Rational Redesign of
Inhibitors of Furin/kexin Processing Proteases
YE Yu-Zhen, FEI Hao, DING Da-Fu*
( Institute of Biochemistry and Cell Biology, Shanghai Institutes for
Biological Sciences, the Chinese Academy of Sciences, Shanghai 200031,
China )
Abstract Furin/kexin
processing proteases catalyze the proteolysis of large protein precursors
involved in many biological processes, such as zymogen activation, peptide
hormone synthesis, viral protein processing and receptor maturation, making
them potential targets for therapeutic agents. Herein, homology modeling and
weighted evolutionary tracing were combined to investigate the
interactionmechanism of furin/kex2 with eglin C mutants. The model structures
showed that there were many acidic residues in the furin (kex2) binding
interface, contributing to specificity for multiple basic residues of their
corresponding substrates or inhibitors. Besides, some rational explanations
were presented for the different inhibitor/substrate specificity of the
furin/kexin members by combining the model structures with results of
evolutionary tracing. Based on these analyses,an attempt was made to rationally
redesign the eglin C by interface engineering with heterogeneous
self-consistent ensemble optimization to improve its inhibitory specificity on
furin/kex2. With the model complex structures of furin/kex2 and eglin C
variants as structural templates, the P1, P2 and P4
of eglin C were redesigned, respectively. The design results show that both
furin and kex2 favored basic residues at P1, P2 and P4
in eglin C, in good agreement with the experimental data. The detection of many
specific residues in S′ part of furin/kexin sequences made possible designing
inhibitors with high specific binding to furin and kex2, respectively. As for
furin, the best inhibitor designed was eglin C-P2′Glu-P3′Asp-P4′Arg
(only these three positions were shown), while the best eglin C variant for
kex2 designed was P2′Arg-P3′Arg-P4′Glu. The
structures show that furin and kex2 form distinct interactions with these two
eglin C variants. Herein, a strategy was proposed that combine homology
modeling, evolutionary tracing and rational interface redesign to investigate
enzyme inhibitor interactions and inhibitor engineering. This computational
design gives some rational guidance to further experimental inhibitor
engineering.
Key words homology modeling； weighted evolutionary tracing； interface redesign； processing proteases； eglin C
*Corresponding author： Tel, 86-21-64374430-254； Fax, 86-21-64338357； e-mail,
[email protected]