Ribosomal production and in vitro selection of natural product-like peptidomimetics: The FIT and RaPID systems
Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan. Current opinion in chemical biology
(Impact Factor: 6.81).
03/2012; 16(1-2):196-203. DOI: 10.1016/j.cbpa.2012.02.014
Bioactive natural product peptides have diverse architectures such as non-standard sidechains and a macrocyclic backbone bearing modifications. In vitro translation of peptides bearing these features would provide the research community with a diverse collection of natural product peptide-like molecules with a potential for drug development. The ordinary in vitro translation system, however, is not amenable to the incorporation of non-proteinogenic amino acids or genetic encoding of macrocyclic backbones. To circumvent this problem, flexible tRNA-acylation ribozymes (flexizymes) were combined with a custom-made reconstituted translation system to produce the flexible in vitro translation (FIT) system. The FIT system was integrated with mRNA display to devise an in vitro selection technique, referred to as the random non-standard peptide integrated discovery (RaPID) system. It has recently yielded an N-methylated macrocyclic peptide having high affinity (Kd=0.60 nM) for its target protein, E6AP.
Available from: Hiroshi Murakami
- "In 2011, Suga's group published an important study in which highly diverse non-standard peptide libraries containing multiple different nonproteinogenic amino acids were constructed in an mRNA display format, and a novel non-standard peptide was selected from the libraries [5, 123]. Previously, the same group used the flexizyme system to examine the synthesis of various non-standard peptides in a ribosomal translation system  and reported the following findings: (1) an N-chloroacetyl-amino acid residue and cysteine residue on the same peptide were spontaneously reacted in situ using a reconstituted translation system to give a thioether-cyclized peptide without an intermolecular side reaction between the N-terminal chloroacetyl group on the peptide and the sulfhydryl group of the other translation component such as a cysteine monomer and DTT [3, 108, 112, 113, 115, 125]; (2) N-methyl amino acids with an aromatic side chain or noncharged and nonbulky side chains are efficiently incorporated into peptides by the ribosome, and multiple N-methyl amino acids can be incorporated simultaneously into a peptide to give various sequences of thioether-cyclized N-methyl-peptides ; and (3) the translation initiation apparatus accepts D-amino acids with hydrophobic side chain as relatively good initiators, and pre-N-acylation of D-aa-tRNA dramatically increases the efficiency of translation initiation . "
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ABSTRACT: The presence of a nonproteinogenic moiety in a nonstandard peptide often improves the biological properties of the peptide. Non-standard peptide libraries are therefore used to obtain valuable molecules for biological, therapeutic, and diagnostic applications. Highly diverse non-standard peptide libraries can be generated by chemically or enzymatically modifying standard peptide libraries synthesized by the ribosomal machinery, using posttranslational modifications. Alternatively, strategies for encoding non-proteinogenic amino acids into the genetic code have been developed for the direct ribosomal synthesis of non-standard peptide libraries. In the strategies for genetic code expansion, non-proteinogenic amino acids are assigned to the nonsense codons or 4-base codons in order to add these amino acids to the universal genetic code. In contrast, in the strategies for genetic code reprogramming, some proteinogenic amino acids are erased from the genetic code and non-proteinogenic amino acids are reassigned to the blank codons. Here, we discuss the generation of genetically encoded non-standard peptide libraries using these strategies and also review recent applications of these libraries to the selection of functional non-standard peptides.
Available from: Piotr Ruchala
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ABSTRACT: Since the discovery of human immunodeficiency virus (HIV) as a causative agent of acquired immune deficiency syndrome (AIDS) various strategies were employed to counter its devastating actions. One such concept relies on the prevention of HIV entry into host's "competent" cells by means of compounds known as entry inhibitors. HIV entry inhibitors comprise a group of immensely diverse compounds ranging from proteins/antibodies to small organic molecules and capable of targeting various stages of viral entry. Although already in clinical use, this approach to HIV therapy is still being investigated to produce new promising antiviral compounds. Here, we review the latest advances in this area.
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ABSTRACT: Owing to their excellent binding properties, high stability, and low off-target toxicity, polycyclic peptides are an attractive molecule format for the development of therapeutics. Currently, only a handful of polycyclic peptides are used in the clinic; examples include the antibiotic vancomycin, the anticancer drugs actinomycin D and romidepsin, and the analgesic agent ziconotide. All clinically used polycyclic peptide drugs are derived from natural sources, such as soil bacteria in the case of vancomycin, actinomycin D and romidepsin, or the venom of a fish-hunting coil snail in the case of ziconotide. Unfortunately, nature provides peptide macrocyclic ligands for only a small fraction of therapeutic targets. For the generation of ligands of targets of choice, researchers have inserted artificial binding sites into natural polycyclic peptide scaffolds, such as cystine knot proteins, using rational design or directed evolution approaches. More recently, large combinatorial libraries of genetically encoded bicyclic peptides have been generated de novo and screened by phage display. In this Minireview, the properties of existing polycyclic peptide drugs are discussed and related to their interesting molecular architectures. Furthermore, technologies that allow the development of unnatural polycyclic peptide ligands are discussed. Recent application of these technologies has generated promising results, suggesting that polycyclic peptide therapeutics could potentially be developed for a broad range of diseases.
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