scholarly journals Antimalarial Properties of Isoquinoline Derivative from Streptomyces hygroscopicus subsp. Hygroscopicus: An In Silico Approach

2020 ◽  
Vol 2020 ◽  
pp. 1-15
Author(s):  
Rivo YB. Nugraha ◽  
Icha FD. Faratisha ◽  
Kana Mardhiyyah ◽  
Dio G. Ariel ◽  
Fitria F. Putri ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Antimalarial Activity ◽  
Pharmacokinetic Profile ◽  
Streptomyces Hygroscopicus ◽  
Protein Targets ◽  
Pharmacokinetic Profiles ◽  
Bond Interaction ◽  
In Silico Studies ◽  
Isoquinoline Derivative

Malaria is one of the life-threatening diseases in the world. The spread of resistance to antimalarial drugs is a major challenge, and resistance to artemisinin has been reported in the Southeast Asian region. In the previous study, the active compound of Streptomyces hygroscopicus subsp. Hygroscopicus (S. hygroscopicus), eponemycin, has been shown to have antimalarial effects. To further analyze the effects of other active compounds on the Plasmodium parasite, identifying and analyzing the effectiveness of compounds contained in S. hygroscopicus through instrumentation of liquid chromatography/mass spectrometry (LC/MS) and in silico studies were very useful. This study aimed at identifying other derivative compounds from S. hygroscopicus and screening the antimalarial activity of the compound by assessing the binding affinity, pharmacokinetic profile, and bond interaction. The derivative compounds were identified using LC/MS. Protein targets for derivative compounds were found through literature studies, and the results of identification of compounds and protein targets were reconstructed into three-dimensional models. Prediction of pharmacokinetic profiles was carried out using Swiss ADME. Screening of protein targets for the derivative compound was carried out using the reverse molecular docking method. Analyzing bond interaction was done by LigPlot. One compound from S. hygroscopicus, i.e., 6,7-dinitro-2-[1, 2, 4]triazole-4-yl-benzo[de]isoquinoline-1,3-dione, was successfully identified using LC/MS. This compound was an isoquinoline derivative compound. Through literature studies with inclusion criteria, thirteen protein targets were obtained for reverse molecular docking. This isoquinoline derivative had the potential to bind to each protein target. The pharmacokinetic profile showed that this compound had the drug-likeness criteria. Conclusion. 6,7-Dinitro-2-[1, 2, 4]triazole-4-yl-benzo[de]isoquinoline-1,3-dione has antimalarial activity as shown by reverse molecular docking studies and pharmacokinetic profiles. The best inhibitory ability of compounds based on bond affinity is with adenylosuccinate synthetase.

scholarly journals IN SILICO STUDIES ON DIACYL DERIVATIVES OF PHLOROGLUCINOL TO ENHANCE PHARMACODYNAMIC AND PHARMACOKINETIC PROFILES OF 2,4,6-TRIHYDROXY-3-GERANYL-ACETOPHENONE

2021 ◽  
pp. 173-179
Author(s):  
SHEAU WEI CHIONG ◽  
CHEAN HUI NG ◽  
KHOZIRAH SHAARI
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Chain Length ◽  
In Silico ◽  
Van Der Waals ◽  
Side Chains ◽  
Amino Acid Residues ◽  
Pharmacokinetic Profiles ◽  
In Silico Studies ◽  
Derivatives Of

Objective: The purpose of this study was to evaluate the LOX inhibitory activity, and predict the drug likeness properties of designed diacyl derivatives of phloroglucinol, using in silico method. Methods: The designed derivatives were subjected to molecular docking using AUTODOCK while the receptor used in this study was built from SWISS MODEL. Drug likeness properties of the derivatives were calculated by online programs i.e. MOLINSPIRATION and PreADMET. Results: Molecular docking study revealed that designed tHGA derivative with four-carbon chain length exhibited the best binding affinity with the docking scores of -7.26kcal/mol. Three types of binding interactions were observed between the derivatives and the receptor site i.e H-bonding, hydrophobic and Van der Waals interactions. The important amino acid residues involved in H-bonding were Gln495 and Gln697, while other amino acid residues, such as Leu754 and Ile 553, were involved in the Van der Waals interaction. The designed tHGA derivatives were mainly stabilized through hydrophobic interactions with His499, His504, Ile538, Phe557 and Val750. In silico physicochemical calculations predicted that all the designed derivatives passed the Lipinski’s Rule of 5, and have good human intestinal absorption property (HIA>70%). Further, all the designed derivatives showed moderate central nervous system absorption (0.6<BBB<2.0), except for the derivative with a longer (5-Cs) chain length. Conclusion: The findings of the present study suggested that changing the acyl and geranyl side chains of the natural product molecule, tHGA, into two acyl bearing side chains, will improve its pharmacodynamic and pharmacokinetic profiles.

scholarly journals Sterols from Jatropha tanjorensis leaves exhibit anti-inflammatory potential: in vitro and in silico studies

