A RaPID way to discover nonstandard macrocyclic peptide modulators of drug targets.

Studies of the fundamental nature of RNA catalysis and the potential mechanism of a shift from the "RNA world" to proteinaceous life lead us to identify a set of ribozymes (flexizymes) capable of promiscuous tRNA acylation. Whilst theoretically and mechanistically interesting in their own right, flexizymes have turned out to have immense practical value for the simple synthesis of tRNAs acylated with unusual amino acids, which in turn can be used for the ribosomal synthesis of peptides containing non-canonical residues. Using this technique, it is possible to synthesise peptides containing a range of structural features (macrocyclic backbones, backbone N-methylation, d-stereochemistry, etc.) commonly observed in natural product secondary metabolites, a chemical class that has historically been a rich source of drug-like molecules. Moreover, when combined with biochemical display screening technologies, this synthetic approach can be used to generate (and screen for target affinity) extremely diverse (in excess of 1012 compound) chemical libraries, making it an extraordinary tool for drug discovery. The current review charts the history of flexizyme technology and its use for non-canonical peptide synthesis and screening.

[1]  A. Hopkins,et al.  The druggable genome , 2002, Nature Reviews Drug Discovery.

[2]  A. Adholeya,et al.  The Pharmacological Potential of Non-ribosomal Peptides from Marine Sponge and Tunicates , 2016, Front. Pharmacol..

[3]  K. Watanabe,et al.  Concurrent molecular recognition of the amino acid and tRNA by a ribozyme. , 2001, RNA.

[4]  G. Winter,et al.  Phage-encoded combinatorial chemical libraries based on bicyclic peptides. , 2009, Nature chemical biology.

[5]  H. Murakami,et al.  A flexizyme that selectively charges amino acids activated by a water-friendly leaving group. , 2009, Bioorganic & medicinal chemistry letters.

[6]  H. Murakami,et al.  Messenger RNA-programmed incorporation of multiple N-methyl-amino acids into linear and cyclic peptides. , 2008, Chemistry & biology.

[7]  S. Blacklow,et al.  Programming peptidomimetic syntheses by translating genetic codes designed de novo , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[8]  H. Murakami,et al.  Polymerization of α‐Hydroxy Acids by Ribosomes , 2008, Chembiochem : a European journal of chemical biology.

[9]  M. Marahiel.  A structural model for multimodular NRPS assembly lines. , 2016, Natural product reports.

[10]  Hiroshi Murakami,et al.  Ribosomal synthesis of peptidase-resistant peptides closed by a nonreducible inter-side-chain bond. , 2008, ACS chemical biology.

[11]  H. Suga,et al.  An in vitro evolved precursor tRNA with aminoacylation activity , 2001, The EMBO journal.

[12]  Matthew P. Jacobson,et al.  Beyond cyclosporine A: conformation-dependent passive membrane permeabilities of cyclic peptide natural products. , 2015, Future medicinal chemistry.

[13]  H. Murakami,et al.  Nonstandard peptide expression under the genetic code consisting of reprogrammed dual sense codons. , 2013, ACS chemical biology.

[14]  H. Murakami,et al.  Ribosomal synthesis of dehydrobutyrine- and methyllanthionine-containing peptides. , 2009, Chemical communications.

[15]  H. Suga,et al.  A ribozyme exclusively aminoacylates the 3'-hydroxyl group of the tRNA terminal adenosine. , 2001, Journal of the American Chemical Society.

[16]  Hiroshi Murakami,et al.  Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme , 2008, Nature.

[17]  H. Suga,et al.  Ribosomal synthesis of an amphotericin-B inspired macrocycle. , 2014, Journal of the American Chemical Society.

[18]  H. Murakami,et al.  Ribosomal Synthesis of Cyclic Peptides with a Fluorogenic Oxidative Coupling Reaction , 2009, Chembiochem : a European journal of chemical biology.

[19]  J. Kovarik,et al.  The pharmacokinetics of Sandimmun Neoral: a new oral formulation of cyclosporine. , 1994, Transplantation proceedings.

[20]  Yuuki Hayashi,et al.  Discovery of macrocyclic peptides armed with a mechanism-based warhead: isoform-selective inhibition of human deacetylase SIRT2. , 2012, Angewandte Chemie.

[21]  T. Katoh,et al.  Natural product-like macrocyclic N-methyl-peptide inhibitors against a ubiquitin ligase uncovered from a ribosome-expressed de novo library. , 2011, Chemistry & biology.

[22]  H. Murakami,et al.  Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids. , 2008, Journal of the American Chemical Society.

[23]  H. Murakami,et al.  Synthesis of polyester by means of genetic code reprogramming. , 2007, Chemistry & biology.

[24]  T. Katoh,et al.  A Fluorescent Imaging Probe Based on a Macrocyclic Scaffold That Binds to Cellular EpCAM , 2015, Journal of Molecular Evolution.

[25]  Stephen P. Hale,et al.  The exploration of macrocycles for drug discovery — an underexploited structural class , 2008, Nature Reviews Drug Discovery.

[26]  H. Suga,et al.  Translation initiation with initiator tRNA charged with exotic peptides. , 2009, Journal of the American Chemical Society.

[27]  Takuya Ueda,et al.  Cell-free translation reconstituted with purified components , 2001, Nature Biotechnology.

