scholarly journals Comparative Shape and Electrostatic Study of Highly Potent and Selective CYP1B1 Inhibitor: Assessment of Active Site of CYP1B1 by Binding Mode Analysis Using Site Map Tool

2018 ◽  
Vol 52 (1) ◽  
pp. 159-165
Author(s):  
Mohd Usman Mohd Siddique ◽  
Barij Nayan Sinha ◽  
Venkatesan Jayaprakash
Keyword(s):  
Active Site ◽  
Binding Mode ◽  
Mode Analysis

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).

High throughput virtual screening based discovery of dengue protease inhibitor

2017 ◽  
Vol 4 (3) ◽  
pp. 35-40
Author(s):  
Sounak Bagchi ◽  
Uzma Alia ◽  
Faiz Mohammad ◽  
Mohd Usman Mohd Siddique
Keyword(s):  
Virtual Screening ◽  
Drug Design ◽  
Protease Inhibitor ◽  
Protease Inhibitors ◽  
High Throughput ◽  
Active Site ◽  
Binding Mode ◽  
Mode Analysis ◽  
Active Site Residues ◽  
High Throughput Virtual Screening

High throughput virtual screening (HTVS) has been proved a successful tool for getting LEADs in drug design and discovery. In an attempt to design new Dengue protease inhibitors, we performed HTVS using Zinc13 database containing 13,195,609 drug-like molecules. ZINC42678127 was identified as potential HIT against Dengue protease. It’s shape and electrostatic complimentary was found to be 0.608 and 0.078, respectively. Qikprop analysis of the compound complied with the Rule of Five (Ro5) and other drug- likeliness properties. Binding mode analysis of docked conformer of ZINC42678127, displayed favorable interaction with the active site residues of DENV protease. The identified HIT has a potential to become a LEAD against Dengue protease.

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>

Recent insights into lytic polysaccharide monooxygenases (LPMOs)

2018 ◽  
Vol 46 (6) ◽  
pp. 1431-1447 ◽  
Author(s):  
Tobias Tandrup ◽  
Kristian E. H. Frandsen ◽  
Katja S. Johansen ◽  
Jean-Guy Berrin ◽  
Leila Lo Leggio
Keyword(s):  
Active Site ◽  
Room Temperature ◽  
Experimental Studies ◽  
Binding Mode ◽  
Structural Features ◽  
Oxygen Species ◽  
Animal Kingdom ◽  
X Ray ◽  
Lytic Polysaccharide Monooxygenases ◽  
Polysaccharide Monooxygenases

Lytic polysaccharide monooxygenases (LPMOs) are copper enzymes discovered within the last 10 years. By degrading recalcitrant substrates oxidatively, these enzymes are major contributors to the recycling of carbon in nature and are being used in the biorefinery industry. Recently, two new families of LPMOs have been defined and structurally characterized, AA14 and AA15, sharing many of previously found structural features. However, unlike most LPMOs to date, AA14 degrades xylan in the context of complex substrates, while AA15 is particularly interesting because they expand the presence of LPMOs from the predominantly microbial to the animal kingdom. The first two neutron crystallography structures have been determined, which, together with high-resolution room temperature X-ray structures, have putatively identified oxygen species at or near the active site of LPMOs. Many recent computational and experimental studies have also investigated the mechanism of action and substrate-binding mode of LPMOs. Perhaps, the most significant recent advance is the increasing structural and biochemical evidence, suggesting that LPMOs follow different mechanistic pathways with different substrates, co-substrates and reductants, by behaving as monooxygenases or peroxygenases with molecular oxygen or hydrogen peroxide as a co-substrate, respectively.

New hypotheses for the binding mode of 4- and 7-substituted indazoles in the active site of neuronal nitric oxide synthase

2012 ◽  
Vol 20 (17) ◽  
pp. 5296-5304 ◽  
Author(s):  
Elodie Lohou ◽  
Jana Sopkova-de Oliveira Santos ◽  
Pascale Schumann-Bard ◽  
Michel Boulouard ◽  
Silvia Stiebing ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Nitric Oxide Synthase ◽  
Active Site ◽  
Neuronal Nitric Oxide Synthase ◽  
Binding Mode ◽  
Oxide Synthase
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