Dynamic Docking Study of the Binding of 1-Chloro-2,4- Dinitrobenzene in the Putative Electrophile Binding Site of Naturally Occurring Human Glutathione

1999 ◽  
Author(s):  
John Buolamwini ◽  
Francis Ali-Osman
Keyword(s):  
Binding Site ◽  
Docking Study ◽  
Naturally Occurring ◽  
Dynamic Docking

A New Reactive Ketenaminal: Synthesis, Coupling Reaction, Tautomeric Study, Docking and Antimicrobial Evaluation of the Products

2020 ◽  
Vol 16 (6) ◽  
pp. 761-773
Author(s):  
Huda K. Mahmoud ◽  
Hanadi A. Katouah ◽  
Marwa F. Harras ◽  
Thoraya A. Farghaly
Keyword(s):  
Binding Site ◽  
Antimicrobial Agents ◽  
Coupling Reaction ◽  
Docking Study ◽  
Binding Mode ◽  
Binding Energies ◽  
Simple Method ◽  
Antimicrobial Evaluation ◽  
New Compounds ◽  
Active Methylene

Background: One of the most successful reagents used in the synthesis of the reactive enaminone is DMF-DMA, but it is very expensive with harmful effects on the human health and reacts with special compounds to generate the enaminone such as active methylene centers. Aim: In this article, we synthesized a new ketenaminal by simple method with inexpensive reagents (through desulfurization in diphenylether). Methods: Thus, a novel reactive ketenaminal (enaminone) was synthesized from the desulfurization of 2-((2-(4-chlorophenyl)-2-oxoethyl)thio)-5,7-bis(4-methoxyphenyl)pyrido[2,3-d]pyrimidin- 4(3H)-one with diphenylether. The starting keteneaminal was coupled with diazotized anilines via the known coupling conditions to give a new series of 2-(4-chlorophenyl)-1-(2-(arylhydrazono)-2- oxoethyl)-5,7-bis(4-methoxy-phenyl)pyrido[2,3-d]pyrimidin-4(1H)-ones. Results: The structures of the new compounds were elucidated based on their IR, 1H-NMR, 13CNMR, and Mass spectra. Moreover, the potency of these compounds as antimicrobial agents has been evaluated. The results showed that some of the products have high activity nearly equal to that of the used standard antibiotic. Additionally, the docking study was done to get the binding mode of the synthesized compounds with the binding site of the DHFR enzyme. The results of molecular docking of the synthesized arylhydrazono compounds are able to fit in DHFR binding site with binding energies ranging from -4.989 to -8.178 Kcal/mol. Conclusion: Our goal was achieved in this context by the synthesis of new ketenaminal from inexpensive reagents, which was utilized in the preparation of bioactive arylhydrazone derivatives.

scholarly journals In-silico Investigation of the Interaction between Beta-class Glutathione S-Transferase and Five Antibiotics, namely; Ampicillin, Tetracycline, Chloramphenicol, Ciprofloxacin and Cephalexin

2021 ◽  
Vol 25 (4) ◽  
pp. 497-502
Author(s):  
D. Shehu ◽  
S Danlami ◽  
M. Ya’u ◽  
A. Babandi ◽  
H.M. Yakasai ◽  
...  
Keyword(s):  
Amino Acids ◽  
Antibiotic Resistance ◽  
Molecular Docking ◽  
Binding Site ◽  
Substrate Binding ◽  
Docking Study ◽  
Glutathione S Transferase ◽  
Molecular Docking Study ◽  
Substrate Binding Site ◽  
Glutathione S Transferases

Glutathione s-transferases(GSTs) are enzymes involved in the conjugation and deactivation of various xenobiotics including drugs. Thisin-silico study was undertaken in order to investigate the interaction between beta-class glutathione s-transferase and five selected antibiotics, namely; ampicillin, tetracycline, chloramphenicol, ciprofloxacin and cephalexin using molecular docking study. RaptorX server was used to predict the amino acids involved at the binding sitewhile molecular docking study was employed in order to investigate the binding interactions.RaptorX predicted several amino acids which were different from the ones observed in molecular docking because of the variability in the substrate binding site of GSTs however, all the amino acids predicted by RaptorX were also found to be involved in the GSH binding.Lys107, Phe109, Ser110, Leu113, Trp114, His115 and Arg123, Leu168 were the amino acids involved in the binding of various antibiotics to the substrate binding site of the protein while Ala9, Cys10, Leu32, Tyr51, Val52, Pro53, Glu65 and Ala66were involved in the binding of the co-substrate GSH to the binding site of the protein. The results indicated that all the antibiotics showed a good binding affinity with the beta class GST and are therefore capable of deactivating the drugs. With these, finding a beta class GST inhibitors alongside antibiotics during a treatment of diseases will be of beneficial in the current fight against antibiotic resistance.

scholarly journals Dual Binding Site and Selective Acetylcholinesterase Inhibitors Derived from Integrated Pharmacophore Models and Sequential Virtual Screening

2014 ◽  
Vol 2014 ◽  
pp. 1-21 ◽  
Author(s):  
Shikhar Gupta ◽  
C. Gopi Mohan
Keyword(s):  
Molecular Docking ◽  
Binding Site ◽  
Enzyme Inhibitors ◽  
Acetylcholinesterase Inhibitors ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Test Set ◽  
Zinc Database ◽  
Pharmacophore Hypotheses ◽  
Pharmacophore Models

