Incorporation of modified amino acids into proteins in vivo

Transition Metal-Free N-Arylation of Amino Acid Esters with Diaryliodonium Salts

A transition metal-free approach for the N-arylation of amino acid derivatives has been developed. Key to this method is the use of unsymmetric diaryliodonium salts with anisyl ligands, which proved important to obtain high chemoselectivity and yields. The scope includes the transfer of both electron deficient, electron rich and sterically hindered aryl groups with a variety of different functional groups. Furthermore, a cyclic diaryliodonium salt was successfully employed in the arylation. The N-arylated products were obtained with retained enantiomeric excess.

RNA Display Methods for the Discovery of Bioactive Macrocycles

The past two decades have witnessed the emergence of macrocycles, including macrocyclic peptides, as a promising yet underexploited class of de novo drug candidates. Both rational/computational design and in vitro display systems have contributed tremendously to the development of cyclic peptide binders of either traditional targets such as cell-surface receptors and enzymes or challenging targets such as protein-protein interaction surfaces. mRNA display, a key platform technology for the discovery of cyclic peptide ligands, has become one of the leading strategies that can generate natural-product-like macrocyclic peptide binders with antibody-like affinities. On the basis of the original cell-free transcription/translation system, mRNA display is highly evolvable to realize its full potential by applying genetic reprogramming and chemical/enzymatic modifications. In addition, mRNA display also allows the follow-up hit-to-lead development using high-throughput focused affinity maturation. Finally, mRNA-displayed peptides can be readily engineered to create chemical conjugates based on known small molecules or biologics. This review covers the birth and growth of mRNA display and discusses the above features of mRNA display with success stories and future perspectives and is up to date as of August 2018.

Strategies for cell membrane functionalization

The ability to rationally manipulate and augment the cytoplasmic membrane can be used to overcome many of the challenges faced by conventional cellular therapies and provide innovative opportunities when combined with new biotechnologies. The focus of this review is on emerging strategies used in cell functionalization, highlighting both pioneering approaches and recent developments. These will be discussed within the context of future directions in this rapidly evolving field.

Stereoselective Pd-catalyzed etherification and asymmetric synthesis of furanomycin and its analogues from a chiral aziridine

A chiral aziridine was utilized for the synthesis of the anti-bacterial natural amino acid L-(+)-furanomycin, and its analogues including 5'-epi-furanomycin and norfuranomycin. Key steps of this synthesis are the stereoselective Pd-catalyzed etherification for diallyl ethers and ring closing metathesis.

Room temperature N-arylation of amino acids and peptides using copper(i) and β-diketone

A mild and efficient Cu-catalyzed procedure for the N-arylation of zwitterionic amino acids, amino acid esters and peptides is described.

Cyclobutane amino acid analogues of furanomycin obtained by a formal [2 + 2] cycloaddition strategy promoted by methylaluminoxane

The synthesis and conformational analysis of a new type of conformationally restricted alpha-amino acid analogue of the amino acid antibiotic furanomycin is presented. The restriction involves the cis-fused cyclobutane and tetrahydrofuran units, generating the unusual 2-oxabicyclo[3.2.0]heptane core, which is found in a great number of biologically active natural products. The synthetic strategy is based on a formal [2 + 2] cycloaddition between 2-(acylamino)acrylates as acceptor alkenes and 2,3-dihydrofuran as a donor alkene, promoted by bulky aluminum-derived Lewis acids, particularly by methylaluminoxane (MAO). Additionally, following the same strategy, the synthesis of furanomycin analogues incorporating the 2-oxabicyclo[4.2.0]octane is reported.

