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The results showed that the methylene blue derivatives 6a c were able to bind to the c-myc G-quadruplex with greater binding affinity compared to the known G-quadruplex binding ligand, crystal violet.
Previous work demonstrated that the Bak 72 87) peptide also binds to the anti-apoptotic protein Bcl-2, albeit with lower binding affinity compared to Bcl-xL.
Modified drug N1 showed greater binding affinity compared to EN in most conformations.
We reveal that this design can enhance fluorescence turn-on and ligand binding affinity compared to the non-permuted topology.
Nα-Methylated analogues (8 11) also were prepared for increased lipophilicity of the inhibitors, but they had 4- to 5-fold weaker binding affinity compared to their parent compounds.
Among them, 5-butyl-1-[[2′- 2H-tetrazol-5-yl biphenyl-4-yl]methyl]imidazole-2-carboxylic acid (30) exhibited higher binding affinity compared to the other analogues tested (−log IC50 = 8.46).
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Notably, chrysin and flavone have no hydroxyl groups in their B-rings, but they could still bind to the same binding sites of the COX enzymes with relatively-lower binding affinities compared to myricetin and quercetin.
This may also go as far as identifying tetra-peptides with potentially superior binding affinities compared to the tri-peptides we have considered here.
Whereas PharmDock provided a high Pearson correlation coefficient between the estimated binding energy and experimentally measured binding affinities compared to other programs, the overall binding affinity prediction is still not accurate enough for drug optimization purposes.
Requiring that peptides in the non-ligand data set were found both with stronger and weaker binding affinities compared to the reference ligand further reduced the set of ligand:non-ligand binder pairs to 459.
However, such substitution in each segment of the peptide dimers (6 and 10) resulted in a loss of Y1 receptor-binding affinity compared to their DOTA-free counterparts (5 and 9).
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