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Three-step structure-activity relationship exploration led to promising compounds 19e and 19h with unique chemical structure and binding mode from the other third-generation tyrosine kinase inhibitors.
d The absolute values of Vina scores (kcal/mol) of T790M decreased by 29.13 and 13.48% for erlotinib and gefitinib, respectively, compared to those of the wild type Fig. 6 Predicted binding mode from the docking analysis.
Interestingly, the cocrystal structure revealed a significantly different binding mode from the typical ATP-competitive interaction pattern.
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Simultaneous replacement of the R 3-phenol-4-methoxy groups of 1 with a 2-pyridyl unit, and truncation of the R benzyl group to a directly linked phenyl, resulted in compound 7 and an unexpected inversion of the binding mode from that observed for 6, giving rise to binding mode T2.
In the case of one inhibitor, melibionic acid (galactose-α- 1-6 -gluconic acid), the majority of the higalactose-α- 1-6 -gluconic from the dockingalactose-α- 1-6 -gluconicalactose residue in a similar position to that found in the crystal structure.
Removing the aldehyde moiety in 1 converts the binding mode from a slow to a fast exchange regime.
Strangely, when DB00631's (clofarabine) binding mode from XP + P1 was superimposed with the XP + P2 or XP + P3 clofarabine binding modes the measured RMSD was 1.6 and 1.2 Å, respectively; while the superimposition of the XP + P2 and XP + P3 binding modes had a measured RMSD of 0.8 Å.
After migratory insertion, the free energy of the σ-alkyl complex is lowered when the acetate counterion changes binding mode from mono- to bidentate (IV to V, Figure 1).
b 2D binding mode from SP P1. c 2D binding mode from SP P1.
In a molecular docking model, compounds 9 and 15c interacted with Topo I-DNA through a different binding mode from 1 and 3.
The X-ray analysis confirmed the binding mode expected from the design hypothesis.
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