Binding mode analysis of chaetomallic acids (A and B) as farnesyltransferase inhibitors

2021 ◽  
Author(s):  
Ns Hari Moorthy ◽  
C Karthikeyn ◽  
E Manivannan
Keyword(s):  
Binding Mode ◽  
Mode Analysis ◽  
Farnesyltransferase Inhibitors

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>

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

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

scholarly journals Finding biologically relevant protein domain interactions: Conserved binding mode analysis

2006 ◽  
Vol 15 (2) ◽  
pp. 352-361 ◽  
Author(s):  
Benjamin A. Shoemaker ◽  
Anna R. Panchenko ◽  
Stephen H. Bryant
Keyword(s):  
Binding Mode ◽  
Protein Domain ◽  
Mode Analysis ◽  
Biologically Relevant ◽  
Domain Interactions

scholarly journals Synthesis, structure–activity relationship and binding mode analysis of 4-thiazolidinone derivatives as novel inhibitors of human dihydroorotate dehydrogenase

MedChemComm ◽  
2017 ◽  
Vol 8 (6) ◽  
pp. 1297-1302 ◽  
Author(s):  
Fanxun Zeng ◽  
Tiantian Qi ◽  
Chunyan Li ◽  
Tingfang Li ◽  
Honglin Li ◽  
...  
Keyword(s):  
Binding Mode ◽  
Structure Activity Relationship ◽  
Mode Analysis ◽  
Activity Relationship ◽  
Dihydroorotate Dehydrogenase ◽  
Structure Activity

A series of 4-thiazolidinone derivatives were synthesized and evaluated as novel human dihydroorotate dehydrogenase (hDHODH) inhibitors.

Amide Analogues of TSA: Synthesis, Binding Mode Analysis and HDAC Inhibition.

ChemInform ◽  
2003 ◽  
Vol 34 (36) ◽  
Author(s):  
K. Van Ommeslaeghe ◽  
G. Elaut ◽  
V. Brecx ◽  
P. Papeleu ◽  
K. Iterbeke ◽  
...  
Keyword(s):  
Binding Mode ◽  
Mode Analysis ◽  
Hdac Inhibition

scholarly journals Synthesis, antibacterial activities, binding mode analysis and predictive ADME studies of novel 1-(aryl)-2-(1H-imidazol-1-yl)methanones

2020 ◽  
Vol 2 (02) ◽  
pp. 39-45
Author(s):  
Priyanka Chandra ◽  
Swastika Ganguly ◽  
Rajdeep Dey ◽  
Biswatrish Sarkar
Keyword(s):  
Antibacterial Activity ◽  
Spectral Analysis ◽  
Nmr Spectroscopy ◽  
Active Compound ◽  
Active Site ◽  
Antibacterial Property ◽  
Binding Mode ◽  
Antibacterial Activities ◽  
Mode Analysis ◽  
Benzoyl Chlorides

Introduction: In the present study a novel series of twelve 1-(aryl)-2-(1H-imidazol-1-yl)methanones 3(a-l) were synthesized and characterised by physicochemical and spectral analysis,viz. elemental analysis, IR spectroscopy, NMR spectroscopy. The antibacterial property of the compounds were examined, in order to develop new broad spectrum antibiotics. Methods: The compounds 3(a-l) were synthesised by reacting the corresponding 2-(aryl)-1H-imidazoles 2 with substituted benzoyl chlorides. Binding mode analysis of the most active compound was carried out. Predictive ADME studies were carried out for all the compounds. Results and Discussions: Among the synthesized compounds, (2-(3-nitrophenyl) (2,4-dichlorophenyl) -1Himidazol-1-yl)methanone 3i exhibited highest antibacterial activity. Binding mode analysis of the highest active compound was carried out in the active site of glucosamine-6-phosphate synthase (2VF5).

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