scholarly journals Impact of the Herbicide Oxyfluorfen on the Activities of Some Enzymes Found in Soil and on the Populations of Soil Microorganisms

Agronomy ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1702
Author(s):  
Marioara Nicoleta Filimon ◽  
Diana Larisa Roman ◽  
Despina Maria Bordean ◽  
Adriana Isvoran
Keyword(s):  
Molecular Docking ◽  
Soil Microorganisms ◽  
Inhibitory Effect ◽  
Soil Samples ◽  
Field Conditions ◽  
Soil Physicochemical Properties ◽  
Normal Dose ◽  
Dependent Behavior ◽  
Docking Approach ◽  
Dose Dependent

This study assesses the effects of the herbicide oxyfluorfen on the activities of enzymes and on the populations of soil microorganisms by considering experiments on soil samples maintained in both laboratory and in field conditions. Furthermore, the molecular docking approach was used to evaluate the interactions of oxyfluorfen with enzymes found in soil. There was a dose dependent inhibitory effect of oxyfluorfen against the activities of dehydrogenase, phosphatase, protease and urease. The enzymes activities obtained for the soil samples maintained under field conditions usually reflected a different trend than those obtained under laboratory conditions, emphasizing the influence of the soil physicochemical properties. For soil samples maintained in field conditions and for the normal dose of oxyfluorfen, dehydrogenase activity recovered after 14 days and a minimum of 21 days was necessary for the recovery of phosphatase, urease and protease activity, respectively. The most important parameters of soil influencing the activities of enzymes and the populations of microorganisms were the pH, N-NO3 and N-NH4 contents. A dose dependent behavior of populations of microorganisms found in soil treated with oxyfluorfen has been shown. There was a slight grows of the colonies of microorganisms when oxyfluorfen was applied, but this growth decreased with increasing the oxyfluorfen concentration.

scholarly journals Computational Molecular Docking and Virtual Screening Revealed Promising SARS-CoV-2 Drugs

2020 ◽  
Author(s):  
Maryam Hosseini ◽  
Wanqiu Chen ◽  
Charles Wang
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Virtual Screening ◽  
Clinical Studies ◽  
Inhibitory Effect ◽  
Docking Approach ◽  
Novel Coronavirus ◽  
Approved Drugs ◽  
Potential Inhibitors ◽  
Computational Molecular Docking

The pandemic of novel coronavirus disease 2019 (COVID-19) is rampaging the world with more than 1.4 million of confirmed cases and more than 85,000 of deaths across world by April 9th, 2020. There is an urgent need to identify effective drugs to fight against the virus. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the family of coronaviruses consisting of four structural and 16 non-structured proteins. Three non-structural proteins such as main protease, papain like protease, and RNA-dependent RNA polymerase are believed to play a crucial role in the virus replication. We applied a computational ligand-receptor binding modeling and performed a comprehensive virtual screening on the FDA-approved drugs against these three SARS-CoV-2 proteins using AutoDock Vina. Our computational studies indicated that Simeprevir, Ledipasvir, Idarubicin, Saquinavir, Ledipasivir, Partitaprevir, Glecaprevir, and Velpatasvir are all promising inhibitors, which displayed a lower binding energy (higher inhibitory effect) than Remdesivir, Lopinavir, and Ritonavir. However, we found that chloroquine and hydroxychloroquine, which showed efficacy in treating the COVID-19 in recent clinical studies, had high binding energy with all three proteins, suggesting they may work through a different mechanism. We also identified several novel drugs as potential inhibitors against SARS-CoV-2, including antiviral Raltegravir; antidiabetic Amaryl; antibiotics Retapamulin, Rifimixin, and Rifabutin; antiemetic Fosaprepitant and Netupitant. In summary, our computational molecular docking approach and virtual screening identified some promising candidate SARS-CoV-2 drugs that may be considered for further clinical studies.

scholarly journals Antioxidant and Antiproliferative Potential of Bioactive Molecules Ursolic Acid and Thujone Isolated from Memecylon edule and Elaeagnus indica and Their Inhibitory Effect on Topoisomerase II by Molecular Docking Approach