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Damilola Alex Omoboyowa
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Diclofenac Sodium ◽  
Ethanol Extract ◽  
Pharmacokinetic Profile ◽  
Gas Chromatography Mass Spectrometry ◽  
Toxicity Screening ◽  
In Silico Studies ◽  
Anti Inflammatory

Abstract Background Inflammation has continued to raise global challenges and Jatropha tanrogenesis (JT) is used traditionally for its management. In this study, the in silico and in vitro anti-inflammatory potential of bioactive sterols were investigated. The active compounds of ethanol extract of JT leaves were identified using Gas chromatography-mass spectrometry (GC.MS) followed by molecular docking against COX-1 and COX-2 using maestro Schrödinger and pharmacokinetic profile prediction using webserver tools. The in vitro anti-inflammatory and anti-oxidantive potentials were investigated using standard protocols. Results GC–MS analysis of ethanol extract of JT leaves revealed the presence of eight (8) compounds, the molecular docking analysis of these compounds demonstrated varying degrees of binding affinities against the target proteins. The extract exhibit concentration dependent anti-oxidant activity with IC50 of 106.383 and 6.00 Fe2+E/g for DPPH and FRAP respectively. The extract showed significant (P < 0.05) reduction in percentage inhibition of hemolysis at 200 µg/ml while non-significant (P > 0.05) increase was observed at 600 and 1000 µg/ml compared to 200 µg/ml of diclofenac sodium. At lower concentration of 25 and 50 µg/ml, percentage inhibition of albumin denaturation was significantly (P < 0.05) higher compared to 200 µg/ml of diclofenac sodium. Drug likeness prediction and ADME/toxicity screening showed that the bioactive compounds possess no side effects. Conclusion The results obtained in this study suggested that, JT leaves possess anti-inflammatory activity and could be used as a source of new drug.

The Molecular Docking of Flavonoids Isolated from Daucus carota as a Dual Inhibitor of MDM2 and MDMX

2020 ◽  
Vol 15 (2) ◽  
pp. 154-164 ◽  
Author(s):  
Ijaz Muhammad ◽  
Noor Rahman ◽  
Gul E. Nayab ◽  
Sadaf Niaz ◽  
Mohibullah Shah ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Cancer Therapy ◽  
Natural Product ◽  
Signaling Pathway ◽  
In Silico ◽  
P53 Protein ◽  
Dual Inhibitor ◽  
P53 Signaling ◽  
In Silico Studies ◽  
P53 Signaling Pathway

Background: Cancer is characterized by overexpression of p53 associated proteins, which down-regulate P53 signaling pathway. In cancer therapy, p53 activity can be restored by inhibiting the interaction of MDMX (2N0W) and MDM2 (4JGR) proteins with P53 protein. Objective: In the current, study in silico approaches were adapted to use a natural product as a source of cancer therapy. Methods: In the current study in silico approaches were adapted to use a natural product as a source of cancer therapy. For in silico studies, Chemdraw and Molecular Operating Environment were used for structure drawing and molecular docking, respectively. Flavonoids isolated from D. carota were docked with cancerous proteins. Result: Based on the docking score analysis, we found that compound 7 was the potent inhibitor of both cancerous proteins and can be used as a potent molecule for inhibition of 2N0W and 4JGR interaction with p53. Conclusion: Thus the compound 7 can be used for the revival of p53 signaling pathway function however, intensive in vitro and in vivo experiments are required to prove the in silico analysis.

Enzymatic Textile Dyes Decolorization by In vitro and In silico Studies

2019 ◽  
Vol 13 (4) ◽  
pp. 268-276
Author(s):  
Sridevi Ayla ◽  
Monika Kallubai ◽  
Suvarnalatha Devi Pallipati ◽  
Golla Narasimha
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Docking Studies ◽  
Textile Dyes ◽  
Crude Enzyme ◽  
Eastern Ghats ◽  
Textile Dye ◽  
Phanerochaete Sordida ◽  
Molecular Docking Studies ◽  
In Silico Studies

Background:Laccase, a multicopper oxidoreductase (EC: 1.10.3.2), is a widely used enzyme in bioremediation of textile dye effluents. Fungal Laccase is preferably used as a remediating agent in the treatment and transformation of toxic organic pollutants. In this study, crude laccase from a basidiomycetes fungus, Phanerochaete sordida, was able to decolorize azo, antroquinone and indigoid dyes. In addition, interactions between dyes and enzyme were analysed using molecular docking studies.Methods:In this work, a white rot basidiomycete’s fungus, Phanerochaete sordida, was selected from forest soil isolates of Eastern Ghats, and Tirumala and lignolytic enzymes production was assayed after 7 days of incubation. The crude enzyme was checked for decolourisation of various synthetic textile dyes (Vat Brown, Acid Blue, Indigo, Reactive Blue and Reactive Black). Molecular docking studies were done using Autodock-4.2 to understand the interactions between dyes and enzymes.Results:Highest decolourisation efficiency was achieved with the crude enzyme in case of vat brown whereas the lowest decolourisation efficiency was achieved in Reactive blue decolourisation. Similar results were observed in their binding affinity with lignin peroxidase of Phanerochaete chrysosporium through molecular docking approach.Conclusion:Thus, experimental results and subsequent in silico validation involving an advanced remediation approach would be useful to reduce time and cost in other similar experiments.

