Radicalic cleavage pathway and DNA docking studies of novel chemotherapic platinum agent of 5,6-di-2-ithienyl-2,3-dihydropyrazine

Polyhedron ◽  
2019 ◽  
Vol 170 ◽  
pp. 25-33
Author(s):  
Rabia El Hag ◽  
Mohamed Musbah Abdusalam ◽  
Ceyda Acilan ◽  
Hakan Kayı ◽  
Şeniz Özalp-Yaman
Keyword(s):  
Docking Studies ◽  
Platinum Agent ◽  
Dna Docking

scholarly journals Optimized structure of monoubiquitinated FANCD2 (human) at Lys 561: a theoretical approach

2021 ◽  
Author(s):  
Sudipa Mondal ◽  
Subba Reddy ◽  
Sudit S. Mukhopadhyay
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Theoretical Approach ◽  
Md Simulation ◽  
Docking Studies ◽  
Fanconi Anaemia ◽  
Cross Linking ◽  
Structural Differences ◽  
The Stability ◽  
Dna Docking

AbstractFanconi anaemia pathway repairs inter-strand cross linking damage (ICL) of the DNA. Monoubiquitination of FANCD2 and FANCI is very crucial for ICL repairing. In this work we have tried to understand the monoubiquitinated FANCD2 structure, which facilitates the FANCD2 for binding the damage part of the chromatin. Crystal structure of the monoubiquitinated FANCD2 alone is not available, therefore we have developed the optimized structure of the human monoubiquitinated (Lys 561) FANCD2. As there is no suitable software or web server we have developed a method for building up monoubiquitinated product and validated on simplest monoubiquitinated protein, diubiquitin. We have predicted the structure of human monoubiquitinated FANCD2 by using our method and studied the interaction with DNA by docking studies. Molecular Dynamics (MD) simulation was used to understand the stability of the structure. Large structural differences have been observed between FANCD2 and monoubiquitinated FANCD2. DNA docking studies suggest that the binding site varies for the FANCD2 and monoubiquitinated FANCD2.

Homology Modeling of Mus Musculus CDK5 and Molecular Docking Studies with Flavonoids

2017 ◽  
Vol 9 (6) ◽  
Author(s):  
Sowmya Suri ◽  
Rumana Waseem ◽  
Seshagiri Bandi ◽  
Sania Shaik
Keyword(s):  
Molecular Docking ◽  
3D Model ◽  
Structural Features ◽  
Docking Studies ◽  
Amino Acid Residues ◽  
Cyclin Dependent Kinase ◽  
Ligand Complex ◽  
Ligand Interaction ◽  
Molecular Docking Studies ◽  
Cyclin Dependent Kinase 5

A 3D model of Cyclin-dependent kinase 5 (CDK5) (Accession Number: Q543f6) is generated based on crystal structure of P. falciparum PFPK5-indirubin-5-sulphonate ligand complex (PDB ID: 1V0O) at 2.30 Å resolution was used as template. Protein-ligand interaction studies were performed with flavonoids to explore structural features and binding mechanism of flavonoids as CDK5 (Cyclin-dependent kinase 5) inhibitors. The modelled structure was selected on the basis of least modeler objective function. The model was validated by PROCHECK. The predicted 3D model is reliable with 93.0% of amino acid residues in core region of the Ramachandran plot. Molecular docking studies with flavonoids viz., Diosmetin, Eriodictyol, Fortuneletin, Apigenin, Ayanin, Baicalein, Chrysoeriol and Chrysosplenol-D with modelled protein indicate that Diosmetin is the best inhibitor containing docking score of -8.23 kcal/mol. Cys83, Lys89, Asp84. The compound Diosmetin shows interactions with Cys83, Lys89, and Asp84.

Insights Studies for Certain Natural FDA Approved Polyphenolics and Repurposing for COVID-19

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 1390-1395
Author(s):  
Arafa Musa ◽  
Ehab M. Mostafa ◽  
Mohammad M. Al-Sanea ◽  
Shaimaa R. Ahmed ◽  
Gomaa Mostafa-Hedeab ◽  
...  
Keyword(s):  
Docking Studies ◽  
Human Populations ◽  
Energy Score ◽  
Protease Enzyme ◽  
Human Disorders ◽  
Variable Chemical ◽  
Pancreatic Disorders ◽  
New Treatment ◽  
New Applications ◽  
Death Cases

Natural polyphenolic drugs were approved for treatment of various diseases. Diosmin, rutin, quercetin, aesculin, genistein, hesperidin and silybin are known for their safety and have been applied for several human disorders including cancer, cardiovascular disorders, atherosclerosis, oxidative stress, capillary fragility, liver and pancreatic disorders and others. As the structures of the selected polyphenolic compounds possess variable chemical moieties with diverse chemical and electronic characters, these properties have been employed for further insights studies to predict new applications concerning the newly occurred pandemic. COVID-19 is a terrible disease that attacked millions of human populations at the end of year 2019. As the number of death cases has increased to exceed one million of humans, the early discovery of new treatment from previously approved and safe drugs is the main target of this study. Employing the putative docking studies for the selected polyphenolic drugs were done and the results were promising, all tested drugs exhibited high affinity with the selected five proteins of protease enzyme, the docking score ranged from -8.4461 to -26.1691 kcal/mol with 3-7 variable interaction bonds. Among the tested drugs, diosmin appeared as the most promising drug as it exhibited the highest energy score and interaction bonds with the most of proteins.

Computational and Docking Studies of 5,6-dihydroxy-7,8, 4'-trimethoxyflavone: A α-Glucosidase Inhibitory Constituent from Limnophila indica

2018 ◽  
Vol 8 (3) ◽  
pp. 548-561
Author(s):  
Dipak Kumar Rana ◽  
Dipanwita Saha ◽  
Partha Sarathi Sengupta ◽  
Bipul Sarkar ◽  
Palash Mondal ◽  
...  
Keyword(s):  
Docking Studies
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