scholarly journals MOLECULAR DOCKING STUDIES OF ISOLATED FLAVONOIDS COMPOUNDS FROM AMARANTHUS TRISTIS LINN. AS ALPHA-AMYLASE AND ALPHA-GLUCOSIDASE ACTIVATORS

2018 ◽  
Vol 11 ◽  
Author(s):  
Sundar Rajan T ◽  
Vijey Aanandhi M
Keyword(s):  
Molecular Docking ◽  
Experimental Studies ◽  
Three Dimensional ◽  
Data Bank ◽  
Docking Studies ◽  
Alpha Amylase ◽  
Dimensional Structure ◽  
Novel Targets ◽  
Alpha Glucosidase ◽  
Protein Data Bank Database

Aim: Aim of this work on in silico approach to used to access the use of flavonids compounds of nutritionally enriched plant Amaranthus tristis Linn.Methods: Bioflavonoids of rutin isolated from A. tristis Linn. and active agents receptor such as alpha-amylase (1SMD) and alpha-glucosidase (3wy1) activators. Three-dimensional structure of receptors was obtained from protein data bank database and biocomponents such as isoflavones and flavonones of A. tristis were downloaded from database like USDA. Docking studies of insulin receptor with A. tristis biocomponents for isoflavones and flavonones were performed using AutoDock - 1.5.6 software.Results: Compounds from A. tristis Linn. showed better binding features with the alpha-amylase and alpha-glycosidase. Thus, these compounds can be effectively used as drugs for treating diabetes which is predicted on the basis of docking scores.Conclusion: The insights gained in this work can be further used in experimental studies for designing antidiabetic drugs with novel targets and mode of action.

scholarly journals SOLATION, CHARACTERIZATION, AND DOCKING STUDIES OF ISOLATED COMPOUNDS AS ANTIDIABETIC MOLECULES FROM CRESSA CRETICA

2020 ◽  
pp. 84-91
Author(s):  
SANGEETA RANI ◽  
KAVITA GAHLOT ◽  
ARVIND KUMAR
Keyword(s):  
Molecular Docking ◽  
Spectroscopic Analysis ◽  
Three Dimensional ◽  
Data Bank ◽  
Docking Study ◽  
Docking Studies ◽  
Dimensional Structure ◽  
Lead Target ◽  
Coarse Powder ◽  
Autodock 4.0

Objective: The purpose of this study was to investigate the diabetic effect of phytocompounds isolated from Cressa cretica Linn. using spectroscopic analysis and molecular docking studies. Methods: Coarse powder of the whole plant of C. cretica was extracted with methanol, extracted part was subjected to silica column isolation, and two compounds: 2-Isopropyl-4-(1-methyl-dodeca-2,4-dienyloxy)-benzene-1,3,5-triol (Compound CN-01) and 11-Methyl-dodeca-2,4,6,8,10-pentenoic acid 2,3-dihydroxy-5-methyl-phenyl ester (Compound CN-02) were isolated in pure form. The three-dimensional structure of target protein was downloaded from PDB (www.rcsb.org) Protein Data Bank, Ligand file CN – 01 and CN – 02 were converted to MDL Molfile (V2000) format using ChemSketch 2017.2.1. These files could not be used directly in AutoDock 4.0 tools; thus, they were first converted to PDB files using an open babel tool. Results: Compounds were revealed through spectroscopic analysis and screened using AutoDock 4.0 tools. Docking study recommended that CN – 01 and CN – 02 an existing phytochemical from the plant of C. cretica had the highest fitness docking score and hence could be a potent antidiabetic drug. Conclusion: In this investigation, we docked the receptor (glycogen phosphorylase protein) holds a promising lead target formation against diabetes based on molecular docking analysis (minimum hydrogen bond length and maximum docked score). Thus, these compounds can be effectively used as drugs for treating diabetes which is predicted on the basis of docking scores.

Exploration of Diosmin to control diabitis and its complications-an in vitro and in silico approach

2020 ◽  
Vol 16 ◽  
Author(s):  
Kushagra Dubey ◽  
Raghvendra Dubey ◽  
Revathi Gupta ◽  
Arun Gupta
Keyword(s):  
Molecular Docking ◽  
Aldose Reductase ◽  
Inhibitory Activity ◽  
Blood Lipid ◽  
Docking Studies ◽  
Alpha Amylase ◽  
Lipid Lowering ◽  
Molecular Docking Studies ◽  
Alpha Glucosidase

