scholarly journals Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations

Biochemistry ◽  
2011 ◽  
Vol 50 (28) ◽  
pp. 6157-6169 ◽  
Author(s):  
Markus A. Lill
Keyword(s):  
Molecular Docking ◽  
Protein Flexibility ◽  
Docking Simulations

In Silico Approach to Inhibition of Tyrosinase by Ascorbic Acid Using Molecular Docking Simulations

2014 ◽  
Vol 14 (12) ◽  
pp. 1469-1472 ◽  
Author(s):  
F. Senol ◽  
M. Khan ◽  
Gurdal Orhan ◽  
Erdem Gurkas ◽  
Ilkay Orhan ◽  
...  
Keyword(s):  
Ascorbic Acid ◽  
Molecular Docking ◽  
In Silico ◽  
Docking Simulations

scholarly journals Discovery of novel potential KIT inhibitors for the treatment of gastrointestinal stromal tumor

2021 ◽  
Vol 16 (1) ◽  
pp. 303-310
Author(s):  
Lili Jiang ◽  
Zhongmin Zhang ◽  
Zhen Wang ◽  
Yong Liu
Keyword(s):  
Molecular Docking ◽  
Gastrointestinal Stromal Tumor ◽  
Pharmacophore Modeling ◽  
Stromal Tumor ◽  
Strong Hydrogen Bond ◽  
Ligand Complex ◽  
Hydrogen Bond Interaction ◽  
Mutant Proteins ◽  
Docking Simulations ◽  
Pharmacophore Models

Abstract Numerous inhibitors of tyrosine-protein kinase KIT, a receptor tyrosine kinase, have been explored as a viable therapy for the treatment of gastrointestinal stromal tumor (GIST). However, drug resistance due to acquired mutations in KIT makes these drugs almost useless. The present study was designed to screen the novel inhibitors against the activity of the KIT mutants through pharmacophore modeling and molecular docking. The best two pharmacophore models were established using the KIT mutants’ crystal complexes and were used to screen the new compounds with possible KIT inhibitory activity against both activation loop and ATP-binding mutants. As a result, two compounds were identified as potential candidates from the virtual screening, which satisfied the potential binding capabilities, molecular modeling characteristics, and predicted absorption, distribution, metabolism, excretion, toxicity (ADMET) properties. Further molecular docking simulations showed that two compounds made strong hydrogen bond interaction with different KIT mutant proteins. Our results indicated that pharmacophore models based on the receptor–ligand complex had excellent ability to screen KIT inhibitors, and two compounds may have the potential to develop further as the future KIT inhibitors for GIST treatment.

scholarly journals An Androsterone‐H 2 @C 60 hybrid: Synthesis, Properties and Molecular Docking Simulations with SARS‐Cov‐2

ChemPlusChem ◽  
2021 ◽  
Author(s):  
Margarita Suárez ◽  
Kamil Makowski ◽  
Reinier Lemos ◽  
Luis Almagro ◽  
Hortensia Rodríguez ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Simulations ◽  
Synthesis Properties

Web Services for Molecular Docking Simulations

2019 ◽  
pp. 221-229 ◽  
Author(s):  
Nelson J. F. da Silveira ◽  
Felipe Siconha S. Pereira ◽  
Thiago C. Elias ◽  
Tiago Henrique
Keyword(s):  
Molecular Docking ◽  
Web Services ◽  
Docking Simulations

scholarly journals In silicoidentification of putativeTrypanosoma cruzienolase inhibitors

2019 ◽  
Author(s):  
Edward A. Valera-Vera ◽  
Melisa Sayé ◽  
Chantal Reigada ◽  
Mariana R. Miranda ◽  
Claudio A. Pereira
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Virtual Screening ◽  
Active Site ◽  
Screening Strategy ◽  
Glycolytic Enzyme ◽  
Docking Simulations ◽  
Enzyme Active Site ◽  
Key Enzyme

AbstractEnolase is a glycolytic enzyme that catalyzes the interconversion between 2-phosphoglycerate and phosphoenolpyruvate. In trypanosomatids enolase was proposed as a key enzyme afterin silicoandin vivoanalysis and it was validated as a protein essential for the survival of the parasite. Therefore, enolase constitutes an interesting enzyme target for the identification of drugs against Chagas disease. In this work, a combined virtual screening strategy was implemented, employing similarity virtual screening, molecular docking and molecular dynamics. First, two known enolase inhibitors and the enzyme substrates were used as queries for the similarity screening on the Sweetlead database using five different algorithms. Compounds retrieved in the top 10 of at least three search algorithms were selected for further analysis, resulting in six compounds of medical use (etidronate, pamidronate, fosfomycin, acetohydroximate, triclofos, and aminohydroxybutyrate). Molecular docking simulations predicted acetohydroxamate and triclofos would not bind to the active site of the enzyme, and a re-scoring of the obtained poses signaled fosfomycin and aminohydroxybutyrate as bad enzyme binders. Docking poses obtained for etidronate, pamidronate, and PEP, were used for molecular dynamics calculations to describe their mode of binding. From the obtained results, we propose etidronate as a possibleTcENO inhibitor, and describe desirable and undesirable molecular motifs to be taken into account in the repurposing or design of drugs aiming this enzyme active site.

scholarly journals Molecular Docking Simulations to Determine Organic Cation Sorption to Organic Matter

2020 ◽  
Author(s):  
Sharon Scott ◽  
Christopher Hadad ◽  
Joseph Fernandez ◽  
Allison MacKay
Keyword(s):  
Organic Matter ◽  
Molecular Docking ◽  
Organic Cation ◽  
Docking Simulations

scholarly journals Molecular Docking Study of Anthocyanidin Compounds Against Epidermal Growth Factor Receptor (EGFR) as Anti-Lung Cancer

2021 ◽  
Vol 8 (1) ◽  
pp. 8
Author(s):  
Riska Prasetiawati ◽  
Meilia Suherman ◽  
Benny Permana ◽  
Rahmawati Rahmawati
Keyword(s):  
Lung Cancer ◽  
Epidermal Growth Factor Receptor ◽  
Molecular Docking ◽  
Growth Factor ◽  
Epidermal Growth Factor ◽  
Growth Factor Receptor ◽  
Docking Simulation ◽  
Molecular Docking Study ◽  
Docking Simulations ◽  
Epidermal Growth

It is presumed that antiproliferative activity of anthocyanidin has interaction with Epidermal Growth Factor Receptor (EGFR) which has effect on lung cancer cell growth. This study aimed to observe the interaction between anthocyanidin and EGFR and to find out prediction, absorption, distribution activities as well as anthocyanidin toxicity compared to Gefitinib, an EGFR inhibitor. All test compounds were optimized with Autodock Tools®, then molecular docking simulations and predictions of absorption, distribution and toxicity were carried out. Malvidin was stated to meet the Lipinski's Rule of Five, indicating good bioavailability. Result of molecular docking simulation showed that malvidin had better affinity against EGFR than Gefitinib. Molecular docking visualization result showed that malvidin had interaction with amino acid residue such as Met793, Gln791, Leu718, Thr854, Asp855 and Lys745. Absorption and distribution predictions included percentage scores of Human Intestinal Absorption (HIA), human colon adenocarcinoma (Caco-2), and Plasma Protein Binding. Toxicity test revealed that malvidin was mutagenic compound but not carcinogenic one. The findings indicated that malvidin was potential to be an anti lung cancer candidate through EGFR inhibition.Keywords: Antiproliferative, Anthocyanidin, Epidermal Growth Factor Receptor, Molecular Docking

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