Synthetic mimetics of protein secondary structure domains

Proteins modulate the majority of all biological functions and are primarily composed of highly organized secondary structural elements such as helices, turns and sheets. Many of these functions are affected by a small number of key protein–protein contacts, often involving one or more of these well-defined structural elements. Given the ubiquitous nature of these protein recognition domains, their mimicry by peptidic and non-peptidic scaffolds has become a major focus of contemporary research. This review examines several key advances in secondary structure mimicry over the past several years, particularly focusing upon scaffolds that show not only promising projection of functional groups, but also a proven effect in biological systems.

[1]  Emad S. Alnemri,et al.  A conserved XIAP-interaction motif in caspase-9 and Smac/DIABLO regulates caspase activity and apoptosis , 2001, Nature.

[2]  Joshua A. Kritzer,et al.  Helical β-Peptide Inhibitors of the p53-hDM2 Interaction , 2004 .

[3]  L. J. Cole,et al.  Antibacterial Action of Melittin, a Polypeptide from Bee Venom , 1968, Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology and Medicine.

[4]  M. Distefano,et al.  Structure and function analysis of peptide antagonists of melanoma inhibitor of apoptosis (ML-IAP). , 2003, Biochemistry.

[5]  E. Giralt,et al.  Trishomocubane Amino Acid as a β‐turn scaffold , 2008, Chemical biology & drug design.

[6]  F. Bernal,et al.  Synthesis and biophysical characterization of stabilized alpha-helices of BCL-2 domains. , 2008, Methods in enzymology.

[7]  Annelise E Barron,et al.  Mimicry of bioactive peptides via non-natural, sequence-specific peptidomimetic oligomers. , 2002, Current opinion in chemical biology.

[8]  A. Schepartz,et al.  Tetrameric β3‐Peptide Bundles , 2008, Chembiochem : a European journal of chemical biology.

[9]  Nathan J. Brown,et al.  Effects of hydrophobic helix length and side chain chemistry on biomimicry in peptoid analogues of SP-C. , 2008, Biochemistry.

[10]  C. Pace,et al.  A helix propensity scale based on experimental studies of peptides and proteins. , 1998, Biophysical journal.

[11]  S. Chowdhury,et al.  How useful is ferrocene as a scaffold for the design of beta-sheet foldamers? , 2008, Angewandte Chemie.

[12]  John A. Robinson,et al.  The design, structures and therapeutic potential of protein epitope mimetics. , 2008, Drug discovery today.

[13]  β-Hairpin Peptidomimetics: Design, Structures and Biological Activities , 2009 .

[14]  R. Zuckermann,et al.  Proteolytic studies of homologous peptide and N-substituted glycine peptoid oligomers , 1994 .

[15]  J. Rebek,et al.  Synthesis of pyridazine-based scaffolds as alpha-helix mimetics. , 2007, Organic letters.

[16]  Joshua A. Kritzer,et al.  β-Peptides as inhibitors of protein–protein interactions , 2005 .

[17]  J. Wells,et al.  High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. , 1989, Science.

[18]  John M. Slattery,et al.  Supramolecular bidentate ligands by metal-directed in situ formation of antiparallel beta-sheet structures and application in asymmetric catalysis. , 2008, Chemistry.

[19]  A Light‐Activated β‐Turn Scaffold within a Somatostatin Analog: NMR Structure and Biological Activity , 2006 .

[20]  W. Fairbrother,et al.  Design, synthesis, and biological activity of a potent Smac mimetic that sensitizes cancer cells to apoptosis by antagonizing IAPs. , 2006, ACS chemical biology.

[21]  Alain Deschenes,et al.  Application of a novel design paradigm to generate general nonpeptide combinatorial templates mimicking beta-turns: synthesis of ligands for melanocortin receptors. , 2007, Journal of combinatorial chemistry.

[22]  Andrew D. Hamilton,et al.  Benzoylurea Oligomers: Synthetic Foldamers That Mimic Extended α Helices , 2007 .

