cDNA display: rapid stabilization of mRNA display

The cDNA display method is a robust in vitro display technology that converts an unstable mRNA-protein fusion (mRNA display) to a stable mRNA/cDNA-protein fusion (cDNA display) whose cDNA is covalently linked to its encoded protein using a well-designed puromycin linker. We provide technical details for preparing cDNA display molecules and for the synthesis of the puromycin linker for the purpose of screening the functional proteins and peptides.

Time-resolved binding of azithromycin to Escherichia coli ribosomes

Azithromycin is a semisynthetic derivative of erythromycin that inhibits bacterial protein synthesis by binding within the peptide exit tunnel of the 50S ribosomal subunit. Nevertheless, there is still debate over what localization is primarily responsible for azithromycin binding and as to how many molecules of the drug actually bind per ribosome. In the present study, kinetic methods and footprinting analysis are coupled together to provide time-resolved details of the azithromycin binding process. It is shown that azithromycin binds to Escherichia coli ribosomes in a two-step process: The first-step involves recognition of azithromycin by the ribosomal machinery and places the drug in a low-affinity site located in the upper part of the exit tunnel. The second step corresponds to the slow formation of a final complex that is both much tighter and more potent in hindering the progression of the nascent peptide through the exit tunnel. Substitution of uracil by cytosine at nucleoside 2609 of 23S rRNA, a base implicated in the high-affinity site, facilitates the shift of azithromycin to this site. In contrast, mutation U754A hardly affects the binding process. Binding of azithromycin to both sites is hindered by high concentrations of Mg(2+) ions. Unlike Mg(2+) ions, polyamines do not significantly affect drug binding to the low-affinity site but attenuate the formation of the final complex. The low- and high-affinity sites of azithromycin binding are mutually exclusive, which means that one molecule of the drug binds per E. coli ribosome at a time. In contrast, kinetic and binding data indicate that in Deinococcus radiodurans, two molecules of azithromycin bind cooperatively to the ribosome. This finding confirms previous crystallographic results and supports the notion that species-specific structural differences may primarily account for the apparent discrepancies between the antibiotic binding modes obtained for different organisms.

Total syntheses of a North methanocarba puromycin analog and its dinucleotide derivative

North methanocarba Puromycin analog 5 and its di-nucleotide derivative 6 were synthesized from D-ribose in respectively 18 and 19 steps, in order to be tested for peptidyl transfer efficiency in ribosomes.

Total synthesis of a xylo-Puromycin analog

N(6)-bis-demethylated xylo-Puromycin analog 2 was synthesized in 56% over 6 steps from adenosine 3, involving a Mattocks bromo acetylation, a regio- and stereo-selective ribo-epoxide ring opening with sodium azide and an efficient Staudinger-Vilarrasa coupling reaction for which the conditions have been optimized.

First Synthesis of 2′-Deoxyfluoropuromycin Analogues: Experimental Insight into the Mechanism of the Staudinger Reaction

The N(6),N(6)-dedimethyl-2'-deoxyfluoro analogue of puromycin (= 3'-deoxy-N(6),N(6)-dimethyl-3'-[O-methyltyrosylamido]adenosine), its 2',3'-regioisomer and a 3'-cytidyl-5'-(2'-deoxyfluoro)puromycyl dinucleotide analogue were synthesized following an approach involving i) the diastereospecific nitrite-assisted formation of a lyxo nucleosidic 2',3'-epoxide from an adenosine-2',3'-ditriflate derivative in a biphasic solvent mixture; ii) the regio- and stereoselective epoxide ring opening with sodium azide under mildly acidic aqueous conditions, iii) the stereospecific introduction of the fluor atom using DAST and iv) the reaction between the nucleosidyl or dinucleotidyl azide and an active ester of the N-protected amino acid using highly efficient solution conditions for the Staudinger-Vilarrasa coupling, to obtain the corresponding carboxamide directly from the in situ formed iminophosphorane. This coupling reaction furnished sterically quite demanding amides in 94 % isolated yields under very mild conditions and should therefore be of a more general value. Under certain reaction conditions we isolated (amino)acyltriazene derivatives from which dinitrogen was not eliminated. These secondary products are trapped and stabilized witnesses of the first intermediate of the Staudinger reaction, the phosphatriazenes (phosphazides, triazaphosphadienes) which usually eliminate dinitrogen in situ and rapidly rearrange into iminophosphoranes, unless they are derived from conjugated or sterically bulky azides and phosphines. The acyltriazenes could either be thermally decomposed or converted to the corresponding N-alkyl carboxamides through proton-assisted elimination of dinitrogen. All compounds were carefully characterized through MS spectrometry, (1)H, (19)F, (31)P and (13)C NMR spectroscopy.