Ribosomal synthesis of unnatural peptides

Combinatorial libraries of non-biological polymers and drug-like peptides could in principle be synthesized from unnatural amino acids by exploiting the broad substrate specificity of the ribosome. The ribosomal synthesis of such libraries would allow rare functional molecules to be identified using technologies developed for the in vitro selection of peptides and proteins. Here, we use a reconstituted E. coli translation system to simultaneously re-assign 35 of the 61 sense codons to 12 unnatural amino acid analogues. This reprogrammed genetic code was used to direct the synthesis of a single peptide containing 10 different unnatural amino acids. This system is compatible with mRNA-display, enabling the synthesis of unnatural peptide libraries of 10(14) unique members for the in vitro selection of functional unnatural molecules. We also show that the chemical space sampled by these libraries can be expanded using mutant aminoacyl-tRNA synthetases for the incorporation of additional unnatural amino acids or by the specific posttranslational chemical derivitization of reactive groups with small molecules. This system represents a first step toward a platform for the synthesis by enzymatic tRNA aminoacylation and ribosomal translation of cyclic peptides comprised of unnatural amino acids that are similar to the nonribosomal peptides.

Prolegomena to Future Experimental Efforts on Genetic Code Engineering by Expanding Its Amino Acid Repertoire

Protein synthesis and its relation to the genetic code was for a long time a central issue in biology. Rapid experimental progress throughout the past decade, crowned with the recently elucidated ribosomal structures, provided an almost complete description of this process. In addition important experiments provided solid evidence that the natural protein translation machinery can be reprogrammed to encode genetically a vast number of non-coded (i.e. noncanonical) amino acids. Indeed, in the set of 20 canonical amino acids as prescribed by the universal genetic code, many desirable functionalities, such as halogeno, keto, cyano, azido, nitroso, nitro, and silyl groups, as well as C=C or C[triple bond]C bonds, are absent. The ability to encode genetically such chemical diversity will enable us to reprogram living cells, such as bacteria, to express tailor-made proteins exhibiting functional diversity. Accordingly, genetic code engineering has developed into an exciting emerging research field at the interface of biology, chemistry, and physics.

Breaking the degeneracy of the genetic code

A mutant yeast phenylalanine transfer RNA (ytRNAPheAAA) containing a modified (AAA) anticodon was generated to explore the feasibility of breaking the degeneracy of the genetic code in Escherichia coli. By using an E. coli strain co-transformed with ytRNAPheAAA and a mutant yeast phenylalanyl-tRNA synthetase, we demonstrate efficient replacement of phenylalanine (Phe) by L-3-(2-naphthyl)alanine (Nal) at UUU, but not at UUC codons.

Substitution of the methionine residues of calmodulin with the unnatural amino acid analogs ethionine and norleucine: biochemical and spectroscopic studies

Calmodulin (CaM) is a 148-residue regulatory calcium-binding protein that activates a wide range of target proteins and enzymes. Calcium-saturated CaM has a bilobal structure, and each domain has an exposed hydrophobic surface region where target proteins are bound. These two "active sites" of calmodulin are remarkably rich in Met residues. Here we have biosynthetically substituted (up to 90% incorporation) the unnatural amino acids ethionine (Eth) and norleucine (Nle) for the nine Met residues of CaM. The substituted proteins bind in a calcium-dependent manner to hydrophobic matrices and a synthetic peptide, encompassing the CaM-binding domain of myosin light-chain kinase (MLCK). Infrared and circular dichroism spectroscopy show that there are essentially no changes in the secondary structure of these proteins compared to wild-type CaM (WT-CaM). One- and two-dimensional NMR studies of the Eth-CaM and Nle-CaM proteins reveal that, while the core of the proteins is relatively unaffected by the substitutions, the two hydrophobic interaction surfaces adjust to accommodate the Eth and Nle residues. Enzyme activation studies with MLCK show that Eth-CaM and Nle-CaM activate the enzyme to 90% of its maximal activity, with little changes in dissociation constant. For calcineurin only 50% activation was obtained, and the K(D) for Nle-CaM also increased 3.5-fold compared with WT-CaM. These data show that the "active site" Met residues of CaM play a distinct role in the activation of different target enzymes, in agreement with site-directed mutagenesis studies of the Met residues of CaM.

