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VOL. 76 (2), 223-239, 2010 PREDICTION OF LIGAND BINDING ENERGY...

Table 2. GR-flavonoids interactions.

Compound LEU33 ASN34 GLN40 ARG81 GLN111 THR205 Others

1 —— ——— 2.2 —

2 — 2.8 ——— 1.9 2.7-3

3 — 2.9-3.5 — — — 3.0 3.3

4 — — 3.2 3.0 — — —

5 —— ——— — —

6 2.8 — 3.0 2.7 — — —

7 —— ——— — —

8 — 2.9-3.0 — — — — 2.8-2.6-3.3

9 —— ——— 2.7 —

10 —— ——— 3.0 —

11 —— ——— 2.9 3.0-2.7

12 — — — — 3.1 2.5 2.9-3.1

13 — 2.4-2.9 3.2 3.0 — — 3.1-2.8

14 — 2.7 3.0 3.2 — 3.0 2,7-3.1-3.1

15 2.9 2.7 3.0 3.2 — 3.0 3.1-3.1-2.7

Dexamethasone 3.5 3.0 3.0 2.6 3.1 2.6-2.7 —

Betamethasone 3.3 3.0 2.9 2.7 3.3 2.9-3.0 —

Cortisol 3.0 3.0 3.1 2.8 3.1 2.6-3.1 —

Distances are shown in amstrong. Other summarizes Cys202, Leu198 and Met30 interactions.

Prior to extract energies from flavonoids complexes, we
constructed a training set as described before. The values of the
calculated and experimental energies are shown in Table 3, and the
results for the best regression test can be seen in Figure 3. Best
correlation was found for the pair values a = 0.42 and ß = 0.5. The
value of a for van der Waals contribution is in good agreement with
the fact that hydrophobic interactions in the case of GR are of great
importance and the value of ß is the same in the original method
proposed for Aqvist et al. (6). However, according to Aqvist et al. (12)
hydroxyl (OH) groups may affect ß, decreasing its value the greater
their number, hence a correction for the number of hydroxyl groups
in molecules of the test set should be done, as in test set all the

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