[23]  Sheng Jiang,et al.  Design, synthesis, and characterization of a potent, nonpeptide, cell-permeable, bivalent Smac mimetic that concurrently targets both the BIR2 and BIR3 domains in XIAP. , 2007, Journal of the American Chemical Society.

[24]  Samuel H. Gellman,et al.  Rational Development of β-Peptide Inhibitors of Human Cytomegalovirus Entry* , 2006, Journal of Biological Chemistry.

[25]  B. Breit,et al.  Supramolecular PhanePhos-analogous ligands through hydrogen-bonding for asymmetric hydrogenation. , 2008, Chemical communications.

[26]  K. Das,et al.  Engineering ML-IAP to produce an extraordinarily potent caspase 9 inhibitor: implications for Smac-dependent anti-apoptotic activity of ML-IAP. , 2005, The Biochemical journal.

[27]  S. Chowdhury,et al.  Amino acid conjugates of 1,1'-diaminoferrocene. Synthesis and chiral organization. , 2005, Organic & biomolecular chemistry.

[28]  Stephen B. H. Kent,et al.  Efficient method for the preparation of peptoids [oligo(N-substituted glycines)] by submonomer solid-phase synthesis , 1992 .

[29]  Alanna Schepartz,et al.  High-Resolution Structure of a β-Peptide Bundle , 2007 .

[30]  S. Korsmeyer,et al.  Reactivation of the p53 tumor suppressor pathway by a stapled p53 peptide. , 2007, Journal of the American Chemical Society.

[31]  K. Dill,et al.  Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer. , 2008, Journal of the American Chemical Society.

[32]  W. DeGrado,et al.  beta-Peptides: from structure to function. , 2001, Chemical reviews.

[33]  S. Gellman,et al.  Inhibition of Herpes Simplex Virus Type 1 Infection by Cationic β-Peptides , 2008, Antimicrobial Agents and Chemotherapy.

[34]  Shaomeng Wang,et al.  Interaction of a cyclic, bivalent smac mimetic with the x-linked inhibitor of apoptosis protein. , 2008, Biochemistry.

[35]  A. Barron,et al.  Peptoids that mimic the structure, function, and mechanism of helical antimicrobial peptides , 2008, Proceedings of the National Academy of Sciences.

[36]  M. Kruppa,et al.  Enhanced Peptide β-Sheet Affinity by Metal to Ligand Coordination , 2005 .

[37]  A. Schepartz,et al.  Toward â-Amino Acid Proteins : Design , Synthesis , and Characterization of a Fifteen Kilodalton â-Peptide Tetramer , 2008 .

[38]  B. König,et al.  Synthesis and structure of 1,4-dipiperazino benzenes: chiral terphenyl-type peptide helix mimetics. , 2008, Organic letters.

[39]  G. Rose,et al.  Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Michael S. Kay,et al.  Inhibiting HIV Fusion with a β-Peptide Foldamer , 2005 .

[41]  D. Seebach,et al.  The Outstanding Biological Stability of β‐ and γ‐Peptides toward Proteolytic Enzymes: An In Vitro Investigation with Fifteen Peptidases , 2001 .

[42]  V. Rapić,,et al.  The first oligopeptide derivative of 1'-aminoferrocene-1-carboxylic acid shows helical chirality with antiparallel strands. , 2004, Chemical communications.

[43]  B. Breit,et al.  Hydrogen bonding as a construction element for bidentate donor ligands in homogeneous catalysis: regioselective hydroformylation of terminal alkenes. , 2003, Journal of the American Chemical Society.

[44]  W. DeGrado,et al.  β-Peptides: From Structure to Function , 2001 .

[45]  Robert L. Baldwin,et al.  α-Helix formation by peptides of defined sequence , 1995 .

[46]  D. Dragoli,et al.  Ordered conformations in bis(amino acid) derivatives of 1,1′-ferrocenedicarboxylic acid , 1996 .

[47]  A. Hamilton,et al.  Toward proteomimetics: terphenyl derivatives as structural and functional mimics of extended regions of an alpha-helix. , 2001, Journal of the American Chemical Society.