Expansion of the genetic code: site-directed p-fluoro-phenylalanine incorporation in Escherichia coli

Site-directed incorporation of the amino acid analogue p-fluoro-phenylalanine (p-F-Phe) was achieved in Escherichia coli. A yeast suppressor tRNA(Phe)amber/phenylalanyl-tRNA synthetase pair was expressed in an analogue-resistant E. coli strain to direct analogue incorporation at a programmed amber stop codon in the DHFR marker protein. The programmed position was translated to 64-75% as p-F-Phe and the remainder as phenylalanine and lysine. Depending on the expression conditions, the p-F-Phe incorporation was 11-21-fold higher at the programmed position than the background incorporation at phenylalanine codons, showing high specificity of analogue incorporation. Protein expression yields of 8-12 mg/L of culture, corresponding to about two thirds of the expression level of the wild-type DHFR protein, are sufficient to provide fluorinated proteins suitable for 19F-NMR spectroscopy and other sample-intensive methods. The use of a nonessential "21st" tRNA/synthetase pair will permit incorporation of a wide range of analogues, once the synthetase specificity has been modified accordingly.

Exploiting unassigned codons in Micrococcus luteus for tRNA-based amino acid mutagenesis

An alternative to suppression of stop codons for the biosynthetic insertion of non-natural amino acids has been developed. Micrococcus luteus , a Gram-positive bacterium, is incapable of translating at least two codons. One of these unused codons was inserted in a gene to act as a nonsense site. An aminoacylated tRNA was synthesized which was complementary to this codon. The gene containing the missing codon was expressed in vitro in a M.luteus transcription/translation system. Read-through of the missing codon occurred only when the complementary tRNA was included. The results demonstrate that M.luteus can be used for incorporation of amino acids via synthetically prepared aminoacylated tRNAs. The use of a M. luteus translation system provides a method for incorporation of non-natural amino acids which avoids the use of stop codons.

Engineered cell surfaces: fertile ground for molecular landscaping

The cell surface contains a wealth of information that determines how cells interact with their environment. Methods for directing the cell surface expression of novel protein-based and oligosaccharide-based epitopes are stimulating new directions in biotechnology and biomedical research.

Towards engineering proteins by site-directed incorporation in vivo of non-natural amino acids

Altering protein structure via the techniques of protein engineering has already allowed the development of proteins displaying both modified and novel activities. The only limitation of conventional site-directed mutagenesis, the cornerstone of protein engineering, is that substitutions are restricted to the 20 naturally occurring, proteinogenic amino acids. However, the discovery of a 21st amino acid, selenocysteine, and the development of novel in vitro translation systems have demonstrated that considerably more substitutions are possible. To this end, a number of experimental approaches have been developed that allow the incorporation of synthetic amino acids into proteins. Some of these have already been successfully applied in vitro and efforts to transfer this technology to in vivo systems are now underway.

Antifibrotic effect of a proline analogue delivered in liposomes to cells in culture

Proline analogues inhibit procollagen triple helix formation and are antifibrotic in vivo. Efficacy of the proline analoguecis-4-hydroxy-L-proline (cHyp) on vascular collagen accumulation is improved by in vivo delivery in liposomes. This effect may be due to local release of drug from liposomes taken up by vascular endothelium. To test this postulate, we used a co-culture system to assess the antifibrotic effect of cHyp in liposomes taken up by endothelium (upper well) by measuring inhibition of growth of smooth muscle cells and fibroblasts (lower well). We also studied whether release of cHyp was prolonged in poly(ethyleneglycol) (PEG)-conjugated liposomes compared to liposomes not conjugated with PEG (control liposomes). In fibroblasts, free (unencapsulated) cHyp (1 mg/ml) added to the upper well inhibited growth for 3 days; an equivalent dose of cHyp in control liposomes inhibited growth for 4 days. cHyp in PEG-liposomes produced greater growth inhibition than cHyp in control liposomes. cHyp in liposomes did not inhibit growth of smooth muscle cells more than free cHyp. Washing free cHyp from endothelium after 1 day incubation restored growth of smooth muscle cells whereas washing liposomes containing cHyp failed to restore cell growth. These results suggest that liposomes enhance drug efficacy of cHyp by prolonging the release of drug from endothelium.