scholarly journals IN SILICO STUDIES ON FUNCTIONALIZED AZAGLYCINE DERIVATIVES CONTAINING 2, 4-THIAZOLIDINEDIONE SCAFFOLD ON MULTIPLE TARGETS

2017 ◽  
Vol 9 (8) ◽  
pp. 209 ◽  
Author(s):  
Arifa Begum ◽  
Shaheen Begum ◽  
Prasad Kvsrg ◽  
Bharathi K.
Keyword(s):  
Molecular Docking ◽  
Oral Bioavailability ◽  
In Silico ◽  
Viral Infections ◽  
Target Prediction ◽  
Docking Studies ◽  
Antidiabetic Activity ◽  
Molecular Docking Studies ◽  
In Silico Studies ◽  
Glycine Derivative

Objective: The 2, 4-thiazolidinedione containing compounds could lead to most promising scaffolds with higher efficiency toward the targets recognized for its antidiabetic activity when combined with azaglycine moiety. The objective of the present work was to merge functionalized aza glycines with 2, 4-thiazolidinediones, perform in silico evaluation by molecular properties prediction and undertake the molecular docking studies with targets relevant to diabetes, bacterial and viral infections using Swiss Dock programme for unraveling the target identification which can be used for further designing.Methods: (i) In silico studies were performed using Molinspiration online tool, Swiss ADME website and Swiss Target Prediction websites to compute the physicochemical descriptors, oral bioavailability and brain penetration. (ii) Molecular docking studies were performed using Swiss Dock web service for enumeration of binding affinities and assess their biological potentiality.Results: The results predicted good drug likeness, solubility, permeability and oral bioavailability for the compounds. All the compounds showed good docking scores as compared to the reference drugs. The N-oleoyl functionalized aza glycine derivative demonstrated superior binding properties towards all the studied target reference proteins, suggesting its significance in pharmacological actions.Conclusion: The binding interactions observed in the molecular docking studies suggest good binding affinity of the oleoyl functionalized aza glycine derivative, indicating that this derivative would be a promising lead for further investigations of anti-viral, anti-inflammatory and anti-diabetic activities.

scholarly journals Reverse Docking, Molecular Docking, Absorption, Distribution, and Toxicity Prediction of Artemisinin as an Anti-diabetic Candidate

Molekul ◽  
2020 ◽  
Vol 15 (2) ◽  
pp. 88
Author(s):  
Ruswanto Ruswanto ◽  
Richa Mardianingrum ◽  
Siswandono Siswandono ◽  
Dini Kesuma
Keyword(s):  
Molecular Docking ◽  
Aldose Reductase ◽  
Glucose Concentration ◽  
In Silico ◽  
Reductase Activity ◽  
Polyol Pathway ◽  
Toxicity Prediction ◽  
In Silico Studies

Aldose reductase is an enzyme that catalyzes one of the steps in the sorbitol (polyol) pathway that is responsible for fructose formation from glucose. In diabetes, aldose reductase activity increases as the glucose concentration increases. The purpose of this research was to identify and develop the use of artemisinin as an anti-diabetic candidate through in silico studies, including reverse docking, receptor analysis, molecular docking, drug scan, absorption, and distributions and toxicity prediction of artemisinin. Based on the results, we conclude that artemisinin can be used as an anti-diabetic candidate through inhibition of aldose reductase

scholarly journals POTENTIAL ANTIVIRAL OF CATECHINS AND THEIR DERIVATIVES TO INHIBIT SARS-COV-2 RECEPTORS OF M pro PROTEIN AND SPIKE GLYCOPROTEIN IN COVID-19 THROUGH THE IN SILICO APPROACH

2020 ◽  
Vol 14 (3) ◽  
Author(s):  
Frengki Frengki ◽  
Deddi Prima Putra ◽  
Fatma Sri Wahyuni ◽  
Daan Khambri ◽  
Henni Vanda ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Pharmacokinetic Profile ◽  
Spike Glycoprotein ◽  
Software Application ◽  
Better Than

Catechin and their derivatives have been studied to have antiviral potential against COVID-19 through in silico method “pharmacokinetics screening and molecular docking”. Pharmacokinetics and toxicity profiles were obtained through the ADMETSAR server and SwissADME server. Then proceed with the prediction of affinity through the method molecular docking using the software application MOE 2007.09. The testmaterial is in the form of a 3D catechin structure and its derivatives as well as several control ligands downloaded via Pubmed. While templatethe Receptor M pro protein and the Spike glycoprotein are downloaded from pdb.org (PDB ID: 6LU7 and 6LXT). The pharmacokinetic profile of catechins is relatively better than all control ligands with the lowest toxicity. Molecular docking results also show that catechins and theirderivatives have a stronger affinity than control ligands. This research proves that catechin has antiviral potential through inhibition of Mpro protein and Spike glycoprotein COVID-19 virus.

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