Predicting subsite interactions of plasmin with substrates and inhibitors through computational docking analysis

Figures & data

Figure 1.  Chemical structures of D/L-Ile-Phe-Lys, YO-2, and PKSI-527. K_M and IC₅₀ values for plasmin are in parentheses^3,4,20.

Figure 2.  Molecular dynamic simulation of plasmin over 11 ns. The root-mean square deviation (RMSD) of simulated structures from the initial structure is plotted versus time. The RMSD calculation is based on the protein main-chain atoms.

Figure 3.  Predicted complex of trypsin with PKSI-527. The structure of trypsin is displayed as a cartoon model (grey) and the inhibitor PKSI-527 is shown as a stick model (yellow). The side-chains of His57, Asp102, Asp189, and Ser195 in the catalytic site of trypsin are shown as stick models (brown).

Figure 4.  Predicted complex of plasmin with D/L-Ile-Phe-Lys substrates. The structure of plasmin is displayed as a surface model (grey) and the ligands D- and L-Ile-Phe-Lys are shown as stick models (magenta for D-Ile-Phe-Lys and blue for L-Ile-Phe-Lys). The side-chains of residues in the binding and catalytic sites are shown as stick models (white). The underlined label is for the substrate. (a) Close-up view of S1/P1 interaction. (b) The overall binding mode of the substrates.

Figure 5.  Predicted complex of plasmin with YO-2. The structure of plasmin is displayed as a surface model (grey) and the inhibitor YO-2 is shown as a stick model (green). The side-chains of residues in the binding and catalytic sites are shown as stick models (white). (a) Identical view as that of Figure 4b. (b) Side-view.

Table 1.  SAR of Tra-Tyr(O-Pic)-CONH-X.

X =	IC50 (μM) for plasmin
–(CH2)7–CH3 (YO-2)	0.53
–(C6H6)–(CH2)4–CH3	0.54
–(C6H6)–CH2–CH3	1.7
–(CH2)2–CH(CH3)–CH3	1.9
–(CH2)7–NH2	3.8
–(CH2)7–COOH	5.5

Figure 6.  Predicted complex of plasmin with PKSI-527. The structure of plasmin is displayed as a surface model (grey) and the inhibitor PKSI-527 is shown as a stick model (yellow). The side-chains of residues in the binding and catalytic sites are shown as stick models (white). (a) Identical view as that of Figure 4b. (b) Comparison of the binding modes of YO-2 (green) and PKSI-527. (c) The structure of PKSI-527 overlapped with YO-2.

Figure 7.  Predicted complex of urokinase with YO-2 and PKSI-527. The structure of urokinase is displayed as a surface model (grey) and the inhibitors YO-2 and PKSI-527 are shown as stick models (green for YO-2 and yellow for PKSI-527). The side-chains of residues in the binding and catalytic sites are shown as stick models (white).

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