scholarly journals PREDIKSI SENYAWA EUCALYPTUS SEBAGAI INHIBITOR POTENSIAL COVID-19 MAIN PROTEASE (Mpro) SECARA MOLECULAR DOCKING

2021 ◽  
Vol 6 (2) ◽  
pp. 77
Author(s):  
Muhammad Fauzi ◽  
Fauzi Rahman ◽  
Yulistia Budianti Soemari ◽  
Richa Purnamasari
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Active Site ◽  
Docking Studies ◽  
Therapeutic Drug ◽  
Free Energies ◽  
Virus Family ◽  
Main Protease ◽  
The World ◽  
Suitable Target

The development of cases infected with the COVID-19 virus in Indonesia continues to increase. COVID-19 is a member of the corona virus family that has spread throughout the world. The COVID-19 Main protease is considered a suitable target for drug design against SARS infection because it plays a role in the processing of polyproteins required for the reproduction of the coronavirus. Eucalyptus are claimed to be able to ward off the COVID-19 virus. Therefore it is necessary to evaluate the content of eucalyptus compounds against Main proteases by docking studies. Based on the results of research conducted using the active site on the Main protease, it is known that eucalyptus (-)-globulol, epiglobulol, and ledol compounds have free energies of -7.23 kcal/mol, -7.91 kcal/mol, and -7.39 kcal/mol, respectively. Remdesivir as a therapeutic drug for COVID-19 has a free energy of -7.67 kcal/mol. These three compounds bind to the amino acid Glu166 as remdisivir with the best binding affinity on the active site of the Main protease. So these three compounds have the potential to inhibit the COVID-19 virus.

scholarly journals Synthesis and Molecular Docking Studies of some Pyrano[2,3-c] Pyrazole as an Inhibitor of SARS-Coronavirus 3CL Protease

2021 ◽  
Vol 11 (3) ◽  
pp. 3780-3801
Keyword(s):  
Molecular Docking ◽  
Active Site ◽  
Antiviral Treatment ◽  
Specific Treatment ◽  
Docking Studies ◽  
Strong Hydrogen Bond ◽  
Active Site Residues ◽  
Hydrogen Bond Interaction ◽  
Main Protease ◽  
3Cl Protease

The widespread global COVID-19 pandemic due to the lack of specific treatment and the urgent situation requires the use of all resources to remedy this scourge. The current study aimed to use molecular docking tools to find potential drug candidates for treatment. The pyrano[2,3-c] pyrazole 5(a-e) was targeted against the Main protease (Mpro), which plays a vital role in the replication and transcription of the Corona viral genome. The 3CL Protease (PDB ID 6LU7) was modeled, and the compounds were docked using Autodock Vina software, and ADMET data have been studied. All synthesized compounds were well engaged into the active site of the main protease with strong hydrogen bond interaction and a good score of energy. The 5b have been classed as the best inhibitor with an energy score of -6.2 kcal/mol, similar to the one given by chloroquine (-6.2Kcal/mol). Moreover, the molecular interaction studies showed that protease structure had multiple active site residues for all studied compounds. Our finding confirms the potential of these derivatives as lead compounds against the selected target protein of coronavirus, which needs further analysis and dynamic simulation studies to propose then develop a new antiviral treatment.

scholarly journals Field-Template, QSAR, Ensemble Molecular Docking, and 3D-RISM Solvation Studies Expose Potential of FDA-Approved Marine Drugs as SARS-CoVID-2 Main Protease Inhibitors

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 936
Author(s):  
Poonam Kalhotra ◽  
Veera C. S. R. Chittepu ◽  
Guillermo Osorio-Revilla ◽  
Tzayhri Gallardo-Velazquez
Keyword(s):  
Molecular Docking ◽  
Protease Inhibitors ◽  
Active Site ◽  
World Health ◽  
Therapeutic Drug ◽  
Eribulin Mesylate ◽  
Infected People ◽  
Molecular Features ◽  
Main Protease

Currently, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has infected people among all countries and is a pandemic as declared by the World Health Organization (WHO). SARS-CoVID-2 main protease is one of the therapeutic drug targets that has been shown to reduce virus replication, and its high-resolution 3D structures in complex with inhibitors have been solved. Previously, we had demonstrated the potential of natural compounds such as serine protease inhibitors eventually leading us to hypothesize that FDA-approved marine drugs have the potential to inhibit the biological activity of SARS-CoV-2 main protease. Initially, field-template and structure–activity atlas models were constructed to understand and explain the molecular features responsible for SARS-CoVID-2 main protease inhibitors, which revealed that Eribulin Mesylate, Plitidepsin, and Trabectedin possess similar characteristics related to SARS-CoVID-2 main protease inhibitors. Later, protein–ligand interactions are studied using ensemble molecular-docking simulations that revealed that marine drugs bind at the active site of the main protease. The three-dimensional reference interaction site model (3D-RISM) studies show that marine drugs displace water molecules at the active site, and interactions observed are favorable. These computational studies eventually paved an interest in further in vitro studies. Finally, these findings are new and indeed provide insights into the role of FDA-approved marine drugs, which are already in clinical use for cancer treatment as a potential alternative to prevent and treat infected people with SARS-CoV-2.