A simple and efficient synthesis of puromycin, 2,2'-anhydro-pyrimidine nucleosides, cytidines and 2',3'-anhydroadenosine from 3',5'-O-sulfinyl xylo-nucleosides

Synthesis of antibiotics, puromycin and 3'-amino-3'-deoxy-N6,N6-dimethyladenosine 11 was achieved by utilizing the cyclic sulfite 6a of the xylo-3',5'-dihydroxy group as a new protective group. The key synthetic step is the deprotection of the sulfite moiety through the intramolecular cyclization of 2-alpha-carbamate 7. In a similar manner 2,2'-anhydro-pyrimidine nucleosides 15, ribo-cytidines 17 and 2',3'-anhydroadenosine 14 were prepared in high yields from the corresponding sulfites 4, 5, and 6b, respectively.

Uncovering the Enzymatic pKa of the Ribosomal Peptidyl Transferase Reaction Utilizing a Fluorinated Puromycin Derivative

The ribosome-catalyzed peptidyl transferase reaction displays a complex pH profile resulting from two functional groups whose deprotonation is important for the reaction, one within the A-site substrate and a second unidentified group thought to reside in the rRNA peptidyl transferase center. Here we report the synthesis and activity of the beta,beta-difluorophenylalanyl derivative of puromycin, an A-site substrate. The fluorine atoms reduce the pK(a) of the nucleophilic alpha-amino group (<5.0) such that it is deprotonated at all pHs amenable to ribosomal analysis (pH 5.2-9.5). In the 50S modified fragment assay, this substrate reacts substantially faster than puromycin at neutral or acidic pH. The reaction follows a simplified pH profile that is dependent only upon deprotonation of a titratable group within the ribosomal active site. This feature will simplify characterization of the peptidyl transferase reaction mechanism. On the basis of the reaction efficiency of the doubly fluorinated substrate compared to the unfluorinated derivative, the Bronsted coefficient for the nucleophile is estimated to be substantially smaller than that reported for uncatalyzed aminolysis reactions, which has important mechanistic implications for the peptidyl transferase reaction.

A practical route to 3'-amino-3'-deoxyadenosine derivatives and puromycin analogues

3'-aminoacylamino-3'-deoxyadenosines, analogues of the antibiotic puromycin, have been synthesized from adenosine. They key 3'-azido derivative 10 was obtained through a 3'-oxidation/reduction/substitution procedure. A modified purification protocol on a larger scale was developed for the oxidation step using the Garegg reagent. The coupling reaction between an Fmoc-l-amino acid and the fully protected form of 3'-amino-3'-deoxyadenosine 11 furnished the aminoacylated compounds 12 in high yields. The puromycin analogues were obtained in 10 steps and up to 23% (14c) overall yield.

Synthesis of a conformationally locked version of puromycin amino nucleoside

[reaction: see text] A conformationally locked carbocyclic version of puromycin amino nucleoside was synthesized via Mitsunobu coupling of a 3-azido-substituted carbocyclic moiety with 6-chloropurine without interference from the azido group reacting with triphenylphosphine. The requisite 3-azido-substituted carbocyclic pseudosugar was prepared by a double inversion of configuration at C3' (nucleoside numbering) involving a nucleophilic displacement with azide.

