scholarly journals Molecular docking study of sappan wood extract to inhibit PBP2A enzyme on methicillin-resistant Staphylococcus aureus (MRSA)

2020 ◽  
Vol 30 (6) ◽  
Author(s):  
Marisca Evalina Gondokesumo ◽  
Ihsan Mulyadi Kurniawan
Keyword(s):  
Staphylococcus Aureus ◽  
Molecular Docking ◽  
Data Bank ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Taste Disturbance ◽  
Methicillin Resistant ◽  
Molegro Virtual Docker ◽  
Important Interaction ◽  
Wood Extract

AbstractBackgroundPBP2a is a type of penicillin-binding proteins (PBPs) that cause resistivity in methicillin-resistant Staphylococcus aureus (MRSA) from β-lactam antibiotics. MRSA susceptible with cefttobiprole (fifth generation of cephalosporin as an anti-MRSA agent) which inhibits PBP2a and stops its growth. Contrary to its efficacy, ceftobiprole causes taste disturbance more than any other cephalosporins; furthermore, its mechanism is unknown. This study aims to explore an in silico study of a natural compound, which serves as a potential alternative to overcome MRSA with minimum adverse side effects.MethodsA molecular docking study was performed using Molegro Virtual Docker version 5.5. Brazilin and proto-sappanins A–E are phytochemical compounds contained in sappan wood extract and are docked into the binding site of PBP2a (Protein Data Bank: ID 4DKI).ResultsBrazilin and proto-sappanins A–E have some interaction with Ser 403 amino acid residue which is an important interaction to inhibit PBP2a protein. The result of the molecular docking study showed that the MolDock score of proto-sappanins D and E is lower than that of methicillin but higher than that of its native ligand (ceftobiprole).ConclusionsThe results of this study suggest that proto-sappanins D and E have an excellent potential activity as an alternative to ceftobiprole in limiting MRSA growth through PBP2A enzyme inhibition.

scholarly journals A Molecular Docking Study of N-Ferrocenylmethylnitroanilines as Potential Anticancer Drugs

2016 ◽  
Vol 2 ◽  
pp. 5-12 ◽  
Author(s):  
Touhami Lanez ◽  
Elhafnaoui Lanez
Keyword(s):  
Escherichia Coli ◽  
Molecular Docking ◽  
Protein Structure ◽  
Dna Gyrase ◽  
Data Bank ◽  
Docking Study ◽  
Docking Studies ◽  
Molecular Docking Study ◽  
Molegro Virtual Docker ◽  
Gyrase A

In the present study, the interaction of the protein structure of Escherichia coli DNA Gyrase-A (EcGyr-A) extracted from protein data bank (PDB Code: 1AB4) with ligands N-ferrocenylmethyl-2-nitroaniline (2FMNA), N-ferrocenylmethyl-3-nitroaniline (3FMNA) and N-ferrocenylmethyl-4-nitroaniline (4FMNA) were investigated by performing docking studies using the Molegro Virtual Docker (MVD) software. The results obtained showed that the best poses which is derived from MolDock score for Escherichia coli DNA Gyrase-A were respectively equal to-92.0111, -96.0866 and-95.6808 with reranking score equal to-40.9575, -73.4476 and-73.6423. Calculations revealed that 3FMNA react strongly with EcGyr-A followed by 4-FMNA and 2-FMNA.

scholarly journals Molecular Docking Study of Novel COVID-19 Protease with Low Risk Terpenoides Compounds of Plants

2020 ◽  
Author(s):  
neda shaghaghi
Keyword(s):  
Molecular Docking ◽  
Data Bank ◽  
Docking Study ◽  
Plant Origin ◽  
Molecular Docking Study ◽  
Molegro Virtual Docker ◽  
High Affinity ◽  
Ginkgolide A ◽  
Inhibitory Activities ◽  
Effectiveness Function

<p><b><i>Background</i></b> :Due to the reported high ability of virulence of COVID_19 in recent months, several studies have been conducted to discover and introduce COVID_19 antiviral drugs. The results of numerous studies have shown that protease inhibitors and compounds, which make up the major part of plant derivatives, especially terpenoids, can therefore be very effective in controlling virus-induced infection. The aim of this research is the bioinformatical study of COVID_19 inhibition by terpenoids of plant origin. </p> <p><b><i>Materials and Methods</i></b>: This is a descriptive-analytic study. In the present study , the structure of terpene comounds and COVID_19 protease was received from the databases such as PubChem and Protein Data Bank (PDB). After that, molecular docking was performed by MVD(molegro virtual docker) software.</p> <p><b><i> Results</i></b>: The results are identified to have inhibitory activities against novel COVID-19 protease. Of these compounds, Ginkgolide A has a stronger bond and high affinity with protease</p> <p><b><i>Conclusion</i></b>: Finally, with due attention to the high effectiveness function of terpenoids, we can conclude that these compounds may be considered as effectire COVID_19 antiprotease drugs</p>

scholarly journals Molecular Docking Study of Several Antiviral Drugs to Defeat Covid-19