Background: Diosmin is a flavonoid obtained from the citrus fruits of the plants. Diosmin has blood lipid lowering activities, antioxidant activity, enhances venous tone and microcirculation, protects capillaries, mainly by reducing systemic oxidative stress. Objective: The present study demonstrates the potential of Diosmin against the enzymes aldose reductase, α-glucosidase, and α-amylase involved in diabetes and its complications by in vitro evaluation and reverse molecular docking studies. Method: The assay of aldose reductase was performed by using NADPH as starting material and DL-Glyceraldehyde as a substrate. DNS method was used for alpha amylase inhibition and in alpha glucosidase inhibitory activity p-nitrophenyl glucopyranoside (pNPG) was used as substrate. The reverse molecular docking studies was performed by using Molegro software (MVD) with grid resolution of 30 Å. Result: Diosmin shows potent inhibitory effect against aldose reductase (IC50:333.88±0.04 µg/mL), α-glucosidase (IC50:410.3±0.01 µg/mL) and α-amylase (IC50: 404.22±0.02 µg/mL) respectively. The standard drugs shows moderate inhibitory activity for enzymes. The MolDock Score of Diosmin was -224.127 against aldose reductase, -168.17 against α-glucosidase and -176.013 against α-amylase respectively, which was much higher than standard drugs. Conclusion: From the result it was concluded that diosmin was a potentially inhibitor of aldose reductase, alpha amylase and alpha glucosidase enzymes then the standard drugs and it will be helpful in the management of diabetes and its complications. This will also be benevolent to decrease the socio economical burden on the middle class family of the society.

scholarly journals Docking studies in targeting proteins involved in cardiovascular disorders using phytocompounds from Terminalia arjuna

2020 ◽  
Author(s):  
Vikas Kumar ◽  
Nitin Sharma ◽  
Anuradha Sourirajan ◽  
Prem Kumar Khosla ◽  
Kamal Dev
Keyword(s):  
Molecular Docking ◽  
3D Structure ◽  
Three Dimensional ◽  
Data Bank ◽  
Docking Studies ◽  
Terminalia Arjuna ◽  
Structure Based Drug Design ◽  
Lipinski’S Rule ◽  
Protein Ligand Interactions ◽  
Ligand Interactions

AbstractTerminalia arjuna (Roxb.) Wight and Arnot (T. arjuna) commonly known as Arjuna has been known for its cardiotonic nature in heart failure, ischemic, cardiomyopathy, atherosclerosis, myocardium necrosis and also has been used in the treatment of different human disorders such as blood diseases, anaemia and viral diseases. Our focus has been on phytochemicals which do not exhibit any cytotoxicity and have significant cardioprotective activity. Since Protein-Ligand interactions play a key role in structure-based drug design, therefore with the help of molecular docking, we screened 19 phytochemicals present in T. arjuna and investigated their binding affinity against different cardiovascular target proteins. The three-dimensional (3D) structure of target cardiovascular proteins were retrieved from Protein Data Bank, and docked with 3D Pubchem structures of 19 phytochemicals using Autodock vina. Molecular docking and drug-likeness studies were made using ADMET properties while Lipinski’s rule of five was performed for the phytochemicals to evaluate their cardio protective activity. Among all selected phytocompounds, arjunic acid, arjungenin, and terminic acid were found to fulfill all ADMET rules, drug likeness, and are less toxic in nature. Our studies, therefore revealed that these three phytochemicals from T. arjuna can be used as promising candidates for developing broad spectrum drugs against cardiovascular diseases.

scholarly journals A computer-based approach for developing linamarase inhibitory agents

2020 ◽  
Vol 5 (7) ◽  
Author(s):  
Lucas Paul ◽  
Celestin N. Mudogo ◽  
Kelvin M. Mtei ◽  
Revocatus L. Machunda ◽  
Fidele Ntie-Kang
Keyword(s):  
Structure Elucidation ◽  
Three Dimensional ◽  
Data Bank ◽  
Competitive Inhibitor ◽  
Industrial Applications ◽  
Dimensional Structure ◽  
Full Understanding ◽  
The Poor ◽  
Computer Based ◽  
Inhibitory Agents

AbstractCassava is a strategic crop, especially for developing countries. However, the presence of cyanogenic compounds in cassava products limits the proper nutrients utilization. Due to the poor availability of structure discovery and elucidation in the Protein Data Bank is limiting the full understanding of the enzyme, how to inhibit it and applications in different fields. There is a need to solve the three-dimensional structure (3-D) of linamarase from cassava. The structural elucidation will allow the development of a competitive inhibitor and various industrial applications of the enzyme. The goal of this review is to summarize and present the available 3-D modeling structure of linamarase enzyme using different computational strategies. This approach could help in determining the structure of linamarase and later guide the structure elucidation in silico and experimentally.

scholarly journals Rutin-Functionalized Multi-Walled Carbon Nanotubes: Molecular Docking, Physicochemistry and Cytotoxicity in Fibroblasts