Syntheses of puromycin from adenosine and 7-deazapuromycin from tubercidin, and biological comparisons of the 7-aza/deaza pair

Protection (O5') of 2',3'-anhydroadenosine with tert-butyldiphenylsilyl chloride and epoxide opening with dimethylboron bromide gave the 3'-bromo-3'-deoxy xylo isomer which was treated with benzylisocyanate to give the 2'-O-(N-benzylcarbamoyl) derivative. Ring closure gave the oxazolidinone, and successive deprotection concluded an efficient route to 3'-amino-3'-deoxyadenosine. Analogous treatment of the antibiotic tubercidin [7-deazaadenosine; 4-amino-7-(beta-D-ribofuranosyl)pyrrolo[2,3-d]pyrimidine] gave 3'-amino-3'-deoxytubercidin. Trifluoroacetylation of the 3'-amino function, elaboration of the heterocyclic amino group into a (1,2,4-triazol-4-yl) ring with N,N'-bis[(dimethylamino)methylene]hydrazine, and nucleophilic aromatic substitution with dimethylamine gave puromycin aminonucleoside [9-(3-amino-3-deoxy-beta-D-ribofuranosyl)-6-(dimethylamino)purine] and its 7-deaza analogue. Aminoacylation [BOC-(4-methoxy-L-phenylalanine)] and deprotection gave puromycin and 7-deazapuromycin. Most reactions gave high yields at or below ambient temperature. Equivalent inhibition of protein biosynthesis in a rabbit reticulocyte system and parallel growth inhibition of several bacteria were observed with the 7-aza/deaza pair. Replacement of N7 in the purine ring of puromycin by "CH" has no apparent effect on biological activity.

Ribosome-catalyzed peptide-bond formation with an A-site substrate covalently linked to 23S ribosomal RNA

In the ribosome, the aminoacyl-transfer RNA (tRNA) analog 4-thio-dT-p-C-p-puromycin crosslinks photochemically with G2553 of 23S ribosomal RNA (rRNA). This covalently linked substrate reacts with a peptidyl-tRNA analog to form a peptide bond in a peptidyl transferase-catalyzed reaction. This result places the conserved 2555 loop of 23S rRNA at the peptidyl transferase A site and suggests that peptide bond formation can occur uncoupled from movement of the A-site tRNA. Crosslink formation depends on occupancy of the P site by a tRNA carrying an intact CCA acceptor end, indicating that peptidyl-tRNA, directly or indirectly, helps to create the peptidyl transferase A site.

Synthesis of N-acetylglucosaminyl asparagine-substituted puromycin analogues

As part of our project aimed to introduce specifically glycosylated amino acids into proteins, new glycosylated puromycin analogues were chemically synthesized. Introduction of a free N-acetylglucosaminyl asparaginyl side chain abolished the activity of puromycin completely, but when the sugar OH groups were rendered increasingly hydrophobic by acetylation or benzylation, up to 8% of the activity was recovered. The results of our preliminary inhibition tests suggest that the interaction of puromycin analogues and therefore also of glycosylated aminoacyl tRNA, with the ribosomal A site increase with hydrophobicity of the modifying protecting groups.

Synthesis, antiviral, antibacterial and antitumor cell activities of 2'-deoxy-2'-fluoropuromycin

A procedure for the synthesis of 2'-deoxy-2'-fluoropuromycin (1b) was developed. Ring opening of the lyxo-epoxide (4) or nucleophilic displacement of the 3'-O-mesylate (5) by an azide ion afforded two azido nucleosides, 6a and 7a. The major product (7a) was reacted with diethylaminosulfur trifluoride (DAST) to give the 2'-fluoronucleoside (8), which was converted to the 3'-aminonucleoside (9) by hydrogenation. Compound 9 was condensed with an amino acid by the conventional method and subsequently deprotected by acid to give 1b. Compounds 1b, 6b and 7b exhibited no selective antiviral activity against several DNA and RNA viruses. Compound 1b had weak antibacterial activity (minimum inhibitory concentration approximately 25-50 micrograms/ml) and was cytotoxic to several tumor cell lines (L1210, Molt 4, CEM) at a concentration of about 5 microM. This antitumor cell activity may be attributed to inhibition of protein biosynthesis.

