Importance of the S1sub pocket

The S1sub pocket of urokinase is formed by the conserved Cys191-Cys220 disulfide bridge and the surrounding residues Gly219, Ser146, Gln192 and Lys143.

urokinase (A, PLS coefficients, no variable selection)

A31 (Ki=0.63 M) 1sqt (Nienaber, et al., 2000; Wendt, et al., 2004)

A30 (Ki=0.035 M) 1sqo (Nienaber, et al., 2000; Wendt, et al., 2004)

Nienaber, V.L., Davidson, D., Edalji, R., Giranda, V.L., Klinghofer, V., Henkin, J., Magdalinos, P., Mantei, R., Merrick, S., Severin, J.M., Smith, R.A., Stewart, K., Walter, K., Wang, J., Wendt, M., Weitzberg, M., Zhao, X. and Rockway, T. (2000) Structure-directed discovery of potent non-peptidic inhibitors of human urokinase that access a novel binding subsite, Structure Fold Des, 8, 553-563.

Wendt, M.D., Geyer, A., McClellan, W.J., Rockway, T.W., Weitzberg, M., Zhao, X., Mantei, R., Stewart, K., Nienaber, V., Klinghofer, V. and Giranda, V.L. (2004) Interaction with the S1 beta-pocket of urokinase: 8-heterocycle substituted and 6,8-disubstituted 2-naphthamidine urokinase inhibitors, Bioorg Med Chem Lett, 14, 3063-3068.

PLS coefficients for electrostatic interaction:

Gly216 ~0

Gln192 ~ +0.07

Arg217 -0.1

A30 (Ki=0.035 M) 1sqo

H bond: NH--Gly216-0

favoured electrostatic interactions: NGln192-N

favoured repulsive (neg. PLS coeff) electrostatic interaction (the disfavoured interaction is less strong): N(=-0.20)Arg217-NH2

(0.9 kcal/mol u^elec * -0.1 PLS coeff = -0.09 kcal/mol)

Ki=0.17 M

H bond: NH--Gly216-0

either no NGln192-N or no NArg217-NH2 interaction

Ki=0.55 M

no H bond: NH--Gly216-0

either no NGln192-N or no NArg217-NH2 interaction

Results:

A qualitative comparison supports the retrieved COMBINE model for the S1sub pocket.