Docking and Molecular Dynamic Simulation of Temozolomide with Carbonic Anhydrase XIII

2020 ◽  
Vol 5 (4) ◽  
pp. 332-339
Author(s):  
R. Meenashi ◽  
K. Selvaraju ◽  
P. Jayalakshmi ◽  
P.V. Nidhin ◽  
A. David Stephen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Carbonic Anhydrase ◽  
Dynamic Simulation ◽  
Alkylating Agent ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Cancer Treatments ◽  
The Stability ◽  
Protein Environment

The effect of inhibition of temozolomide, an alkylating agent widely used in cancer treatments, with carbonic anhydrase XIII protein was investigated using docking studies. The stability of temozolomide in the protein environment was assessed and analyzed by molecular dynamics simulation. The topological and charge density variations of temozolomide were studied in detail to perceive the primary insight of the pharmaceutical actions.

scholarly journals Molecular Modeling of Some Benzodiazole Derivatives with EGFR Protein 1M17

2020 ◽  
pp. 84-95
Author(s):  
A. S. Sony ◽  
Xavier Suresh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modeling ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Simulation Study ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Ligand Complex ◽  
Drug Candidates ◽  
The Stability

Aims: To study the anticancer potential of benzodiazole derivatives using molecular modeling studies. Study Design: Molecular Dynamics simulation study. Place and Duration of Study: Sathyabama Institute of Science and Technology (SIST), Chennai, between June 2020 and August 2020. Methodology: We studied the anticancer potential of benzodiazole derivatives using molecular modeling. Docking studies of the ligands with EGFR protein 1M17 was carried out using AutoDock.Molecular Dynamics simulation study was carried out using Playmolecule was used to verify the stability of the protein-ligand complex. Results: Molecular docking studies showed a good binding affinity of the ligands with the protein 1m17. Benzodiazole derivative 4,6-dichloro-2-(trifluoromethyl)-1H-1,3-benzodiazole exhibited the lowest binding energy of (-6.42 kcal/mol) at the active site of EGFR (PDB code:1M17) consistent with its least inhibition coefficient (Ki =32.54 uM). Molecular dynamics simulation showed better stability of the ligand and protein complex. Conclusion: Molecular modeling study of selected benzodiazole derivatives showed a very good binding affinity to EGFR protein 1m17. MD simulation of the best-docked ligand showed that the complex was stable. Our study demonstrated that benzodiazole derivatives can be potential anticancer drug candidates

Effects of Normal and Aberrant Glycosylation on the Stability of α1-Anti Trypsin Through Molecular Dynamic Simulation

2021 ◽  
Vol 15 (10) ◽  
pp. 3066-3069
Author(s):  
Mujeeb Alam Khan ◽  
Ehtesham . ◽  
Muhammad Shoaib ◽  
Roshan Ali ◽  
Muhammad Idrees
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Dynamics Simulation ◽  
Mean Square ◽  
Glycated Protein ◽  
Alpha 1 Antitrypsin ◽  
The Stability

The Alpha-1 antitrypsin belonging to serpin family is a protease inhibitor, the level of which rises by a factor of ten during inflammation Purpose: To investigate the stability of normal and aberrantly glycosylated α1-antitrypsin through molecular dynamics simulation Study Design: Experimental study Methodology: Current project was conducted in the department of Biochemistry at Institute of Basic Medical Sciences Khyber Medical University, Peshawar. A1AT FASTA sequence was retrieved from UniProt database (UniProt ID: P01009). Post-Translational Modifications (PTM) regions were identified from the same database. GLYCONNECT database was used to understand N-linked glycation with the asparagine residues found at position 70, 107, and 271 amino acid residue regions Statistical analysis: Different bioinformatics analyses such that Root Mean Square Deviation, Radius of gyration, Root Mean Square fluctuation, Hydrogen-bonding, Secondary Structure Determination, and Principal Component Analysis were executed for 100 ns molecular dynamics simulation run Results: RMSd, RMSf, and Rgyr significantly differ between the native type and cancer isoform. More H-bonding and strong protein stability and folding were seen in the native type. PCA analysis further confirms native type compact motion in the parallel direction during MD simulation Conclusion: It was concluded that glycated protein appears to have high structural stability than its aberrant glycated protein. However, it will be utilized for the prompt production of the anti-cancer drugs to effectively treating cancer disease Key Words: Alpha-1 Antitrypsin, Aberrant Glycosylation and Molecular Dynamic Simulation.

Molecular Dynamics Simulation and Docking Studies of Selenocyanate Derivatives as Anti-Leishmanial Agents

2016 ◽  
Vol 19 (10) ◽  
Author(s):  
Maryam Iman ◽  
Hamid Bakhtiari Kaboutaraki ◽  
Rahim Jafari ◽  
Seyed Ayoub Hosseini ◽  
Abolghasem Moghimi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Docking Studies ◽  
Dynamics Simulation

scholarly journals Molecular Docking and Molecular Dynamics Simulation Studies of Triterpenes from Vernonia patula with the Cannabinoid Type 1 Receptor

2021 ◽  
Vol 22 (7) ◽  
pp. 3595
Author(s):  
Md Afjalus Afjalus Siraj ◽  
Md. Sajjadur Rahman ◽  
Ghee T. Tan ◽  
Veronique Seidel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Cannabinoid Type 1 Receptor ◽  
Docking Approach

A molecular docking approach was employed to evaluate the binding affinity of six triterpenes, namely epifriedelanol, friedelin, α-amyrin, α-amyrin acetate, β-amyrin acetate, and bauerenyl acetate, towards the cannabinoid type 1 receptor (CB1). Molecular docking studies showed that friedelin, α-amyrin, and epifriedelanol had the strongest binding affinity towards CB1. Molecular dynamics simulation studies revealed that friedelin and α-amyrin engaged in stable non-bonding interactions by binding to a pocket close to the active site on the surface of the CB1 target protein. The studied triterpenes showed a good capacity to penetrate the blood–brain barrier. These results help to provide some evidence to justify, at least in part, the previously reported antinociceptive and sedative properties of Vernonia patula.

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