Hybrids of antibiotics inhibiting protein synthesis. Synthesis and biological activity

Four hybrid antibiotics combining structural features of chloramphenicol (1a), sparsomycin (2b), lincomycin (5c), and puromycin (6d)--lincophenicol (1c), chloramlincomycin (5a), sparsolincomycin (5b), and sparsopuromycin (6b)--were synthesized. They were investigated as inhibitors of several partial reactions of procaryotic and eucaryotic protein synthesis as well as potential antimicrobial agents. Lincophenicol (1c) was active as inhibitor of Escherichia coli ribosomal peptidyltransferase-catalyzed puromycin reaction. Both lincophenicol (1c) and sparsophenicol (1b) inhibited the binding of the iodophenol analogue of sparsomycin to E. coli ribosomes. The results are discussed in terms of a retro-inverso hypothesis advanced earlier for interpretation of biological activity of chloramphenicol (1a) and sparsophenicol (1b). Chloramlincomycin (5a) suppressed the growth of Streptococcus pyogenes with MIC 6.25 micrograms/mL.

Synthesis and antimicrobial activity of 2'-deoxypuromycin

2'-Deoxypuromycin (2) was synthesized to learn the effect of the 2'-hydroxyl group on the biological activity. Acylated xylose 3 was condensed with silylated 6-chloropurine to give beta-D-xylofuranosyl-6-chloropurine derivative 4, whose 6-dimethylamination, 2'-deoxygenation and deprotection afforded 2'-deoxy-beta-D-xylofuranosyl purine analog 7. The latter was converted to 2'-deoxypuromycin (2) in 8 steps. 2'-Deoxy analog 2 showed only weak antimicrobial activity compared with that of puromycin (1).

Carbocyclic puromycin: synthesis and inhibition of protein biosynthesis

The carbocyclic analogue of puromycin was prepared by the coupling of N-(benzyloxycarbonyl)-p-methoxy-L-phenylalanine to the racemic aminonucleoside (+/-)-9-[3 beta-amino-2 beta-hydroxy-4 alpha-(hydroxymethyl)cyclopent-1 alpha-yl]-6-(dimethylamino)purine, followed by separation of the diastereomers and subsequent removal of the Cbz blocking group. Kinetic studies indicate that carbocyclic puromycin is an excellent substrate for the peptidyltransferase reaction with both prokaryotic and eukaryotic ribosomes. A comparison of carbocyclic puromycin with previously synthesized analogues indicate that the furanosyl ring oxygen and the hydroxymethyl group of puromycin do not contribute to ribosomal binding, but both moieties contribute to the rate of product formation from the enzyme-substrate complex. Carbocyclic puromycin was equal to puromycin when evaluated for cytotoxicity using P-388 mouse lymphoid leukemia cells in culture.

Purine acyclic nucleosides. 6-Dimethylamino-9-[(2-phenylalanylamido-1-substituted- ethoxy)methyl]purines as candidate antivirals

Several acyclic puromycin analogues containing hydrocarbon substituents on the 1'-position of the aminoethoxymethyl moiety were synthesized and tested for antiviral activity. The N-carbobenzoxy intermediate 7c was active in vitro against Mengo and Semliki Forest viruses.