[48]  David R. Liu,et al.  Solving chemical problems through the application of evolutionary principles. , 2007, Current opinion in chemical biology.

[49]  J. Nowick,et al.  Designed molecules that fold to mimic protein secondary structures. , 1999, Current opinion in chemical biology.

[50]  T. Hirao,et al.  Chirality organization of ferrocenes bearing podand dipeptide chains: synthesis and structural characterization. , 2001, Journal of the American Chemical Society.

[51]  K. Meyer Lung Surfactants: Basic Science and Clinical Applications , 2002 .

[52]  A. Debnath,et al.  Solution Structure of a Hydrocarbon Stapled Peptide Inhibitor in Complex with Monomeric C-terminal Domain of HIV-1 Capsid* , 2008, Journal of Biological Chemistry.

[53]  K. Holroyd,et al.  In Vitro Antibacterial Properties of Pexiganan, an Analog of Magainin , 1999, Antimicrobial Agents and Chemotherapy.

[54]  R. Srinivasan,et al.  Local Interactions in Protein Folding: Lessons from the α-Helix* , 1997, The Journal of Biological Chemistry.

[55]  C. Chothia,et al.  The structure of protein-protein recognition sites. , 1990, The Journal of biological chemistry.

[56]  S. Chowdhury,et al.  Rational design of bioorganometallic foldamers: a potential model for parallel beta-helical peptides. , 2006, Angewandte Chemie.

[57]  J. Nowick Exploring β-Sheet Structure and Interactions with Chemical Model Systems , 2009 .

[58]  J. Melinger,et al.  Supramolecular device for artificial photosynthetic mimics as helix-mediated antenna/reaction center ensemble. , 2008, Organic letters.

[59]  Geng Wu,et al.  Structural basis of IAP recognition by Smac/DIABLO , 2000, Nature.

[60]  Philip M. Dean,et al.  Design criteria for molecular mimics of fragments of the β-turn. 1. Cα atom analysis , 1999, J. Comput. Aided Mol. Des..

[61]  B. Breit,et al.  Self-assembly of bidentate ligands for combinatorial homogeneous catalysis: methanol-stable platforms analogous to the adenine-thymine base pair. , 2007, Angewandte Chemie.

[62]  A. Hamilton,et al.  Intramolecular hydrogen bonding allows simple enaminones to structurally mimic the i, i + 4, and i + 7 residues of an α-helix , 2006 .

[63]  M. Weis,et al.  Self-assembly of bidentate ligands for combinatorial homogeneous catalysis: asymmetric rhodium-catalyzed hydrogenation. , 2006, Journal of the American Chemical Society.

[64]  Julius Rebek,et al.  Heterocyclic α-helix mimetics for targeting protein-protein interactions , 2007 .

[65]  K. Mayo,et al.  A journey in structure-based drug discovery: from designed peptides to protein surface topomimetics as antibiotic and antiangiogenic agents. , 2007, Accounts of chemical research.

[66]  A. Schepartz,et al.  Biophysical and structural characterization of a robust octameric beta-peptide bundle. , 2007, Journal of the American Chemical Society.

[67]  A. Hamilton,et al.  Strategies for targeting protein-protein interactions with synthetic agents. , 2005, Angewandte Chemie.

[68]  F. Bernal,et al.  Dissection of the BCL-2 family signaling network with stabilized alpha-helices of BCL-2 domains. , 2008, Methods in enzymology.

[69]  S. Srinivasula,et al.  Mechanism of XIAP-mediated inhibition of caspase-9. , 2003, Molecular cell.

[70]  J. Kelly,et al.  SYNTHESIS AND EFFICACY OF SQUARE PLANAR COPPER COMPLEXES DESIGNED TO NUCLEATE BETA -SHEET STRUCTURE , 1995 .

[71]  E. Letouzé,et al.  Modular alpha-helical mimetics with antiviral activity against respiratory syncitial virus. , 2006, Journal of the American Chemical Society.