scholarly journals Eucalyptol (1,8 cineole) from Eucalyptus Essential Oil a Potential Inhibitor of COVID 19 Corona Virus Infection by Molecular Docking Studies

2020 ◽  
Author(s):  
Arun Dev Sharma ◽  
inderjeet kaur
Keyword(s):  
Molecular Docking ◽  
Essential Oil ◽  
Active Site ◽  
Hydrophobic Interactions ◽  
Rna Virus ◽  
Docking Studies ◽  
Active Site Residues ◽  
Virus Family ◽  
Molecular Docking Studies ◽  
Corona Virus

Background: COVID-19, a member of corona virus family is spreading its tentacles across the world due to lack of drugs at present. Associated with its infection are cough, fever and respiratory problems causes more than 15% mortality worldwide. It is caused by a positive, single stranded RNA virus from the enveloped coronaviruse family. However, the main viral proteinase (Mpro/3CLpro) has recently been regarded as a suitable target for drug design against SARS infection due to its vital role in polyproteins processing necessary for coronavirus reproduction.Objectives: The present in silico study was designed to evaluate the effect of Eucalyptol (1,8 cineole), a essential oil component from eucalyptus oil, on Mpro by docking study.Methods: In the present study, molecular docking studies were conducted by using 1-click dock and swiss dock tools. Protein interaction mode was calculated by Protein Interactions Calculator.Results: The calculated parameters such as RMSD, binding energy, and binding site similarity indicated effective binding of eucalyptol to COVID-19 proteinase. Active site prediction further validated the role of active site residues in ligand binding. PIC results indicated that, Mpro/eucalyptol complexes forms hydrophobic interactions, hydrogen bond interactions and strong ionic interactions.Conclusions: Therefore, eucalyptol may represent potential treatment potential to act as COVID-19 Mpro inhibitor. However, further research is necessary to investigate their potential medicinal use.

scholarly journals Synthesis of Novel Acylhydrazone-Oxazole Hybrids and Docking Studies of SARS-CoV-2 Main Protease

2020 ◽  
Vol 3 (1) ◽  
pp. 1
Author(s):  
Verónica G. García-Ramírez ◽  
Abel Suarez-Castro ◽  
Ma. Guadalupe Villa-Lopez ◽  
Erik Díaz-Cervantes ◽  
Luis Chacón-García ◽  
...  
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
In Silico ◽  
Functional Group ◽  
Docking Studies ◽  
Synthetic Strategy ◽  
Protease Enzyme ◽  
Main Protease ◽  
Target Molecules ◽  
Van Leusen Reaction

A novel synthetic strategy to obtain acylhydrazone-oxazole hybrids in three-step reactions in moderate to good yields is reported. The key step reaction consists in a Van Leusen reaction using a bifunctional component of both an aldehyde and a functional group. The target molecules were evaluated via in-silico by molecular docking with the main protease enzyme of SARS-Cov-2, where two acyl hydralazine-oxazoles yielded good predicted free energy values in comparison to the co-crystalized ligand.

scholarly journals Synthesis, Molecular Docking Studies and Antifungal Activity Evaluation of New Thiazolyl-methylen-1,3,4-oxadiazolines as Potential Lanosterol 14a-demethylase Inhibitors

2019 ◽  
Vol 70 (10) ◽  
pp. 3522-3526
Author(s):  
Smaranda Oniga ◽  
Catalin Araniciu ◽  
Gabriel Marc ◽  
Livia Uncu ◽  
Mariana Palage ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Molecular Docking ◽  
Antifungal Activity ◽  
Active Site ◽  
Docking Studies ◽  
Molecular Docking Studies ◽  
Activity Evaluation ◽  
Lanosterol Demethylase ◽  
Target Enzyme

Considering the well-established antifungal activity of azole compounds, a new series of thiazolyl-methylen-1,3,4-oxadiazolines derivatives were designed and synthesized as lanosterol-demethylase inhibitors. The final compounds were screened for antifungal activity against the Candida albicans ATCC 90028 strain. Molecular docking studies were performed to investigate the interaction modes between the compounds and the active site of lanosterol 14a-demethylase, which is a target enzyme for anticandidal azoles. Theoretical ADME predictions were also calculated for the final compounds 5a-h.

