Suppression of mitochondrial production of reactive oxygen species is a promising strategy against intrinsic apoptosis typical of degenerative diseases. Stable nitroxide radicals such as 4-hydroxy-2,2,6,6-tetramethyl piperidine-1-oxyl (TEMPOL) and its analogs combine several important features, including recycleability, electron acceptance from respiratory complexes, superoxide dismutase mimicry, and radical scavenging. Although successful in antioxidant protection, their effective concentrations are too high for successful in vivo applications. Recently (J Am Chem Soc 127:12460, 2005), we reported that 4-amino 2,2,6,6-tetramethyl-1-piperidinyloxy, covalently conjugated to a five-residue segment of gramicidin S (GS), was integrated into mitochondria and blocked actinomycin D (ActD)-induced superoxide generation and apoptosis. Using a model of ActDinduced apoptosis in mouse embryonic cells, we screened a library of nitroxides to explore structure-activity relationships between their antioxidant/antiapoptotic properties and chemical composition and three-dimensional (3D) structure. High hydrophobicity and effective mitochondrial integration are necessary but not sufficient for high antiapoptotic/antioxidant activity of a nitroxide conjugate. By designing conformationally preorganized peptidyl nitroxide conjugates and characterizing their 3D structure experimentally (circular dichroism and NMR) and theoretically (molecular dynamics), we established that the presence of the -turn/-sheet secondary structure is essential for the desired activity. Monte Carlo simulations in model lipid membranes confirmed that the conservation of the D-Phe-Pro reverse turn in hemi-GS analogs ensures the specific positioning of the nitroxide moiety at the mitochondrial membrane interface and maximizes their protective effects. These new insights into the structure-activity relationships of nitroxidepeptide and -peptide isostere conjugates are instrumental for development of new mechanism-based therapeutically effective agents.Poorly controlled and excessive generation of reactive oxygen species (ROS), coupled with their ability to cause oxidative damage to phospholipids, proteins, and DNA, has been associated with the pathogenesis of a number of major human cardiovascular (Ambrosio and Tritto, 1999) and neurodegenerative diseases (Andersen, 2004) as well as cancer (Szatrowski and Nathan, 1991). Not surprisingly, significant efforts have been directed toward the use of radical scavengers and antioxidants in preventive and therapeutic strategies, albeit with limited success. The search for new protective remedies has been focused on molecules combining antioxidant utilities with recycling capacities (Mitchell et al.,