In this study, we have employedin silicomethodology combining double pharmacophore based screening, molecular docking, and ADME/T filtering to identify dual binding site acetylcholinesterase inhibitors that can preferentially inhibit acetylcholinesterase and simultaneously inhibit the butyrylcholinesterase also but in the lesser extent than acetylcholinesterase. 3D-pharmacophore models of AChE and BuChE enzyme inhibitors have been developed from xanthostigmine derivatives through HypoGen and validated using test set, Fischer’s randomization technique. The best acetylcholinesterase and butyrylcholinesterase inhibitors pharmacophore hypotheses Hypo1_A and Hypo1_B, with high correlation coefficient of 0.96 and 0.94, respectively, were used as 3D query for screening the Zinc database. The screened hits were then subjected to the ADME/T and molecular docking study to prioritise the compounds. Finally, 18 compounds were identified as potential leads against AChE enzyme, showing good predicted activities and promising ADME/T properties.

Docking Study of Ligands into the Colchicine Binding Site of Tubulin

2004 ◽  
Vol 19 (6) ◽  
pp. 541-547 ◽  
Author(s):  
Amaury Farce ◽  
Cedric Loge ◽  
Sebastien Gallet ◽  
Nicolas Lebegue ◽  
Pascal Carato ◽  
...  
Keyword(s):  
Binding Site ◽  
Docking Study ◽  
Colchicine Binding Site

scholarly journals Naturally occurring mutation affecting the MyD88-binding site ofTNFRSF13Bimpairs triggering of class switch recombination

2013 ◽  
Vol 43 (3) ◽  
pp. 805-814 ◽  
Author(s):  
Maria B. Almejun ◽  
Montserrat Cols ◽  
Marta Zelazko ◽  
Matias Oleastro ◽  
Andrea Cerutti ◽  
...  
Keyword(s):  
Binding Site ◽  
Class Switch Recombination ◽  
Class Switch ◽  
Naturally Occurring

scholarly journals Biophysical characterization of a binding site for TLQP-21, a naturally occurring peptide which induces resistance to obesity

2013 ◽  
Vol 1828 (2) ◽  
pp. 455-460 ◽  
Author(s):  
V. Cassina ◽  
A. Torsello ◽  
A. Tempestini ◽  
D. Salerno ◽  
D. Brogioli ◽  
...  
Keyword(s):  
Binding Site ◽  
Biophysical Characterization ◽  
Naturally Occurring

Binding of mitochondrial ATPase from ox heart to its naturally occurring inhibitor protein: Localization by antibody binding

1983 ◽  
Vol 3 (10) ◽  
pp. 921-926 ◽  
Author(s):  
Philip J. Jackson ◽  
David A. Harris
Keyword(s):  
Binding Site ◽  
Protein Localization ◽  
Antibody Binding ◽  
Heart Mitochondria ◽  
Mitochondrial Atpase ◽  
Β Subunit ◽  
Inhibitor Protein ◽  
Atpase Inhibitor ◽  
Naturally Occurring ◽  
The Cross

The naturally occurring ATPase inhibitor protein from ox heart mitochondria was cross-linked to its binding site on the mitochondrial ATPase using 1-ethyl-3-(dimethylamino)propyl carbodiimide. The cross-linked product, when transferred electrophoretically to a nitrocellulose sheet, reacted with antibodies directed against the inhibitor protein and the β-subunit of the ATPase. It was concluded that the binding site for the inhibitor protein lies on the β-subunit.

Exploring the binding site of the human muscarinic M3 receptor: Homology modeling and docking study

2007 ◽  
Vol 107 (8) ◽  
pp. 1794-1802 ◽  
Author(s):  
Liliana Ostopovici ◽  
Maria Mracec ◽  
Mircea Mracec ◽  
Ana Borota
Keyword(s):  
Homology Modeling ◽  
Binding Site ◽  
Docking Study ◽  
M3 Receptor

scholarly journals Theoretical Evaluation of Bortezomib and Other Boron-Containing Compounds as Inhibitors of SARS-CoV-2 Main Protease

2020 ◽  
Author(s):  
Ivan Ricardo Vega Valdez ◽  
Jose-Martin Santiago-Quintana ◽  
MELVIN ROSALEZ ◽  
Eunice Farfan ◽  
Marvin A. Soriano-Ursua
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Boron Atom ◽  
Docking Study ◽  
Theoretical Evaluation ◽  
Main Protease ◽  
Potent Inhibition ◽  
Drug Designing ◽  
Key Residues

The aim of the present docking study was to explore the putative role of boronic moieties in molecules interacting on the binding site of the SARS-CoV-2 main protease. The methodology was based on the conventional docking procedure by means of AutoDock software by assaying boron-free and boron-containing compounds on the recent reported crystal structure of SARS-CoV-2 main protease (PDB code: 6LU7). The most of tested compounds share contact with key residues and poses on the cleavage pocket. Those compounds with a boron atom in its structure often were estimated with higher affinity than boron-free analogues. Interactions and affinity of boron-containing peptidomimetics on the binding site let us to propose the potent inhibition of these compounds on targeted protease. These advances may be relevant for drug designing, but also to suggest the testing of available boron-containing drugs in patients with severe symptoms of COVID19 infection.

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