2020 ◽  
Vol 2020 ◽  
pp. 1-12 ◽  
Author(s):  
Ramalingam Srinivasan ◽  
Arumugam Aruna ◽  
Jong Suk Lee ◽  
Myunghee Kim ◽  
Muthugounder Subramaniam Shivakumar ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Ursolic Acid ◽  
Topoisomerase Ii ◽  
Docking Study ◽  
Inhibitory Effect ◽  
Significant Inhibition ◽  
Bioactive Molecules ◽  
Molecular Docking Study ◽  
Docking Approach ◽  
Free Radicals Scavenging

The present study aimed to evaluate the antioxidant and antiproliferative potential of ursolic acid and thujone isolated from leaves of Elaeagnus indica and Memecylon edule and their inhibitory effect on topoisomerase II using molecular docking study. The isolated ursolic acid and thujone were examined for different types of free radicals scavenging activity, the antiproliferative potential on U-937 and HT-60 cell lines by adopting standard methods. Further, these compounds were docked with the active site of the ATPase region of topoisomerase II. The findings of the research revealed that ursolic acid harbor strong antioxidant and antiproliferative capacity with low IC50 values than the thujone in all tested methods. Moreover, ursolic acid shows significant inhibition effect on topoisomerase II with a considerable docking score (−8.0312) and GLIDE energy (−51.86 kca/mol). The present outcome concludes that ursolic acid possesses significant antioxidant and antiproliferative potential, which can be used in the development of novel antioxidant and antiproliferative agents in the future.

scholarly journals Computational Molecular Docking and Virtual Screening Revealed Promising SARS-CoV-2 Drugs

2020 ◽  
Author(s):  
Maryam Hosseini ◽  
Wanqiu Chen ◽  
Charles Wang
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Virtual Screening ◽  
Clinical Studies ◽  
Inhibitory Effect ◽  
Docking Approach ◽  
Novel Coronavirus ◽  
Approved Drugs ◽  
Potential Inhibitors ◽  
Computational Molecular Docking

The pandemic of novel coronavirus disease 2019 (COVID-19) is rampaging the world with more than 1.4 million of confirmed cases and more than 85,000 of deaths across world by April 9th, 2020. There is an urgent need to identify effective drugs to fight against the virus. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the family of coronaviruses consisting of four structural and 16 non-structured proteins. Three non-structural proteins such as main protease, papain like protease, and RNA-dependent RNA polymerase are believed to play a crucial role in the virus replication. We applied a computational ligand-receptor binding modeling and performed a comprehensive virtual screening on the FDA-approved drugs against these three SARS-CoV-2 proteins using AutoDock Vina. Our computational studies indicated that Simeprevir, Ledipasvir, Idarubicin, Saquinavir, Ledipasivir, Partitaprevir, Glecaprevir, and Velpatasvir are all promising inhibitors, which displayed a lower binding energy (higher inhibitory effect) than Remdesivir, Lopinavir, and Ritonavir. However, we found that chloroquine and hydroxychloroquine, which showed efficacy in treating the COVID-19 in recent clinical studies, had high binding energy with all three proteins, suggesting they may work through a different mechanism. We also identified several novel drugs as potential inhibitors against SARS-CoV-2, including antiviral Raltegravir; antidiabetic Amaryl; antibiotics Retapamulin, Rifimixin, and Rifabutin; antiemetic Fosaprepitant and Netupitant. In summary, our computational molecular docking approach and virtual screening identified some promising candidate SARS-CoV-2 drugs that may be considered for further clinical studies.

scholarly journals Effects Of Herbicides And Fungicides On The Soil Chitinolytic Activity. A Molecular Docking Approach

2015 ◽  
Vol 22 (3) ◽  
pp. 439-450
Author(s):  
Diana Larisa Vlădoiu ◽  
Marioara Nicoleta Filimon ◽  
Vasile Ostafe ◽  
Adriana Isvoran
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Active Sites ◽  
Soil Microorganisms ◽  
Docking Study ◽  
Chitinolytic Activity ◽  
Molecular Docking Study ◽  
Receptor Ligand ◽  
Docking Approach ◽  
Inhibitory Potential

