oral bioavailability and less toxicity. These compounds subjected to molecular docking analysis to determine their binding energies with the 3CLpro. The result of the analysis indicated that the free binding energies of the compounds ranged between ˗5.08 and -10.24kcal/mol, better than the binding energies of 02j (-4.10kcal/mol) and PJE (-5.07kcal.mol). Six compounds (CID_99615 = -10.24kcal/mol, CID_3981360 = 9.75kcal/mol, CID_9910474 = -9.14kcal/mol, CID_11697907 = -9.10kcal/mol, CID_10503282 = -9.09kcal/mol and CID_620012 = -8.53kcal/mol) with good binding energies further selected and subjected to MD Simulation to determine the stability of the protein-ligand complex. The results of the analysis indicated that all the ligands form stable complexes with the protein, although, CID_9910474 and CID_10503282 had a better stability when compared to other selected phytochemicals (CID_99615, CID_3981360, CID_620012, and CID_11697907). </p>

In Silico Molecular Docking and Molecular Dynamic Simulation of Potential Inhibitors of 3C-like Main Proteinase (3CLpro) from Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Using Selected African Medicinal Plants

2020 ◽  
Author(s):  
Sahar Qazi ◽  
Mustafa Alhaji Isa ◽  
Adam Mustapha ◽  
Khalid Raza ◽  
Ibrahim Alkali Allamin ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Severe Acute Respiratory Syndrome ◽  
In Silico ◽  
Md Simulation ◽  
Binding Energies ◽  
Anacardium Occidentale ◽  
Upper Respiratory Tract ◽  
Ligand Complex ◽  
In Silico Docking ◽  
Main Protease

<p>The Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) is an infectious virus that causes mild to severe life-threatening upper respiratory tract infection. The virus emerged in Wuhan, China in 2019, and later spread across the globe. Its genome has been completely sequenced and based on the genomic information, the virus possessed 3C-Like Main Protease (3CLpro), an essential multifunctional enzyme that plays a vital role in the replication and transcription of the virus by cleaving polyprotein at eleven various sites to produce different non-structural proteins. This makes the protein an important target for drug design and discovery. Herein, we analyzed the interaction between the 3CLpro and potential inhibitory compounds identified from the extracts of <i>Zingiber offinale</i> and <i>Anacardium occidentale</i> using in silico docking and Molecular Dynamics (MD) Simulation. The crystal structure of SARS-CoV-2 main protease in complex with 02J (5-Methylisoxazole-3-carboxylic acid) and PEJ (composite ligand) (PDB Code: 6LU7,2.16Å) retrieved from Protein Data Bank (PDB) and subject to structure optimization and energy minimization. A total of twenty-nine compounds were obtained from the extracts of <i>Zingiber offinale </i>and the leaves of <i>Anacardium occidentale. </i>These compounds were screened for physicochemical (Lipinski rule of five, Veber rule, and Egan filter), <i>Pan</i>-Assay Interference Structure (PAINS), and pharmacokinetic properties to determine the Pharmaceutical Active Ingredients (PAIs). Of the 29 compounds, only nineteen (19) possessed drug-likeness properties with efficient oral bioavailability and less toxicity. These compounds subjected to molecular docking analysis to determine their binding energies with the 3CLpro. The result of the analysis indicated that the free binding energies of the compounds ranged between ˗5.08 and -10.24kcal/mol, better than the binding energies of 02j (-4.10kcal/mol) and PJE (-5.07kcal.mol). Six compounds (CID_99615 = -10.24kcal/mol, CID_3981360 = 9.75kcal/mol, CID_9910474 = -9.14kcal/mol, CID_11697907 = -9.10kcal/mol, CID_10503282 = -9.09kcal/mol and CID_620012 = -8.53kcal/mol) with good binding energies further selected and subjected to MD Simulation to determine the stability of the protein-ligand complex. The results of the analysis indicated that all the ligands form stable complexes with the protein, although, CID_9910474 and CID_10503282 had a better stability when compared to other selected phytochemicals (CID_99615, CID_3981360, CID_620012, and CID_11697907). </p>

The Antiviral and Antimalarial Drug Repurposing in Quest of Chemotherapeutics to Combat COVID-19 Utilizing Structure-Based Molecular Docking

2020 ◽  
Vol 23 ◽  
Author(s):  
Sisir Nandi ◽  
Mohit Kumar ◽  
Mridula Saxena ◽  
Anil Kumar Saxena
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Drug Repurposing ◽  
Clinical Settings ◽  
The Novel ◽  
In Silico Docking ◽  
Biochemical Mechanisms ◽  
Novel Coronavirus ◽  
In Silico Molecular Docking

Background: The novel coronavirus disease (COVID-19) is caused by a new strain (SARS-CoV-2) erupted in 2019. Nowadays, it is a great threat that claims uncountable lives worldwide. There is no specific chemotherapeutics developed yet to combat COVID-19. Therefore, scientists have been devoted in the quest of the medicine that can cure COVID- 19. Objective: Existing antivirals such as ASC09/ritonavir, lopinavir/ritonavir with or without umifenovir in combination with antimalarial chloroquine or hydroxychloroquine have been repurposed to fight the current coronavirus epidemic. But exact biochemical mechanisms of these drugs towards COVID-19 have not been discovered to date. Method: In-silico molecular docking can predict the mode of binding to sort out the existing chemotherapeutics having a potential affinity towards inhibition of the COVID-19 target. An attempt has been made in the present work to carry out docking analyses of 34 drugs including antivirals and antimalarials to explain explicitly the mode of interactions of these ligands towards the COVID-19protease target. Results: 13 compounds having good binding affinity have been predicted towards protease binding inhibition of COVID-19. Conclusion: Our in silico docking results have been confirmed by current reports from clinical settings through the citation of suitable experimental in vitro data available in the published literature.

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