scholarly journals Molecular Dynamics of Rab7::REP1::GGTase-II Ternary Complex and Identification of Their Putative Drug Binding Sites

2013 ◽  
Vol 75 (1) ◽  
pp. 23 ◽  
Author(s):  
A Kumar ◽  
Meenakshi Sindhu ◽  
Vandana Saini ◽  
Sakshi Piplani
Keyword(s):  
Molecular Dynamics ◽  
Binding Sites ◽  
Ternary Complex ◽  
Drug Binding ◽  
Drug Binding Sites

Identification of Drug Binding Sites and Action Mechanisms with Molecular Dynamics Simulations

2019 ◽  
Vol 18 (27) ◽  
pp. 2268-2277 ◽  
Author(s):  
Yang Wang ◽  
Cecylia Severin Lupala ◽  
Haiguang Liu ◽  
Xubo Lin
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Binding Sites ◽  
Lipid Membrane ◽  
Md Simulations ◽  
Drug Action ◽  
Drug Binding ◽  
Action Mechanisms ◽  
Drug Binding Sites ◽  
Dynamics Simulations

Identifying drug binding sites and elucidating drug action mechanisms are important components in a drug discovery process. In this review, we briefly compared three different approaches (sequence- based methods, structure-based methods and probe-based molecular dynamics (MD) methods) to identifying drug binding sites, and concluded that probe-based MD methods are much more advantageous in dealing with flexible target macromolecules and digging out druggable macromolecule conformations for subsequent drug screening. The applications of MD simulation to studying drug-target interactions were demonstrated with different types of target molecules, including lipid membrane, protein and DNA. The results indicate that MD simulations with enhanced sampling methods provide a powerful tool to determine free energy profiles/surfaces and identify important intermediate states, which are essential for the elucidation of drug action mechanisms. The future development of methods in MD simulations will benefit and speed up the drug discovery processes.

scholarly journals Systematic exploration of multiple drug binding sites

2017 ◽  
Vol 9 (1) ◽  
Author(s):  
Mónika Bálint ◽  
Norbert Jeszenői ◽  
István Horváth ◽  
David van der Spoel ◽  
Csaba Hetényi
Keyword(s):  
Binding Sites ◽  
Drug Binding ◽  
Multiple Drug ◽  
Systematic Exploration ◽  
Drug Binding Sites

scholarly journals Footprinting studies on the effect of echinomycin on the structure of a bent DNA fragment

1990 ◽  
Vol 269 (1) ◽  
pp. 217-221 ◽  
Author(s):  
K R Fox ◽  
E Kentebe
Keyword(s):  
Binding Sites ◽  
Dna Structure ◽  
Drug Binding ◽  
Micrococcal Nuclease ◽  
Kinetoplast Dna ◽  
Bent Dna ◽  
Diethyl Pyrocarbonate ◽  
Drug Binding Sites ◽  
Dna Fragment

The interaction of echinomycin with a kinetoplast DNA fragment which contains phased runs of adenine residues has been examined by various footprinting techniques. DNAase I footprinting confirms that all drug-binding sites contain the dinucleotide CpG. However, not all such sequences are protected. Three sites, each of which is located between two adenine tracks in the sequence GCGA, are not protected from DNAase I attack. Enhanced cleavage by DNAase I, DNAase II and micrococcal nuclease is observed in regions surrounding drug-binding sites. The results suggest that echinomycin alters the conformation of the AT tracks, making them more like an average DNA structure. Echinomycin renders adenine residues in the sequence CGA hyper-reactive to diethyl pyrocarbonate.

scholarly journals Location of drug binding sites on human serum albumin.

1986 ◽  
Vol 34 (7) ◽  
pp. 2989-2993 ◽  
Author(s):  
KAZUO MARUYAMA ◽  
HIDEO NISHIGORI ◽  
MOTOHARU IWATSURU
Keyword(s):  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Binding Sites ◽  
Drug Binding ◽  
Drug Binding Sites
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