[28]  Yoshiki Tanaka,et al.  Structural basis for the drug extrusion mechanism by a MATE multidrug transporter , 2013, Nature.

[29]  Meng Gao,et al.  Targeting protein−protein interfaces using macrocyclic peptides , 2015, Biopolymers.

[30]  T. Katoh,et al.  Selection-based discovery of druglike macrocyclic peptides. , 2014, Annual review of biochemistry.

[31]  Yuuki Hayashi,et al.  In vitro selection of anti-Akt2 thioether-macrocyclic peptides leading to isoform-selective inhibitors. , 2012, ACS chemical biology.

[32]  Jack W. Szostak,et al.  An Expanded Set of Amino Acid Analogs for the Ribosomal Translation of Unnatural Peptides , 2007, PloS one.

[33]  N. Wiederhold,et al.  The echinocandin antifungals: an overview of the pharmacology, spectrum and clinical efficacy , 2003, Expert opinion on investigational drugs.

[34]  T. Katoh,et al.  Selective thioether macrocyclization of peptides having the N-terminal 2-chloroacetyl group and competing two or three cysteine residues in translation. , 2012, Organic & biomolecular chemistry.

[35]  W. A. van der Donk,et al.  New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products. , 2016, Cell chemical biology.

[36]  H. Murakami,et al.  Translation initiation by using various N-acylaminoacyl tRNAs. , 2006, Nucleic acids symposium series.

[37]  J W Szostak,et al.  RNA-peptide fusions for the in vitro selection of peptides and proteins. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[38]  P G Schultz,et al.  A general method for site-specific incorporation of unnatural amino acids into proteins. , 1989, Science.

[39]  H. Suga,et al.  Outersphere and innersphere coordinated metal ions in an aminoacyl-tRNA synthetase ribozyme. , 2002, Nucleic acids research.

[40]  Hiroshi Murakami,et al.  A highly flexible tRNA acylation method for non-natural polypeptide synthesis , 2006, Nature Methods.

[41]  Hiroshi Murakami,et al.  Expanding the amino acid repertoire of ribosomal polypeptide synthesis via the artificial division of codon boxes. , 2016, Nature chemistry.

[42]  T. Natsume,et al.  Artificial human Met agonists based on macrocycle scaffolds , 2015, Nature Communications.

[43]  Kit S Lam,et al.  Tumor-targeting peptides from combinatorial libraries. , 2017, Advanced drug delivery reviews.

[44]  H. Murakami,et al.  A versatile tRNA aminoacylation catalyst based on RNA. , 2003, Chemistry & biology.

[45]  Hiroshi Murakami,et al.  Ribosomal synthesis of bicyclic peptides via two orthogonal inter-side-chain reactions. , 2008, Journal of the American Chemical Society.

[46]  H. Murakami,et al.  Initiating translation with D-amino acids. , 2008, RNA.

[47]  A. McKillop,et al.  Development of novel ligands for peptide GPCRs. , 2016, Current opinion in pharmacology.

[48]  Peter G Schultz,et al.  An Expanded Eukaryotic Genetic Code , 2003, Science.

[49]  E. Tacconelli,et al.  The pharmacokinetics and pharmacodynamics of vancomycin in clinical practice: evidence and uncertainties. , 2013, The Journal of antimicrobial chemotherapy.

[50]  H. Murakami,et al.  Using a solid-phase ribozyme aminoacylation system to reprogram the genetic code. , 2003, Chemistry & biology.

[51]  Y Husimi,et al.  In vitro virus: Bonding of mRNA bearing puromycin at the 3′‐terminal end to the C‐terminal end of its encoded protein on the ribosome in vitro , 1997, FEBS letters.

[52]  H. Suga,et al.  Synthesis of fused tricyclic peptides using a reprogrammed translation system and chemical modification. , 2015, Bioorganic chemistry.

[53]  J. Szostak,et al.  Enzymatic aminoacylation of tRNA with unnatural amino acids. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[54]  H. Murakami,et al.  Diverse backbone-cyclized peptides via codon reprogramming. , 2009, Nature chemical biology.

[55]  Tilmann Weber,et al.  The evolution of genome mining in microbes - a review. , 2016, Natural product reports.

[56]  H. Murakami,et al.  Ribosomal Synthesis of Peptides with C‐Terminal Lactams, Thiolactones, and Alkylamides , 2009, Chembiochem : a European journal of chemical biology.

[57]  H. Murakami,et al.  Reprogramming the translation initiation for the synthesis of physiologically stable cyclic peptides. , 2008, ACS chemical biology.

[58]  H. Murakami,et al.  Reevaluation of the D-amino acid compatibility with the elongation event in translation. , 2013, Journal of the American Chemical Society.

[59]  G. von Heijne,et al.  Apolar surface area determines the efficiency of translocon-mediated membrane-protein integration into the endoplasmic reticulum , 2011, Proceedings of the National Academy of Sciences.

[60]  O. Nureki,et al.  A Macrocyclic Peptide that Serves as a Cocrystallization Ligand and Inhibits the Function of a MATE Family Transporter , 2013, Molecules.

[61]  T. Katoh,et al.  Flexizymes for genetic code reprogramming , 2011, Nature Protocols.

[62]  T. Doi,et al.  Ribosomal Synthesis of Backbone‐Macrocyclic Peptides Containing γ‐Amino Acids , 2011, Chembiochem : a European journal of chemical biology.