title: Paratope and epitope mapping of the antithrombotic antibody 6B4 in complex with platelet glycoprotein Ibalpha.
abstract: The monoclonal antibody 6B4 has a potent antithrombotic effect in nonhuman primates by binding to the flexible loop, also known as the beta-switch region (amino acids 230-242), of glycoprotein Ibalpha (GPIbalpha). This interaction blocks, in high shear stress conditions, the specific interaction between GPIbalpha and von Willebrand factor suppressing platelet deposition to the damaged vessel wall, a key event in the pathogenesis of arterial thrombosis. To understand the interactions between this antibody and its antigen at the amino acid level, we here report the identification of the paratope and epitope in 6B4 and GPIbalpha, respectively, by using computer modeling and site-directed mutagenesis. The docking programs ZDOCK (rigid body docking) and HADDOCK (flexible docking) were used to model the interaction of 6B4 with GPIbalpha and to delineate the respective paratope and epitope. 6B4 and GPIbalpha mutants were constructed and assayed for their capacity to bind GPIbalpha and 6B4, respectively. From these data, it is found that the paratope of 6B4 is mainly formed by five residues: Tyr(27D), Lys(27E), Asp(28), and Glu(93) located in light chain CDR1 and -3, respectively, and Tyr(100C) of the heavy chain CDR3. These residues form a valley, where the GPIbalpha flexible loop can bind via residues Asp(235) and Lys(237). The experimental results were finally used to build a more accurate docking model. Taken together, this information provides guidelines for the design of new derivatized lead compounds with antithrombotic properties.
authors.affiliation: Laboratory for Thrombosis Research, IRC, KU Leuven Campus Kortrijk, E. Sabbelaan 53, B-8500 Kortrijk, Belgium.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Fontayne
authors.forename: Bauke
authors.initials: B
authors.lastname: De Maeyer
authors.forename: Marc
authors.initials: M
authors.lastname: De Maeyer
authors.forename: Mayo
authors.initials: M
authors.lastname: Yamashita
authors.forename: Tadashi
authors.initials: T
authors.lastname: Matsushita
authors.forename: Hans
authors.initials: H
authors.lastname: Deckmyn
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D000906:Antibodies / Q000737:chemistry*; D000911:Antibodies, Monoclonal / Q000737:chemistry*; D001666:Binding Sites, Antibody; D002626:Chemistry, Pharmaceutical / Q000379:methods; D015195:Drug Design; D018604:Epitope Mapping / Q000379:methods; D000939:Epitopes / Q000737:chemistry; D008562:Membrane Glycoproteins; D008565:Membrane Proteins / Q000737:chemistry*; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D019038:Platelet Glycoprotein GPIb-IX Complex; D012984:Software; D013927:Thrombosis / Q000276:immunology*; D014443:Tyrosine / Q000737:chemistry
chemical_list: D000596:Amino Acids; D000906:Antibodies; D000911:Antibodies, Monoclonal; D000939:Epitopes; D008562:Membrane Glycoproteins; D008565:Membrane Proteins; D019038:Platelet Glycoprotein GPIb-IX Complex; C094990:adhesion receptor; D014443:Tyrosine