Liposome-entrapped antifibrotic agent prevents collagen accumulation in hypertensive pulmonary arteries of rats

We studied the therapeutic efficacy of an intravenously injected antifibrotic agent encapsulated in liposomes on inhibiting collagen accumulation in hypertensive blood vessels. cis-4-Hydroxy-L-proline (cHyp) in liposomes was injected into rats exposed to 10% O2, and drug effect was evaluated by measuring right ventricular pressure and hydroxyproline content of the pulmonary artery. Right ventricular pressure was 11 +/- 1 mm Hg (mean +/- SEM) 5 days after a single intravenous injection of 200 mg/kg cHyp in liposomes compared with 14 +/- 1 mm Hg in rats injected with empty liposomes; hydroxyproline content was also reduced by cHyp treatment (87 +/- 6 versus 107 +/- 7 micrograms per vessel) (p less than 0.05 for both, n = 6-9). Injections of cHyp in liposomes every 5 days partially prevented hypertension and vascular collagen accumulation during a 3-week exposure to hypoxia, and the dose required was one tenth the dose of unencapsulated cHyp. Therapeutic doses of cHyp in liposomes injected for 6 months affected tensile properties of main pulmonary artery and aorta, but there were no apparent histological effects on other organs. Liposomes injected intravenously were identified in pulmonary artery endothelial cells. The prolonged effect of a single injection of cHyp in liposomes may be due to uptake of the liposomes by the endothelium. Liposome delivery of drugs to the arterial wall may be useful in the study and treatment of hypertensive vascular disease.

Investigations on the antiproliferative effects of amino acid antagonists targeting for aminoacyl-tRNA synthetases. Part II--The antileukemic effect

Amino acid antagonists with proven or potential inhibitory activities on aminoacyl-tRNA synthetases were tested for their antiproliferative effect against the murine leukemic cell line P388D1. Micromolar concentrations of the compounds S-tritylcysteine (18), fenitropan and beta-chloroalanine gave strong growth inhibition. In the mouse only 18 was effective against leukemia P388 (T/C = 211%). The inhibitory effect on aminoacyl-tRNA synthetases and the antiproliferative action on P388D1 or P388 could not be correlated.

Investigations on the antiproliferative effects of amino acid antagonists targeting for aminoacyl-tRNA synthetases. Part I--The antibacterial effect

Amino acid antagonists with proven or potentially inhibitory activities on aminoacyl-tRNA synthetases were tested for their antiproliferative effect against E. coli B. The compounds 4- and 6-fluoro-tryptophan, 5-methyltryptophan, selenocystine and beta-(2-thienyl)alanine gave strong growth inhibition in minimal medium, which disappeared after addition of structurally related natural amino acids or in an enriched broth. The inhibitory effect on amino-acyl-tRNA synthetases and the minimal inhibitory concentration for growth inhibition in minimal medium could not be correlated.

Biosynthesis of a protein containing a nonprotein amino acid by Escherichia coli: L-2-aminohexanoic acid at position 21 in human epidermal growth factor

Endeavoring to develop a method to biosynthesize proteins substituted with nonprotein amino acids, we attempted the incorporation of L-2-aminohexanoic acid (Ahx) into human epidermal growth factor (hEGF). Escherichia coli YK537 strain harboring plasmid pTA1522, which has the phoA promoter-phoA signal peptide-hEGF gene, was used. Cells were cultured first in high-phosphate medium and then, for induction of the hEGF-encoding gene, transferred to low-phosphate medium containing Ahx (0.25 mg/ml). hEGF and Ahx-substituted hEGF, [Ahx21]hEGF, secreted into the periplasm were recovered. After treatment with H2O2, [Ahx21]-hEGF was clearly separated from methionine-oxidized hEGF by one-step reverse-phase HPLC. Substitution of the methionine residue of hEGF with Ahx was confirmed by the amino acid analysis of [Ahx21]hEGF. The three biological activities of [Ahx21]hEGF were the same as those of hEGF. From the successful production of [Ahx21]hEGF, a basic strategy was established for preparing proteins substituted with nonprotein amino acid (alloprotein). Induction of the phoA promoter of pho regulon and secretion of the product to the periplasm may depress heat shock-like responses and subsequent hydrolysis of the product by cytoplasmic protease.