Using Affinity Capillary Electrophoresis To Determine Binding Stoichiometries of Protein-Ligand Interactions

Biochemistry ◽  
1994 ◽  
Vol 33 (35) ◽  
pp. 10616-10621 ◽  
Author(s):  
Yen-Ho Chu ◽  
Watson J. Lees ◽  
Adonis Stassinopoulos ◽  
Christopher T. Walsh
Keyword(s):  
Capillary Electrophoresis ◽  
Affinity Capillary Electrophoresis ◽  
Protein Ligand Interactions ◽  
Ligand Interactions

Study of deoxyribonucleic acid–ligand interactions by partial filling affinity capillary electrophoresis

2014 ◽  
Vol 1349 ◽  
pp. 116-121 ◽  
Author(s):  
Martin Růžička ◽  
Martina Čížková ◽  
Michael Jirásek ◽  
Filip Teplý ◽  
Dušan Koval ◽  
...  
Keyword(s):  
Capillary Electrophoresis ◽  
Deoxyribonucleic Acid ◽  
Affinity Capillary Electrophoresis ◽  
Acid Ligand ◽  
Partial Filling ◽  
Ligand Interactions

Affinity Capillary Electrophoresis to Examine Receptor–Ligand Interactions

2004 ◽  
pp. 153-168 ◽  
Author(s):  
Maryam Azad ◽  
John Kaddis ◽  
Valerie Villareal ◽  
Lili Hernandez ◽  
Catherine Silverio ◽  
...  
Keyword(s):  
Capillary Electrophoresis ◽  
Affinity Capillary Electrophoresis ◽  
Receptor Ligand ◽  
Ligand Interactions

scholarly journals Nonequilibrium Capillary Electrophoresis of Equilibrium Mixtures (NECEEM): A Novel Method for Biomolecular Screening

2005 ◽  
Vol 11 (2) ◽  
pp. 115-122 ◽  
Author(s):  
Sergey N. Krylov
Keyword(s):  
Capillary Electrophoresis ◽  
Combinatorial Libraries ◽  
Kinetic And Thermodynamic Parameters ◽  
Transverse Diffusion ◽  
Protein Ligand Interactions ◽  
Dna And Rna ◽  
Ligand Interactions ◽  
Novel Method ◽  
Analytical Power ◽  
Selection Of

Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) is a new separation-based affinity method. It has kinetic capabilities exceeding those of surface plasmon resonance (SPR) and does not require immobilization of molecules on the surface. Another distinctive feature of NECEEM is that—if it is combined with an advanced method for the mixing solutions inside a capillary, termed transverse diffusion of laminar flow profiles (TDLFP)—it requires only nanoliter volumes of solutions. The proven applications of NECEEM to biomolecular screening include 1) measuring kinetic and thermodynamic parameters of protein-ligand interactions, 2) quantitative affinity analyses of proteins and hybridization analyses of DNA and RNA, and 3) selection of binding ligands from combinatorial libraries. NECEEM is easy to automate and parallelize. Because of its simplicity and analytical power, NECEEM has the potential to become a workhorse in studies of biomolecular interactions. The author reviews theoretical bases of NECEEM and its applications to biomolecular screening.

19F-NMR in Target-based Drug Discovery

2019 ◽  
Vol 26 (26) ◽  
pp. 4964-4983 ◽  
Author(s):  
CongBao Kang
Keyword(s):  
Drug Discovery ◽  
Conformational Changes ◽  
Protein Structures ◽  
19F Nmr ◽  
Binding Affinities ◽  
Protein Ligand Interactions ◽  
Compound Libraries ◽  
Ligand Interactions ◽  
Reference Ligand ◽  
Hit Identification

Solution NMR spectroscopy plays important roles in understanding protein structures, dynamics and protein-protein/ligand interactions. In a target-based drug discovery project, NMR can serve an important function in hit identification and lead optimization. Fluorine is a valuable probe for evaluating protein conformational changes and protein-ligand interactions. Accumulated studies demonstrate that 19F-NMR can play important roles in fragment- based drug discovery (FBDD) and probing protein-ligand interactions. This review summarizes the application of 19F-NMR in understanding protein-ligand interactions and drug discovery. Several examples are included to show the roles of 19F-NMR in confirming identified hits/leads in the drug discovery process. In addition to identifying hits from fluorinecontaining compound libraries, 19F-NMR will play an important role in drug discovery by providing a fast and robust way in novel hit identification. This technique can be used for ranking compounds with different binding affinities and is particularly useful for screening competitive compounds when a reference ligand is available.

Combiphore (Structure and Ligand Based Pharmacophore) - Approach for the Design of GPR40 Modulators in the Management of Diabetes

2020 ◽  
Vol 17 (2) ◽  
pp. 233-247
Author(s):  
Krishna A. Gajjar ◽  
Anuradha K. Gajjar
Keyword(s):  
Molecular Docking ◽  
Structural Information ◽  
Docking Studies ◽  
Structural Motif ◽  
Roc Curve Analysis ◽  
Ligand Complex ◽  
Discovery Studio ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Pharmacophore Models

Background: Pharmacophore mapping and molecular docking can be synergistically integrated to improve the drug design and discovery process. A rational strategy, combiphore approach, derived from the combined study of Structure and Ligand based pharmacophore has been described to identify novel GPR40 modulators. Methods: DISCOtech module from Discovery studio was used for the generation of the Structure and Ligand based pharmacophore models which gave hydrophobic aromatic, ring aromatic and negative ionizable as essential pharmacophoric features. The generated models were validated by screening active and inactive datasets, GH scoring and ROC curve analysis. The best model was exposed as a 3D query to screen the hits from databases like GLASS (GPCR-Ligand Association), GPCR SARfari and Mini-Maybridge. Various filters were applied to retrieve the hit molecules having good drug-like properties. A known protein structure of hGPR40 (pdb: 4PHU) having TAK-875 as ligand complex was used to perform the molecular docking studies; using SYBYL-X 1.2 software. Results and Conclusion: Clustering both the models gave RMSD of 0.89. Therefore, the present approach explored the maximum features by combining both ligand and structure based pharmacophore models. A common structural motif as identified in combiphore for GPR40 modulation consists of the para-substituted phenyl propionic acid scaffold. Therefore, the combiphore approach, whereby maximum structural information (from both ligand and biological protein) is explored, gives maximum insights into the plausible protein-ligand interactions and provides potential lead candidates as exemplified in this study.

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