scholarly journals Property-based characterization of kinase-like ligand space for library design and virtual screening

MedChemComm ◽  
2015 ◽  
Vol 6 (10) ◽  
pp. 1898-1904 ◽  
Author(s):  
Dávid Bajusz ◽  
György G. Ferenczy ◽  
György M. Keserű
Keyword(s):  
Virtual Screening ◽  
Library Design ◽  
Large Compound

A property-based desirability scoring scheme has been developed for kinase-focused library design and ligand-based pre-screening of large compound sets.

scholarly journals A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0

2020 ◽  
Vol 21 (14) ◽  
pp. 5152 ◽  
Author(s):  
Silvia Gervasoni ◽  
Giulio Vistoli ◽  
Carmine Talarico ◽  
Candida Manelfi ◽  
Andrea R. Beccari ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Drug Repurposing ◽  
Protein Targets ◽  
In Silico Studies ◽  
Allosteric Sites ◽  
Binding Pockets ◽  
Novel Strategy ◽  
Better Than ◽  
Comprehensive Mapping

(1) Background: Virtual screening studies on the therapeutically relevant proteins of the severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) require a detailed characterization of their druggable binding sites, and, more generally, a convenient pocket mapping represents a key step for structure-based in silico studies; (2) Methods: Along with a careful literature search on SARS-CoV-2 protein targets, the study presents a novel strategy for pocket mapping based on the combination of pocket (as performed by the well-known FPocket tool) and docking searches (as performed by PLANTS or AutoDock/Vina engines); such an approach is implemented by the Pockets 2.0 plug-in for the VEGA ZZ suite of programs; (3) Results: The literature analysis allowed the identification of 16 promising binding cavities within the SARS-CoV-2 proteins and the here proposed approach was able to recognize them showing performances clearly better than those reached by the sole pocket detection; and (4) Conclusions: Even though the presented strategy should require more extended validations, this proved successful in precisely characterizing a set of SARS-CoV-2 druggable binding pockets including both orthosteric and allosteric sites, which are clearly amenable for virtual screening campaigns and drug repurposing studies. All results generated by the study and the Pockets 2.0 plug-in are available for download.

Synthesis and Characterization of Luminescent Rod-Coil Poly[2,7-(9,9- Dihexylfluorene)] - Block-Poly(2-(Dimethylamino) Ethyl Methacrylate) by Atom Transfer Radical Polymerization

2008 ◽  
Vol 47-50 ◽  
pp. 642-645
Author(s):  
Yang Yen Yu ◽  
Wen Chen Chien ◽  
Chia Liang Tsai
Keyword(s):  
Atom Transfer Radical Polymerization ◽  
Radical Polymerization ◽  
Photophysical Properties ◽  
Mixed Solvents ◽  
Solvent System ◽  
Synthesis And Characterization ◽  
Photoluminescence Properties ◽  
Ethyl Methacrylate ◽  
Large Compound

The synthesis, morphology, and photophysical properties of Poly[2,7-(9,9-dihexyl fluorene)]- block-poly(2-(Dimethylamino) ethyl methacrylate) (PF-b-PDMAEMA) copolymers in various mixed solvents, i.e., THF/MeOH, DMF/MeOH, and 1,4-Dioxane/MeOH, with methanol contents of 0, 10, 25, 50, 75, 90 vol.% were reported. TEM images showed that different aggregate morphologies of PF-b-PDMAEMA, including spherical and large compound micelles, cylinder, nanorods, long stick-like structure, could be prepared by introducing different amount of methanol into the copolymer/solvent system. The results indicated that aggregate morphologies of PF-b-PDMAEMA, which obtained from various coil lengths and mixed solvents, had a great influenced on the optical and photoluminescence properties of the prepared PF-b-PDMAEMA copolymers.

scholarly journals Receptor-Based Virtual Screening and Biological Characterization of Human Apurinic/Apyrimidinic Endonuclease (Ape1) Inhibitors

ChemMedChem ◽  
2012 ◽  
Vol 7 (12) ◽  
pp. 2168-2178 ◽  
Author(s):  
Federico M. Ruiz ◽  
Sandrea M. Francis ◽  
Maria Tintoré ◽  
Rubén Ferreira ◽  
Rubén Gil-Redondo ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Biological Characterization

scholarly journals Characterization of Soybean Protein Isolate-Food Polyphenol Interaction via Virtual Screening and Experimental Studies

Foods ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2813
Author(s):  
Le Ao ◽  
Panhang Liu ◽  
Annan Wu ◽  
Jing Zhao ◽  
Xiaosong Hu
Keyword(s):  
Virtual Screening ◽  
Hydrophobic Interactions ◽  
Binding Capacity ◽  
Soybean Protein ◽  
Screening Method ◽  
Experimental Studies ◽  
Protein Isolate ◽  
Soybean Protein Isolate ◽  
Apparent Binding Constant

(1) Background: Protein–polyphenol interactions have been widely studied regarding their influence on the properties of both protein and the ligands. As an important protein material in the food industry, soybean protein isolate (SPI) experiences interesting changes through polyphenols binding. (2) Methods: In this study, a molecular docking and virtual screening method was established to evaluate the SPI–polyphenol interaction. A compound library composed of 33 commonly found food source polyphenols was used in virtual screening. The binding capacity of top-ranking polyphenols (rutin, procyanidin, cyanidin chloride, quercetin) was validated and compared by fluorescence assays. (3) Results: Four out of five top-ranking polyphenols in virtual screening were flavonoids, while phenolic acids exhibit low binding capacity. Hydrogen bonding and hydrophobic interactions were found to be dominant interactions involved in soybean protein–polyphenol binding. Cyanidin chloride exhibited the highest apparent binding constant (Ka), which was followed by quercetin, procyanidin, and rutin. Unlike others, procyanidin addition perturbed a red shift of SPI fluorescence, indicating a slight conformational change of SPI. (4) Conclusions: These results suggest that the pattern of SPI–polyphenol interaction is highly dependent on the detailed structure of polyphenols, which have important implications in uncovering the binding mechanism of SPI–polyphenol interaction.

scholarly journals Characterization of seaweed hypoglycemic property with integration of virtual screening for identification of bioactive compounds

2020 ◽  
Vol 64 ◽  
pp. 103656 ◽  
Author(s):  
Yao Xian Chin ◽  
Xin Chen ◽  
Wan Xiu Cao ◽  
Yurizam Sharifuddin ◽  
Brian D. Green ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Bioactive Compounds

Virtual Screening and Biological Characterization of Novel Histone Arginine Methyltransferase PRMT1 Inhibitors

ChemMedChem ◽  
2009 ◽  
Vol 4 (1) ◽  
pp. 69-77 ◽  
Author(s):  
Ralf Heinke ◽  
Astrid Spannhoff ◽  
Rene Meier ◽  
Patrick Trojer ◽  
Ingo Bauer ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Biological Characterization ◽  
Arginine Methyltransferase
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