2020 ◽  
Vol 19 (3) ◽  
pp. 37-46
Author(s):  
Jasdev S. Tuteja ◽  
Priti Patidar ◽  
Shilpa E. Mathew ◽  
Anil Prajapati
Keyword(s):  
Molecular Docking ◽  
Severe Acute Respiratory Syndrome ◽  
Active Drug ◽  
Data Bank ◽  
Docking Study ◽  
Antiviral Drugs ◽  
Binding Affinities ◽  
Molecular Docking Study ◽  
Molegro Virtual Docker ◽  
Docking Approach

Corona virus is one of the significant pathogens that destructs the human respiratory functioning. Deaths and casualties caused by coronaviruses (CoVs) include the severe acute respiratory syndrome (SARS)-CoV and the Middle East respiratory syndrome (MERS)-CoV. The aim of the work was to compare several antiviral drugs and find out which is the most active drug that might be used in treatment for COVID -19. In this study Molecular Docking approach was used to determine the binding affinities of 62 antiviral molecules. The study was carried out using Molegro Virtual Docker 6.0 with PDB 2GTB procured from RCSB Protein Data Bank. Simeprevir and Telaprevir were discovered to be most potent having high MolDock and Rerank scores of -225.158, -78.4383 and -209.467, -136.155 respectively. Further studies may be conducted to design more potent analogue and defeat COVID-19.

scholarly journals Molecular Docking Study of Novel COVID-19 Protease with Low Risk Terpenoides Compounds of Plants

2020 ◽  
Author(s):  
neda shaghaghi
Keyword(s):  
Molecular Docking ◽  
Data Bank ◽  
Docking Study ◽  
Plant Origin ◽  
Molecular Docking Study ◽  
Molegro Virtual Docker ◽  
High Affinity ◽  
Ginkgolide A ◽  
Inhibitory Activities ◽  
Effectiveness Function

<p><b><i>Background</i></b> :Due to the reported high ability of virulence of COVID_19 in recent months, several studies have been conducted to discover and introduce COVID_19 antiviral drugs. The results of numerous studies have shown that protease inhibitors and compounds, which make up the major part of plant derivatives, especially terpenoids, can therefore be very effective in controlling virus-induced infection. The aim of this research is the bioinformatical study of COVID_19 inhibition by terpenoids of plant origin. </p> <p><b><i>Materials and Methods</i></b>: This is a descriptive-analytic study. In the present study , the structure of terpene comounds and COVID_19 protease was received from the databases such as PubChem and Protein Data Bank (PDB). After that, molecular docking was performed by MVD(molegro virtual docker) software.</p> <p><b><i> Results</i></b>: The results are identified to have inhibitory activities against novel COVID-19 protease. Of these compounds, Ginkgolide A has a stronger bond and high affinity with protease</p> <p><b><i>Conclusion</i></b>: Finally, with due attention to the high effectiveness function of terpenoids, we can conclude that these compounds may be considered as effectire COVID_19 antiprotease drugs</p>

scholarly journals A Molecular Docking of New 9β-Halogenated Prostaglandin Analogues

Proceedings ◽  
2019 ◽  
Vol 41 (1) ◽  
pp. 21
Author(s):  
Constantin I. Tanase ◽  
Lucia Pintilie ◽  
Elena Mihai
Keyword(s):  
Molecular Docking ◽  
Acid Catalysis ◽  
Data Bank ◽  
Docking Study ◽  
Ester Group ◽  
Prostaglandin Analogue ◽  
Molecular Docking Study ◽  
Prostaglandin Analogues ◽  
Cytoprotective Activity ◽  
Long Time

Prostaglandins (PGs) with cytoprotective activity were studied for a long time, and a few PGE1 and PGE2 stable analogues were promoted as drugs: arbaprostil, enprostil, misoprostol, and rioptostol. Similarly, nocloprost, a 9β-chlorine prostaglandin analogue, and many 9β- and 11β-substituted prostaglandins were synthesized and studied for their biological activity. We previously synthesized new 9β-halogenated prostaglandins with an ester group at the carbon atom 6 (PGs numbering) by the reaction of a δ-lactone intermediate with diols in acid catalysis. These compounds were used in the current molecular docking study to determine their potential cytoprotective (anti-ulcer) activity. The current study was done with the CLC Drug Discovery Workbench 2.4. software and an oxidoreductase enzyme receptor, chosen from the Protein Data Bank, ID: 4KEW (www.rcsb.org). We used two recognized drugs, omeprazole (co-crystallized with the enzyme) and nocloprost, as the standard. The 9β-halogenated prostaglandin analogs were docked. Nocloprost and all 9β-halogenated compounds had docking scores greater than that of omeprazole. The majority of the 9β-halogenated analogs had docking scores even greater than that of nocloprost, indicating that these compounds could have potential cytoprotective (anti-ulcer) activity. A few correlations between docking score and substituents on the prostaglandin skeleton were found.

