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Virtual screening for compounds that mimic protein–protein interface epitopes
Author(s) -
Geppert Tim,
Reisen Felix,
Pillong Max,
Hähnke Volker,
Tanrikulu Yusuf,
Koch Christian P.,
Perna Anna Maria,
Perez Tatiana Batista,
Schneider Petra,
Schneider Gisbert
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.22894
Subject(s) - epitope , virtual screening , interface (matter) , chemistry , computer science , computational biology , biochemistry , biology , genetics , drug discovery , antigen , pulmonary surfactant , gibbs isotherm
Modulation of protein–protein interactions (PPI) has emerged as a new concept in rational drug design. Here, we present a computational protocol for identifying potential PPI inhibitors. Relevant regions of interfaces (epitopes) are predicted for three‐dimensional protein models and serve as queries for virtual compound screening. We present a computational screening protocol that incorporates two different pharmacophore models. One model is based on the mathematical concept of autocorrelation vectors and the other utilizes fuzzy labeled graphs. In a proof‐of‐concept study, we were able to identify serine protease inhibitors using a predicted trypsin epitope as query. Our virtual screening framework may be suited for rapid identification of PPI inhibitors and suggesting bioactive tool compounds. Copyright for JCC Journal: © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011