Bacterial proteins, target peptides

Steps in bacterial protein synthesis and targets of (1) chloramphenicol (2) macrolides, clindamycin, and type B streptogramins and (3) tetracyclines. The 70S ribosomal mRNA complex is shown with its 50S and 30S subunits. The peptidyl tRNA at the donor site donates the growing peptide chain to the aminoacyl tRNA at the acceptor site in a reaction catalyzed by peptidyl transferase. The tRNA, discharged of its peptide, is released from the donor site to make way for translocation of the newly formed peptidyl tRNA. The acceptor site is then free to be occupied by the next "charged" aminoacyl tRNA. 

Peptide deformylase (PDF), which is not found in mammalian cells, is an essential bacterial met-alloenzyme that has received much attention as one of the targets for developing novel antibiotics (Clements et al., 2001 Hackbarth et al., 2002). Bacterial protein synthesis, unlike cytosolic protein synthesis in mammalian cells, is initiated by A-formylmethionine (Adams and Capecchi, 1966). 

Only two compounds presently in the clinic act on unconventional targets oxazolidinones (which inhibit bacterial protein synthesis initiation by binding the 50S ribosomal subunit) and cationic peptides (which permeabilize bacterial membranes). 

C-terminal peptide a-thioester, mUdly activated peptide ester acting as a valuable key intermediate for the synthesis/semi-synthesis of polypeptides and proteins by both chemical ligation and the Aimoto thioester approach. The synthesis of the peptide a-thioester (—r thioester) can be performed by standard SPPS using Boc- or Fmoc-based chemistry or, for larger target polypeptides, by application of intein-based bacterial expression systems. Peptide a-thioester synthesis can also be carried out based on an N-S acyl shift reaction mediated by a thiol ligation auxiliary [F. B. Perler, E. Adams, Curr. Opin. Biotechnol. 2000, 377 D. Swinnen, D. Hilvert, Org. Lett. 2000, 2, 2439 R. Quaderer, D. Hilvert, Org. Lett. 2001, 3, 3181 T. W. Muir, Annu. Rev. Biochem. 2003, 72, 249 T. Kawakami et al.. Tetrahedron Lett. 2005, 46, 8805 J. A. Camarero, A. R. Mitchell, Prot. Pept. Lett. 2005, 12, 723]. 

Nearly all bacterial proteins are synthesized with a formyl-methionine as the first amino acid, as described above. Yet most proteins isolated from cell culture do not contain an N-terminal fMet or Met residue, indicating that the maturation process involves proteolytic removal of this amino acid. Some proteolytic events release a functional protein from a synthesized precursor, or proprotein. An example is insulin, which is released from its proinsulin precursor by excision of an internal 33-residue peptide. Another type of proteolytic processing is the removal of N-terminal signal peptides, which target some proteins for insertion into membranes or for secretion from the cell. 

Many antibiotics, which inhibit protein synthesis, do not bind to ribosomes but block any of a variety of vital chemical processes needed for growth. Among them are pseudomonic acid, which inhibits isoleucyl-tRNA synthetase from many gram-positive bacteria.1111/VV Rapamycin, best known as an immunosuppressant (Box 9-F), inhibits phosphoinositide-3-kinase and also phosphorylation of the cap-binding protein 4G, a component of the eukaryotic initiation factor complex (Fig. 29-11 ).ww The bacterial enzyme peptide deformylase, which is absent from the human body, has been suggested as a target for design of synthetic antibiotics. 01... 

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