title: Design of protein membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V.
abstract: Most orally bioavailable drugs on the market are competitive inhibitors of catalytic sites, but a significant number of targets remain undrugged, because their molecular functions are believed to be inaccessible to drug-like molecules. This observation specifically applies to the development of small-molecule inhibitors of macromolecular interactions such as protein-membrane interactions that have been essentially neglected thus far. Nonetheless, many proteins containing a membrane-targeting domain play a crucial role in health and disease, and the inhibition of such interactions therefore represents a very promising therapeutic strategy. In this study, we demonstrate the use of combined in silico structure-based virtual ligand screening and surface plasmon resonance experiments to identify compounds that specifically disrupt protein-membrane interactions. Computational analysis of several membrane-binding domains revealed they all contain a druggable pocket within their membrane-binding region. We applied our screening protocol to the second discoidin domain of coagulation factor V and screened >300,000 drug-like compounds in silico against two known crystal structure forms. For each C2 domain structure, the top 500 molecules predicted as likely factor V-membrane inhibitors were evaluated in vitro. Seven drug-like hits were identified, indicating that therapeutic targets that bind transiently to the membrane surface can be investigated cost-effectively, and that inhibitors of protein-membrane interactions can be designed.
authors.affiliation: Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, 6229 Maastricht, The Netherlands.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Segers
authors.forename: Olivier
authors.initials: O
authors.lastname: Sperandio
authors.forename: Markus
authors.initials: M
authors.lastname: Sack
authors.forename: Rainer
authors.initials: R
authors.lastname: Fischer
authors.forename: Maria A
authors.initials: MA
authors.lastname: Miteva
authors.forename: Jan
authors.initials: J
authors.lastname: Rosing
authors.forename: Gerry A F
authors.initials: GA
authors.lastname: Nicolaes
authors.forename: Bruno O
authors.initials: BO
authors.lastname: Villoutreix
mesh_terms: D001665:Binding Sites; D002462:Cell Membrane / Q000378:metabolism*; D004353:Drug Evaluation, Preclinical; D005165:Factor V / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D020128:Inhibitory Concentration 50; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D017186:Titrimetry
chemical_list: D008024:Ligands; D005165:Factor V