Binding mode analysis of topoisomerase inhibitors, 6-arylamino-7-chloro-quinazoline-5,8-diones, within the cleavable complex of human topoisomerase I and DNA

2007 ◽  
Vol 30 (12) ◽  
pp. 1526-1535 ◽  
Author(s):  
Inhee Choi ◽  
Choonmi Kim ◽  
Sun Choi
Keyword(s):  
Topoisomerase I ◽  
Binding Mode ◽  
Mode Analysis ◽  
Topoisomerase Inhibitors ◽  
Cleavable Complex

Application of the ESMACS Binding Free Energy Protocol to a Highly Varied Ligand Dataset: Lactate Dehydogenase A

2019 ◽  
Author(s):  
David Wright ◽  
Fouad Husseini ◽  
Shunzhou Wan ◽  
Christophe Meyer ◽  
Herman Van Vlijmen ◽  
...  
Keyword(s):  
Free Energy ◽  
Surface Area ◽  
Binding Free Energy ◽  
Normal Mode Analysis ◽  
Binding Mode ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Mode Analysis ◽  
Energy Calculation ◽  
Accessible Surface

<div>Here, we evaluate the performance of our range of ensemble simulation based binding free energy calculation protocols, called ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) for use in fragment based drug design scenarios. ESMACS is designed to generate reproducible binding affinity predictions from the widely used molecular mechanics Poisson-Boltzmann surface area (MMPBSA) approach. We study ligands designed to target two binding pockets in the lactate dehydogenase A target protein, which vary in size, charge and binding mode. When comparing to experimental results, we obtain excellent statistical rankings across this highly diverse set of ligands. In addition, we investigate three approaches to account for entropic contributions not captured by standard MMPBSA calculations: (1) normal mode analysis, (2) weighted solvent accessible surface area (WSAS) and (3) variational entropy. </div>

Binding mode and affinity studies of DNA-binding agents using topoisomerase I DNA unwinding assay

2007 ◽  
Vol 17 (4) ◽  
pp. 1013-1017 ◽  
Author(s):  
Ruel E. McKnight ◽  
Aaron B. Gleason ◽  
James A. Keyes ◽  
Sadia Sahabi
Keyword(s):  
Dna Binding ◽  
Topoisomerase I ◽  
Binding Mode ◽  
Dna Unwinding ◽  
Binding Agents ◽  
Dna Binding Agents

scholarly journals SUMO-1 conjugation to intact DNA topoisomerase I amplifies cleavable complex formation induced by camptothecin

Oncogene ◽  
2002 ◽  
Vol 21 (52) ◽  
pp. 7913-7922 ◽  
Author(s):  
Koji Horie ◽  
Akihiro Tomida ◽  
Yoshikazu Sugimoto ◽  
Toshiharu Yasugi ◽  
Hiroyuki Yoshikawa ◽  
...  
Keyword(s):  
Complex Formation ◽  
Topoisomerase I ◽  
Dna Topoisomerase I ◽  
Dna Topoisomerase ◽  
Cleavable Complex

Structural Evaluation and Binding Mode Analysis of CCL19 and CCR7 Proteins—Identification of Novel Leads for Rheumatic and Autoimmune Diseases: An Insilico study

2017 ◽  
Vol 10 (2) ◽  
pp. 346-366 ◽  
Author(s):  
Santhi Prada Vellanki ◽  
Ramasree Dulapalli ◽  
Bhargavi Kondagari ◽  
Navaneetha Nambigari ◽  
Rajender Vadija ◽  
...  
Keyword(s):  
Autoimmune Diseases ◽  
Binding Mode ◽  
Mode Analysis ◽  
Structural Evaluation

Pyrrolidine Derivatives as Plasmepsin Inhibitors: Binding Mode Analysis Assisted by Molecular Dynamics Simulations of a Highly Flexible Protein

ChemMedChem ◽  
2010 ◽  
Vol 5 (3) ◽  
pp. 443-454 ◽  
Author(s):  
Torsten Luksch ◽  
Andreas Blum ◽  
Nina Klee ◽  
Wibke E. Diederich ◽  
Christoph A. Sotriffer ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Mode ◽  
Mode Analysis ◽  
Flexible Protein ◽  
Dynamics Simulations

scholarly journals The structure–activity relationships of A-ring-substituted aromathecin topoisomerase I inhibitors strongly support a camptothecin-like binding mode

2010 ◽  
Vol 18 (15) ◽  
pp. 5535-5552 ◽  
Author(s):  
Maris A. Cinelli ◽  
Andrew E. Morrell ◽  
Thomas S. Dexheimer ◽  
Keli Agama ◽  
Surbhi Agrawal ◽  
...  
Keyword(s):  
Topoisomerase I ◽  
Binding Mode ◽  
Structure Activity Relationships ◽  
Topoisomerase I Inhibitors ◽  
Structure Activity

Amide analogues of TSA: synthesis, binding mode analysis and HDAC inhibition

2003 ◽  
Vol 13 (11) ◽  
pp. 1861-1864 ◽  
Author(s):  
K Van Ommeslaeghe ◽  
G Elaut ◽  
V Brecx ◽  
P Papeleu ◽  
K Iterbeke ◽  
...  
Keyword(s):  
Binding Mode ◽  
Mode Analysis ◽  
Hdac Inhibition
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