Design, synthesis, structural analysis and biochemical studies of stapled AIF(370-394) analogues as ligand of CypA

• Published in: Biochimica et biophysica acta. General subjects Vol. 1864; no. 12; p. 129717
• Main Authors: Monti, Alessandra, Sturlese, Mattia, Caporale, Andrea, Roger, Jessica De Almeida, Mascanzoni, Fabiola, Ruvo, Menotti, Doti, Nunzianna
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.12.2020
• Subjects: AIF(370–394) stapled peptide; AIF/CypA complex; apoptosis; Apoptosis Inducing Factor - chemistry; Apoptosis Inducing Factor - metabolism; calorimetry; chromatin; Circular dichroism (CD); circular dichroism spectroscopy; Click chemistry; cyclophilin A; Cyclophilin A - metabolism; disulfides; DNA; Drug Design; Enspire label free; Humans; Isothermal Titration Calorimetry (ITC); Ligands; Molecular Docking Simulation; neurodegenerative diseases; neurons; Neuroprotective Agents - chemical synthesis; Neuroprotective Agents - chemistry; Neuroprotective Agents - pharmacology; neuroprotective effect; NMR and molecular modeling analysis; nuclear magnetic resonance spectroscopy; peptides; Peptides - chemical synthesis; Peptides - chemistry; Peptides - pharmacology; therapeutics; thermodynamics; titration; Enspire label free; Circular dichroism (CD); AIF/CypA complex; Click chemistry; Isothermal Titration Calorimetry (ITC); NMR and molecular modeling analysis; AIF(370–394) stapled peptide
• DOI: 10.1016/j.bbagen.2020.129717
• ISSN: 0304-4165; 1872-8006

The neuronal apoptotic process requires the nuclear translocation of Apoptosis Inducing Factor (AIF) in complex with Cyclophilin A (CypA) with consequent chromatin condensation and DNA degradation events. Targeting CypA by delivering an AIF-blocking peptide (AIF(370–394)) provides a significant neuroprotection, demonstrating the biological relevance of the AIF/CypA complex. To date pharmaceutical compounds targeting this complex are missing. We designed and synthesized a set of mono and bicyclic AIF(370–394) analogs containing both disulfide and 1,2,3-triazole bridges, in the attempt to both stabilize the peptide conformation and improve its binding affinity to CypA. Peptide structures in solution and in complex with CypA have been studied by circular dichroism (CD), Nuclear Magnetic Resonance (NMR) and molecular modeling. The ability of stapled peptides to interact with CypA was evaluated by using Epic Corning label free technique and Isothermal Titration Calorimetry experiments. We identified a stapled peptide analogue of AIF(370–394) with a ten-fold improved affinity for CypA. Molecular modeling studies reveal that the new peptide acquires β-turn/β-fold structures and shares with the parent molecule the same binding region on CypA. Data obtained provide invaluable assistance in designing new ligand of CypA for therapeutic approaches in neurodegenerative diseases. Due to the crucial role of AIF/CypA complex formation in neurodegeneration, identification of selective inhibitors is of high importance for targeted therapies. We describe new bicyclic peptide inhibitors with improved affinity for CypA, investigating the kinetic, thermodynamic and structural effects of conformational constraints on the protein−ligand interaction, and their utility for drug design. •Design of stapled peptides mimicking AIF peptide inhibitor of AIF/CypA complex•Identification of a stapled peptide as a potent binder of CypA•Evaluation on the rigidity/flexibility effects in peptide-protein complex formation