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According to a comment from one of the reviewers, the degree of steric overlap between the thiophene 3,4-positions of compound 11 and the wall of the S1′ pocket was examined. For each atom in the thiophene ring, van der Waals interaction energy with the protein was calculated in each of 500 snapshots during the docking simulation and then statistically analyzed. Similar energy calculation was done for each atom in the corresponding benzene ring of compound 9. As a result, the hydrogens at the 3,4-positions of the thiophene ring gave negative mean energy values (-2.38 ± 0.26 and -2.42 ± 0.16 kcal/mol), suggesting that there was no severe steric overlap between these positions of the thiophene ring and the wall of the S1′ pocket during the simulation. Interestingly, mean values for the two hydrogens at the corresponding positions on the benzene ring of 9 were less negative (-0.41 ± 0.22 and -0.45 ± 0.27 kcal/mol). Mean vdW energies of whole rings, which were calculated as the sum of the contribution from each ring atom in each snapshot, also showed that the thiophene ring (-13.60 ± 0.82 kcal/mol) of 11 can be accommodated in the S1′ pocket more favorably than the benzene ring (-11.75 ± 1.05 kcal/mol) of 9. With these calculation results, it was reasonably confirmed that there is no severe steric overlap of the thiophene ring of compound 11 with the wall of the S1′ pocket.
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Compound 3 was synthesized from the corresponding tert-butyl ester using methyl iodide and potassium carbonate in dimethylformamide, followed by trifluoroacetic acid (TFA) hydrolysis.
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