Toxics ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. 173
Author(s):  
Conrado M. S. Neto ◽  
Felipe C. Lima ◽  
Renata P. Morais ◽  
Lucas R. M. de Andrade ◽  
Renata de Lima ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Docking ◽  
Thermal Analyses ◽  
Three Dimensional ◽  
Morphological Structure ◽  
Dose Effect ◽  
Dimensional Structure ◽  
3T3 Fibroblasts ◽  
Multi Walled Carbon Nanotubes ◽  
Walled Carbon Nanotubes

Multi-Walled Carbon Nanotubes (MWCNT) have been functionalized with rutin through three steps (i. reaction step; ii. purification step; iii. drying step) and their physicochemical properties investigated with respect to morphological structure, thermal analysis, Fourier Transform Infrared Spectroscopy (FTIR), and cytotoxicity. The molecular docking suggested the rutin-functionalized MWCNT occurred by hydrogen bonds, which was confirmed by FTIR assays, corroborating the results obtained by thermal analyses. A tubular shape, arranged in a three-dimensional structure, could be observed. Mild cytotoxicity observed in 3T3 fibroblasts suggested a dose–effect relationship after exposure. These findings suggest the formation of aggregates of filamentous structures on the cells favoring the cell penetration.

Design of Dual COX-2 and 5-LOX Inhibitors with Iron-Chelating Properties Using Structure-Based and Ligand-Based Methods

2021 ◽  
Vol 18 ◽  
Author(s):  
Jelena Bošković ◽  
Dušan Ružić ◽  
Olivera Čudina ◽  
Katarina Nikolic ◽  
Vladimir Dobričić
Keyword(s):  
Molecular Docking ◽  
External Validation ◽  
Three Dimensional ◽  
3D Qsar ◽  
Quantitative Structure Activity Relationship ◽  
Docking Studies ◽  
Qsar Analysis ◽  
In Silico Admet ◽  
Cox 2 ◽  
Lox Inhibitors

Background: Inflammation is common pathogenesis of many diseases progression, such as malignancy, cardiovascular and rheumatic diseases. The inhibition of the synthesis of inflammatory mediators by modulation of cyclooxygenase (COX) and lipoxygenase (LOX) pathways provides a challenging strategy for the development of more effective drugs. Objective: The aim of this study was to design dual COX-2 and 5-LOX inhibitors with iron-chelating properties using a combination of ligand-based (three-dimensional quantitative structure-activity relationship (3D-QSAR)) and structure-based (molecular docking) methods. Methods: The 3D-QSAR analysis was applied on a literature dataset consisting of 28 dual COX-2 and 5-LOX inhibitors in Pentacle software. The quality of developed COX-2 and 5-LOX 3D-QSAR models were evaluated by internal and external validation methods. The molecular docking analysis was performed in GOLD software, while selected ADMET properties were predicted in ADMET predictor software. Results: According to the molecular docking studies, the class of sulfohydroxamic acid analogues, previously designed by 3D-QSAR, was clustered as potential dual COX-2 and 5-LOX inhibitors with iron-chelating properties. Based on the 3D-QSAR and molecular docking, 1j, 1g, and 1l were selected as the most promising dual COX-2 and 5-LOX inhibitors. According to the in silico ADMET predictions, all compounds had an ADMET_Risk score less than 7 and a CYP_Risk score lower than 2.5. Designed compounds were not estimated as hERG inhibitors, and 1j had improved intrinsic solubility (8.704) in comparison to the dataset compounds (0.411-7.946). Conclusion: By combining 3D-QSAR and molecular docking, three compounds (1j, 1g, and 1l) are selected as the most promising designed dual COX-2 and 5-LOX inhibitors, for which good activity, as well as favourable ADMET properties and toxicity, are expected.

MRPC (Missing Regions in Polypeptide Chains): a knowledgebase

2019 ◽  
Vol 52 (6) ◽  
pp. 1422-1426
Author(s):  
Rajendran Santhosh ◽  
Namrata Bankoti ◽  
Adgonda Malgonnavar Padmashri ◽  
Daliah Michael ◽  
Jeyaraman Jeyakanthan ◽  
...  
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Protein Molecule ◽  
Data Bank ◽  
Protein Crystal ◽  
Dimensional Structure ◽  
Protein Structure Analysis ◽  
Three Dimensional Structure ◽  
X Ray Crystallography ◽  
Polypeptide Chains

