title: A NMR and computational study of Smac mimics targeting both the BIR2 and BIR3 domains in XIAP protein.
abstract: In this paper we report an extensive NMR analysis of small ligands (Smac mimics) complexed with different constructs of XIAP. The mimics-binding site of XIAP is known as the BIR3 domain - primary, and the linker BIR2 region - secondary site. Interactions between the BIR3 domain and Smac mimics have been extensively studied by X-ray but, as of today, there are scarce data about the interaction between BIR2, or the whole linker-BIR2-BIR3 construct, and Smac mimics. In order to characterize our Smac mimics, we performed a STD NMR study between our 4-substituted, 1-aza-2-oxobicyclo[5.3.0]decane scaffold-based molecules and three different XIAP fragments: single BIR2 and BIR3 domains, and bifunctional linker-BIR2-BIR3. The results were integrated with docking calculations and molecular dynamics simulations. NMR data, which are consistent with biological tests, indicated that the two BIR subunits interact differently with our Smac mimics and suggest that the ligands enter into more intimate contact with the linker-BIR2-BIR3. In conclusion, we observe that the SMAC mimics showed with the construct linker-BIR2-BIR3 a series of NOE contacts that were not observed in the mono-domain ligand:BIR2 or :BIR3 complexes. So, in agreement with the computational models we believe that the linker moieties of the binding site play a key role in the stability of the protein complex.
authors.affiliation: Università degli Studi di Milano, Dipartimento di Chimica Organica e Industriale, Centro Interdipartimentale C.I.S.I., Istituto di Scienze e Tecnologie Molecolari-CNR, Via Venezian 21, 20133 Milano, Italy. donatella.potenza@unimi.it
authors.forename: Donatella
authors.initials: D
authors.lastname: Potenza
authors.forename: Laura
authors.initials: L
authors.lastname: Belvisi
authors.forename: Francesca
authors.initials: F
authors.lastname: Vasile
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Moroni
authors.forename: Federica
authors.initials: F
authors.lastname: Cossu
authors.forename: Pierfausto
authors.initials: P
authors.lastname: Seneci
mesh_terms: D001665:Binding Sites; D040761:Biomimetic Materials / Q000737:chemistry*; D006801:Humans; D008024:Ligands; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D017434:Protein Structure, Tertiary; D051636:X-Linked Inhibitor of Apoptosis Protein / Q000737:chemistry*
chemical_list: D008024:Ligands; D051636:X-Linked Inhibitor of Apoptosis Protein