Abstract A molecular docking study was undertaken using the programs SwissDock and PatchDock to assess the interactions of the bacterial chitinases belonging to the GH18 and GH19 families with two herbicides (chlorsulfuron and nicosulfuron) and two fungicides (difenoconazole and drazoxolon). Both molecular docking programs predict that all considered pesticides bind to the active sites of chitinases produced by soil microorganisms. There are correlations for predicted binding energy values for receptor-ligand complexes obtained using the two programs consolidating the prediction of the chitinases-pesticides interactions. The interactions of chitinases with pesticides involve the same residues as their interactions with known inhibitors suggesting the inhibitory potential of pesticides. Pesticides interact stronger with chitinases belonging to the GH18 family, their active sites reflecting higher polarity than those of the GH19 chitinases. Also, herbicides reveal a higher inhibitory potential to bacterial chitinases than fungicides.

scholarly journals Computational molecular docking and virtual screening revealed promising SARS-CoV-2 drugs

2021 ◽  
Author(s):  
Maryam Hosseini ◽  
Wanqiu Chen ◽  
Daliao Xiao ◽  
Charles Wang
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
Protein Complexes ◽  
Inhibitory Effect ◽  
Dynamics Simulation ◽  
The World ◽  
Docking Approach ◽  
Novel Coronavirus ◽  
Approved Drugs ◽  
Computational Molecular Docking

Abstract The pandemic of novel coronavirus disease 2019 (COVID-19) has rampaged the world with more than 58.4 million confirmed cases and over 1.38 million deaths across the world by November 23, 2020. There is an urgent need to identify effective drugs and vaccines to fight against the virus. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the family of coronaviruses consisting of four structural and 16 non-structured proteins. Three non-structural proteins such as main protease (Mpro), papain-like protease (PLpro), and RNA-dependent RNA polymerase (RdRp) are believed to play a crucial role in the virus replication. We applied a computational ligand-receptor binding modeling and performed a comprehensive virtual screening on the FDA-approved drugs against these three SARS-CoV-2 proteins using AutoDock Vina, Glide, and rDock. Our computational studies identified six novel ligands as potential inhibitors against SARS-CoV-2, including antiemetics Rolapitant and Ondansetron for Mpro; Labetalol and Levomefolic acid for PLpro; and Leucal and antifungal Natamycin for RdRp. Molecular dynamics simulation confirmed the stability of the ligand-protein complexes. The result of our analysis with some other suggested drugs indicated that chloroquine and hydroxychloroquine had high binding energy (low inhibitory effect) with all three proteins—Mpro, PLpro, and RdRp. In summary, our computational molecular docking approach and virtual screening identified some promising candidate SARS-CoV-2 inhibitors that may be considered for further clinical studies.

Soil response to chemicals used in a field experiment

2013 ◽  
Vol 27 (2) ◽  
pp. 151-158 ◽  
Author(s):  
S. Jezierska-Tys ◽  
A. Rutkowska
Keyword(s):  
Alkaline Phosphatase ◽  
Enzymatic Activity ◽  
Field Experiment ◽  
Soil Microorganisms ◽  
Block Design ◽  
Soil Samples ◽  
Alkaline Phosphatases ◽  
Soil Response ◽  
Negative Effect ◽  
Set Up

Abstract The effect of chemicals (Reglone 200 SL and Elastiq 550 EC) on soil microorganisms and their enzymatic activity was estimated. The study was conducted in a field experiment which was set up in the split-block design and comprised three treatments. Soil samples were taken six times, twice in each year of study. The results showed that the application of chemicals generally had no negative effect on the number of soil microorganisms. The application of Reglone 200 SL caused an increase of proteolytic and ureolytic activity and affected the activity of dehydrogenases, acid and alkaline phosphatases in the soil. The soil subjected of Elastiq 550 EC was characterized by lower activity of dehydrogenases, protease, urease and alkaline phosphatase.