Missing regions in protein crystal structures are those regions that cannot be resolved, mainly owing to poor electron density (if the three-dimensional structure was solved using X-ray crystallography). These missing regions are known to have high B factors and could represent loops with a possibility of being part of an active site of the protein molecule. Thus, they are likely to provide valuable information and play a crucial role in the design of inhibitors and drugs and in protein structure analysis. In view of this, an online database, Missing Regions in Polypeptide Chains (MRPC), has been developed which provides information about the missing regions in protein structures available in the Protein Data Bank. In addition, the new database has an option for users to obtain the above data for non-homologous protein structures (25 and 90%). A user-friendly graphical interface with various options has been incorporated, with a provision to view the three-dimensional structure of the protein along with the missing regions using JSmol. The MRPC database is updated regularly (currently once every three months) and can be accessed freely at the URL http://cluster.physics.iisc.ac.in/mrpc.

scholarly journals BLASTing away preconceptions in crystallization trials

2019 ◽  
Vol 75 (3) ◽  
pp. 184-192 ◽  
Author(s):  
Gabriel Jan Abrahams ◽  
Janet Newman
Keyword(s):  
Protein Data Bank ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Protein Sequences ◽  
Protein Molecule ◽  
Data Bank ◽  
Dimensional Structure ◽  
Critical Step ◽  
Quantitative Verification ◽  
Better Than

Crystallization is in many cases a critical step for solving the three-dimensional structure of a protein molecule. Determining which set of chemicals to use in the initial screen is typically agnostic of the protein under investigation; however, crystallization efficiency could potentially be improved if this were not the case. Previous work has assumed that sequence similarity may provide useful information about appropriate crystallization cocktails; however, the authors are not aware of any quantitative verification of this assumption. This research investigates whether, given current information, one can detect any correlation between sequence similarity and crystallization cocktails. BLAST was used to quantitate the similarity between protein sequences in the Protein Data Bank, and this was compared with three estimations of the chemical similarities of the respective crystallization cocktails. No correlation was detected between proteins of similar (but not identical) sequence and their crystallization cocktails, suggesting that methods of determining screens based on this assumption are unlikely to result in screens that are better than those currently in use.

scholarly journals AN IN SILICO STUDY OF NARINGENIN-MEDIATED NEUROPROTECTION IN PARKINSON’S DISEASE

2017 ◽  
Vol 10 (8) ◽  
pp. 171
Author(s):  
Saurabh Kumar Jha ◽  
Pravir Kumar
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Molecular Docking ◽  
In Silico ◽  
E3 Ligase ◽  
Docking Studies ◽  
Dimensional Structure ◽  
Molecular Docking Studies ◽  
Lipinski’S Rule ◽  
Ubiquitin E3 Ligase

  Objective: Naringenin is a dietary biomolecule with broad spectrum of activities which protects neurons from various neurotoxic insults and improves cognition and motor function in neurodegenerative diseases. DJ-1 has both, ubiquitin E3 ligase as well as chaperonic activity, and loss of ubiquitin E3 ligase activity of DJ-1 has been found to be associated with familial Parkinson’s disease (PD). Naringenin induced E3 ligase activity of DJ-1 which can have possible clinical relevance in PD.Methods: Various in silico parameters such as phylogenetic analysis, homology modeling, active site prediction, and molecular docking studies using AutoDock 4.2.1 and LIGPLOT1.4.5 were carried out.Results: Three-dimensional structure of DJ-1 was generated and Ramachandran plot was obtained for quality assessment. RAMPAGE displayed 99.5% of residues in the most favored regions. 0% residues in additionally allowed and 0.5% disallowed regions of DJ-1 protein. Further, initial screenings of the molecules were done based on Lipinski’s rule of five. CastP server used to predict the ligand binding site suggests that this protein can be utilized as a potential drug target. Finally, we have found naringenin to be most effective among four biomolecules in modulating DJ-1 based on minimum inhibition constant, Ki, and highest negative free energy of binding with maximum interacting surface area in the course of docking studies.Conclusion: Our study suggests that based on different in silico parameters and molecular docking studies, naringenin can provide a new avenue for PD therapeutics.

Evaluation of anti-diabetic and alpha glucosidase inhibitory action of anthraquinones from Rheum emodi

2015 ◽  
Vol 6 (8) ◽  
pp. 2693-2700 ◽  
Author(s):  
Aditya Arvindekar ◽  
Tanaji More ◽  
Pavan V. Payghan ◽  
Kirti Laddha ◽  
Nanda Ghoshal ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Inhibitory Action ◽  
Docking Studies ◽  
Molecular Docking Studies ◽  
Alpha Glucosidase

The 1,8-dihydroxyanthraquinones from the culinary and medicinally important plant Rheum emodi exert anti-hyperglycemic potential but notably different α-glucosidase actions as established by in vitro, in vivo, kinetics and molecular docking studies.

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