Potential Bioactive glycosylated flavonoids as SARS-CoV-2 Main protease Inhibitors: A molecular Docking Study

2020 ◽  
Author(s):  
sabri ahmed cherrak ◽  
merzouk hafida ◽  
mokhtari soulimane nassima
Keyword(s):  
Molecular Docking ◽  
Data Bank ◽  
Docking Study ◽  
Docking Studies ◽  
Molecular Docking Study ◽  
Chemical Structures ◽  
In Vivo Experiments ◽  
Main Protease

A novel (COVID-19) responsible of acute respiratory infection closely related to SARS-CoV has recently emerged. So far there is no consensus for drug treatment to stop the spread of the virus. Discovery of a drug that would limit the virus expansion is one of the biggest challenges faced by the humanity in the last decades. In this perspective, testing existing drugs as inhibitors of the main COVID-19 protease is a good approach.Among natural phenolic compounds found in plants, fruit, and vegetables; flavonoids are the most abundant. Flavonoids, especially in their glycosylated forms, display a number of physiological activities, which makes them interesting to investigate as antiviral molecules.The flavonoids chemical structures were downloaded from PubChem and protease structure 6lu7 was from the Protein Data Bank site. Molecular docking study was performed using AutoDock Vina. Among the tested molecules Quercetin-3-O-rhamnoside showed the highest binding affinity (-9,7 kcal/mol). Docking studies showed that glycosylated flavonoids are good inhibitors for the covid-19 protease and could be further investigated by in vitro and in vivo experiments for further validation.

scholarly journals Identification of Potent COVID-19 Main Protease (Mpro) Inhibitors from Natural Polyphenols: An in Silico Strategy Unveils a Hope against CORONA

2020 ◽  
Author(s):  
Sevki Adem ◽  
Volkan Eyupoglu ◽  
Iqra Sarfraz ◽  
Azhar Rasul ◽  
Muhammad Ali
Keyword(s):  
Molecular Docking ◽  
Drug Target ◽  
Docking Study ◽  
Binding Energies ◽  
Therapeutic Drug ◽  
Molecular Docking Study ◽  
Molegro Virtual Docker ◽  
Main Protease ◽  
Chinese Researcher ◽  
Native Ligand

COVID-19, a rapidly spreading new strain of coronavirus, has affected more than 150 countries and received worldwide attention. The lack of efficacious drugs or vaccines against SARS-CoV-2 has further worsened the situation. Thus, there is an urgent need to boost up research for the development of effective therapeutics and affordable diagnostic against COVID-19. The crystallized form of SARS-CoV-2 main protease (Mpro) was demonstrated by a Chinese researcher Liu et al. (2020) which is a novel therapeutic drug target. This study was conducted to evaluate the efficacy of medicinal plant-based bioactive compounds against COVID-19 Mpro by molecular docking study. Molecular docking investigations were performed by using Molegro Virtual Docker 7 to analyze the inhibition probability of these compounds against COVID-19. COVID-19 Mpro was docked with 80 flavonoid compounds and the binding energies were obtained from the docking of (PDB ID: 6LU7: Resolution 2.16 Å) with the native ligand. According to obtained results, hesperidin, rutin, diosmin, apiin, diacetylcurcumin, (E)-1-(2-Hydroxy-4-methoxyphenyl)-3-[3-[(E)-3-(2-hydroxy-4- methoxyphenyl)-3-oxoprop-1-enyl]phenyl]prop-2-en-1-one, and beta,beta'-(4-Methoxy-1,3- phenylene)bis(2'-hydroxy-4',6'-dimethoxyacrylophenone have been found as more effective on COVID-19 than nelfinavir. So, this study will pave a way for doing advanced experimental research to evaluate the real medicinal potential of these compounds to cure COVID-19.

scholarly journals Mechanistic Insights into Biological Activities of Polyphenolic Compounds from Rosemary Obtained by Inverse Molecular Docking

Foods ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 67
Author(s):  
Samo Lešnik ◽  
Urban Bren
Keyword(s):  
Molecular Docking ◽  
Pathogenic Bacteria ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Biological Activities ◽  
Data Bank ◽  
Docking Study ◽  
Antimicrobial Activities ◽  
Carnosic Acid ◽  
Molecular Docking Study

Rosemary (Rosmarinus officinalis L.) represents a medicinal plant known for its various health-promoting properties. Its extracts and essential oils exhibit antioxidative, anti-inflammatory, anticarcinogenic, and antimicrobial activities. The main compounds responsible for these effects are the diterpenes carnosic acid, carnosol, and rosmanol, as well as the phenolic acid ester rosmarinic acid. However, surprisingly little is known about the molecular mechanisms responsible for the pharmacological activities of rosemary and its compounds. To discern these mechanisms, we performed a large-scale inverse molecular docking study to identify their potential protein targets. Listed compounds were separately docked into predicted binding sites of all non-redundant holo proteins from the Protein Data Bank and those with the top scores were further examined. We focused on proteins directly related to human health, including human and mammalian proteins as well as proteins from pathogenic bacteria, viruses, and parasites. The observed interactions of rosemary compounds indeed confirm the beforementioned activities, whereas we also identified their potential for anticoagulant and antiparasitic actions. The obtained results were carefully checked against the existing experimental findings from the scientific literature as well as further validated using both redocking procedures and retrospective metrics.

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