Mutation of surface residues to promote crystallization of activated factor XI as a complex with benzamidine: an essential step for the iterative structure-based design of factor XI inhibitors.
Activated factor XI (FXIa) is a key enzyme in the amplification phase of the blood-coagulation cascade. Thus, a selective FXIa inhibitor may have lesser bleeding liabilities and provide a safe alternative for antithrombosis therapy to available drugs on the market. In a previous report, the crystal structures of the catalytic domain of FXIa (rhFXI(370-607)) in complex with various ecotin mutants have been described. However, ecotin forms a matrix-like interaction with rhFXI(370-607) and is impossible to displace with small-molecule inhibitors; ecotin crystals are therefore not suitable for iterative structure-based ligand design. In addition, rhFXI(370-607) did not crystallize in the presence of small-molecule ligands. In order to obtain the crystal structure of rhFXI(370-607) with a weak small-molecule ligand, namely benzamidine, several rounds of surface-residue mutation were implemented to promote crystal formation of rhFXI(370-607). A quadruple mutant of rhFXI(370-607) (rhFXI(370-607)-S434A,T475A,C482S,K437A) readily crystallized in the presence of benzamidine. The benzamidine in the preformed crystals was easily exchanged with other FXIa small-molecule inhibitors. These crystals have facilitated the structure-based design of small-molecule FXIa inhibitors.
Jin
Lei
L
Daiichi Asubio Medical Research Laboratories LLC, USA. leijin05@yahoo.com
Pandey
Pramod
P
Babine
Robert E
RE
Weaver
David T
DT
Abdel-Meguid
Sherin S
SS
Strickler
James E
JE
D001550:Benzamidines / Q000737:chemistry*; D001665:Binding Sites; D001779:Blood Coagulation Factors / Q000737:chemistry; D002384:Catalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D018076:DNA, Complementary / Q000378:metabolism; D005172:Factor XI / Q000037:antagonists & inhibitors*; D015945:Factor XIa / Q000737:chemistry* / Q000235:genetics*; D006801:Humans; D006860:Hydrogen Bonding; D020128:Inhibitory Concentration 50; D008024:Ligands; D046911:Macromolecular Substances / Q000737:chemistry; D008958:Models, Molecular; D016296:Mutagenesis; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D010455:Peptides / Q000737:chemistry; D010843:Pichia / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry; D012694:Serine / Q000737:chemistry
D001550:Benzamidines; D001779:Blood Coagulation Factors; D018076:DNA, Complementary; D008024:Ligands; D046911:Macromolecular Substances; D010455:Peptides; D011994:Recombinant Proteins; D012694:Serine; D005172:Factor XI; D015945:Factor XIa; C032157:benzamidine