scholarly journals Molecular Docking Studies of Possible Treatment of Diabetes using Vasicine against Islet Amyloid Polypeptide

2021 ◽  
Vol 9 (VI) ◽  
pp. 4202-4209
Author(s):  
Tushar Kumar
Keyword(s):  
Type 2 Diabetes ◽  
Insulin Secretion ◽  
Molecular Docking ◽  
Islet Amyloid Polypeptide ◽  
Docking Studies ◽  
Islet Amyloid ◽  
Molecular Docking Studies ◽  
The World ◽  
Treatment Of Diabetes

Diabetes is the becoming one of the most common problem all over the world. About 1 in 10 persons are suffering from diabetes and most from type 2 diabetes. It occurs due to problem in pancreas which further results defect in the insulin secretion, as insulin maintains blood glucose level. The effect of Alpha-Amyrin Acetate, Myrcene and Vasicine compounds against Islet Amyloid polypeptide (IAPP) protein was seen through molecular docking studies. IAPP acts as complementary to insulin in regulating the sugar level for the treatment of diabetes disease by virtual screening. Different tools and software used in this research were Uniprot, Pubchem, Swiss ADMS, PyRx, Auto dock Vina/MGL tool and PyMOL.

Synthesis, characterization and molecular docking studies on some new N-substituted 2-phenylpyrido[2,3-d]pyrimidine derivatives

2021 ◽  
pp. 3846-3854
Author(s):  
Vivek B. Panchabhai ◽  
Santosh R. Butle ◽  
Parag G. Ingole
Keyword(s):  
Crystal Structure ◽  
Antibacterial Activity ◽  
Molecular Docking ◽  
Active Site ◽  
Docking Studies ◽  
Biotin Carboxylase ◽  
Active Site Residues ◽  
Pyrimidine Derivatives ◽  
Molecular Docking Studies ◽  
Novel Scaffold

We report a novel scaffold of N-substituted 2-phenylpyrido(2,3-d)pyrimidine derivatives with potent antibacterial activity by targeting this biotin carboxylase enzyme. The series of eighteen N-substituted 2-phenylpyrido(2,3-d)pyrimidine derivatives were synthesized, characterized and further molecular docking studied to determine the mode of binding and energy changes with the crystal structure of biotin carboxylase (PDB ID: 2V58) was employed as the receptor with compounds 6a-r as ligands. The results obtained from the simulation were obtained in the form of dock score; these values represent the minimum energies. Compounds 6d, 6l, 6n, 6o, 6r and 6i showed formation of hydrogen bonds with the active site residues and van Der Walls interactions with the biotin carboxylase enzyme in their molecular docking studies. This compound can be studied further and developed into a potential antibacterial lead molecule.

scholarly journals Molecular docking and pharmacokinetic screening of eucalyptol (1,8 cineole) from eucalyptus essential oil against SARS-CoV-2

2020 ◽  
Vol 12 (3) ◽  
pp. 536-545
Author(s):  
Arun D. SHARMA ◽  
Inderjeet KAUR
Keyword(s):  
Molecular Docking ◽  
Essential Oil ◽  
Active Site ◽  
In Silico ◽  
Hydrophobic Interactions ◽  
Rna Virus ◽  
In Silico Analysis ◽  
Active Site Residues ◽  
Virus Family

SARS-CoV-2 (COVID-19), member of corona virus family, is a positive single stranded RNA virus. Due to lack of drugs it is spreading its tentacles across the world. Being associated with cough, fever, and respiratory distress, this disease caused more than 15% mortality worldwide. Mpro/3CLpro has recently been regarded as a suitable target for drug design due to its vital role in virus replication. The current study focused on the inhibitory activity of eucalyptol (1,8 cineole), an essential oil component from eucalyptus oil, against Mpro/3CLprofrom SARS-CoV-2. Till date there is no work is undertaken on in-silico analysis of this compound against Mpro/3CLproof SARS-CoV-2. Molecular docking studies were conducted by using 1-click dock tool and Patchdock analysis. In-silico absorption, distribution, metabolism, excretion and toxicity (ADMET) profile were also studied. The calculated parameters such as docking score indicated effective binding of eucalyptol to COVID-19 Mpro protein. Active site prediction revealed the involvement of active site residues in ligand binding. Interactions results indicated that, Mpro/3CLpro/eucalyptol complexes forms hydrophobic interactions. ADMET studies provided guidelines and mechanistic scope for identification of potent anti-COVID 19 drug. Therefore, eucalyptol may represent potential herbal treatment to act as COVID-19 Mpro/3CLproinhibitor, a finding which must be validated in vivo.

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