Molecular Docking Approaches to Suggest the Anti-Mycobacterial Targets of Natural Products

2020 ◽  
Author(s):  
Rafael Baptista ◽  
Sumana Bhowmick ◽  
Shen Jianying ◽  
Luis Mur
Keyword(s):  
Natural Products ◽  
Molecular Docking ◽  
Free Energies ◽  
Antibiotic Resistant ◽  
Drug Lead ◽  
Bisbenzylisoquinoline Alkaloids ◽  
Docking Approach ◽  
Global Threat ◽  
Physicochemical And Structural Properties

Tuberculosis (TB) is a major global threat mostly due to the development of antibiotic resistant forms of Mycobacterium tuberculosis, the causal agent of the disease. Driven by the pressing need for new anti-mycobacterial agents, several natural products (NPs) have been shown to have in vitro activities against M. tuberculosis. The utility of any NP as a drug lead is augmented when the anti-mycobacterial target(s) is unknown. To suggest these, we used a molecular docking approach to predict the interactions of 53 selected anti-mycobacterial NPs against known ‘druggable’ mycobacterial targets ClpP1P2, DprE1, InhA, KasA, PanK, PknB and Pks13. The docking scores / binding free energies were predicted and calculated using AutoDock Vina along with physicochemical and structural properties of the NPs, using PaDEL descriptors. These were compared to the established inhibitor (control) drugs for each mycobacterial target. The specific interactions of the bisbenzylisoquinoline alkaloids 2-nortiliacorinine, tiliacorine and 13’-bromotiliacorinine against the targets PknB and DprE1 (-11.4, -10.9 and -9.8 kcal.mol-1 ; -12.7, -10.9 and -10.3 kcal.mol-1 , respectively) and the lignan αcubebin and Pks13 (-11.0 kcal.mol-1 ) had significantly superior docking scores compared to controls. Our approach can be used to suggest predicted targets for the NP to be validated experimentally but these in silico steps are likely to facilitate drug optimisation.

Synthesis and Assessment of Novel Anti-chlamydial Benzylidene Acylhydrazides Derivatives

2018 ◽  
Vol 15 (1) ◽  
pp. 31-36 ◽  
Author(s):  
Xiaofeng Bao ◽  
Ying Xue ◽  
Chao Xia ◽  
Yin Lu ◽  
Ningjing Yang ◽  
...  
Keyword(s):  
Inhibitory Effect ◽  
Dependent Manner ◽  
Iron Starvation ◽  
Hydrochloride Salt ◽  
Obligate Intracellular ◽  
Biphasic Life Cycle ◽  
Ic50 Value ◽  
Ic50 Values ◽  
Dose Dependent ◽  
Better Than

Background: Chlamydiae, characterized by a unique biphasic life cycle, are a group of Gram-negative obligate intracellular bacterial pathogens responsible for diseases in a range of hosts including humans. Benzylidene acylhydrazide CF0001 could inhibit chlamydiae independent of iron starvation and T3SS inhibition. This finding promoted us to design and synthesize more benzylidene acylhydrazides to find novel anti-chlamydial agents. Methods: The carboxylic acids 1a-1d were coupled with Boc-hydrazide inpresence of EDCI and DMAP to obtain the intermediate 2a-2d in 60-62% yields. N-Boc deprotections were performed to obtain hydrazide hydrochloride salt 3a-3d. Nextly, the hydrazides were subjected to condensation with aldehydes to obtain benzylidene acylhydrazides 4a-4g in 30-52% yields in two steps. Results: Compound 4d exhibited best inhibitory effect on the formation and growth of chlamydial inclusions. The IC50 value of compound 4d for infectious progenies was 3.55 µM, better than 7.30 µM of CF0001. Conclusion: To find novel anti-chlamydial agents, we have designed and synthesized benzylidene acylhydrazides 4a-4g. Compounds 4a, 4d, 4g showed inhibitory activity on C. muridarum with the IC50 values from 3.55-12 µM. The 3,5-dibromo-4-hydroxyl substitutes on ring B are critical to keep their anti-chlamydial activity. Compound 4d inhibited C. muridarum in a dose-dependent manner without apparent cytotoxicity.

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