5'Chloropuromycin. Inhibition of protein synthesis and antitrypanosomal activity

A facile, two-step conversion of puromycin aminonucleoside (PAN) into 5'-deoxy-PAN (5) via 5'-chloro-5'-deoxy-PAN (1) was accomplished. Replacement of the 5'-OH group of PAN with H or Cl resulted in the elimination of kidney toxicity associated with the administration of PAN. The corresponding puromycin derivatives, 5'-chloro-5'-deoxypuromycin (4) and 5'-deoxypuromycin (6), derived from 1 and 5, respectively, were compared in a ribosomal peptidyltransferase assay. Both compounds were excellent substrates for the transpeptidation reaction, confirming our previous observations with 6 that the 5'-OH of puromycin is not essential for activity at the ribosomal level. Thus, 4 represents a new puromycin derivative that retains puromycin-like activity at the ribosomal site but is capable of releasing only a nonnephrotoxic aminonucleoside upon enzymatic release of the p-methoxyphenylalanyl side chain. The chloro derivative 4 exhibited significant antitrypanosomal activity in mice infected with Trypanosoma rhodesiense. The 5'-deoxy derivative 6 was inactive against trypanosomes.

Puromycin analogues. Effect of aryl-substituted puromycin analogues on the ribosomal peptidyltransferase reaction

A series of ortho- and para-substituted L-phenylalanylpuromycin analogues were synthesized and evaluated as substrates for the peptidyltransferase reaction of Escherichia coli ribosomes. Kinetic results reveal that substitution of the p-methoxy group of the puromycin molecule alters the peptidyltransferase activity of the molecule with the following decreasing order of substrate efficiencies: p-NH2 greater than p-NHCOCH3 greater than p-NO2 = p-NHCO(CH2)2CH3 greater than p-NHCOCH2Br. However, the inability of the ribosome to tolerate a nitro group at the ortho position of the phenylalanine ring precluded the use of the photosensitive puromycin analogue, 2-nitro-4-azidophenylalanylpuromycin aminonucleoside (7a), as a photoaffinity label for the peptidyltransferase site.

Peptidyl transferase substrate specificity with nonaromatic aminoacyl analogues of puromycin

A series of puromycin analogues, 3'-N-(S-substituted L-cysteinyl) puromycin aminonuleosides, has been prepared and examined as substrates for ribosomal peptidyl transferase. S-Substituted N-tert-butyloxycarbonyl-L-cysteines were coupled with puromycin aminonucleoside using dicyclohexylcarbodiimide and N-hydroxysuccinimide. Removal of the t-Boc blocking group with anhydrous trifluoroacetic acid gave the desired puromycin analogues. Kinetic studies indicate that the nonaromatic aminoacyl analogues of puromycin are effective substrates for the peptidyl transferase reaction. In addition, the discovery of the existence of hydrophilic character beyond the region normally occupied by hydrophobic amino acid R groups of the aminoacyladenyl termini of tRNA molecules, and the proper exploitation of this information, has provided the first active purmoycin analogue possessing a hydrophilic amino acid.

The synthesis of a photoreactive puromycin analogue and its application for labeling proteins in the 50-S subunit of Escherichia coli ribosomes

A photoreactive puromycin analogue, 6-dimethylamino-9-[3-(p-azido-L-beta-phenylalanylamino)-3-deoxy-beta-ribofuranosyl] purine, was synthesized. Biological activity was demonstrated by inhibition of the poly (U)-directed phenylalanine-incorporation system and by decomposition of isolated polysomes from Escherichia coli. The 3H-labeled puromycin analogue was covalently attached to the 50-S subunit of isolated 70-S ribosomes from Escherichia coli after irradiation. More than 90% of the radioactivity was bound to the protein fraction. The 70-S proteins were separated by two-dimensional gel electrophoresis. The proteins labeled primarily were those of the 50-S subunit, identified as L6, L13, L18, L22 and L25. On the basis of the affinity label used and supportive data from the literature, it is concluded that these proteins are at the active center of the 50-S particle and probably belong to the region of the ribosomal A site.

Synthesis of cyclohexylpuromycin and its reaction with N-acetylphenylalanyl-transfer ribonucleic acid on rat liver ribosomes

1. Cyclohexylpuromycin, an anlogue of puromycin in which a cyclohexane ring replaces the aromatic benzene ring of the L-phenylalanyl moeity of the nucleoside., has been synthesized and examined for its ability to release N-acetylphenylalanine from tRNA attached to rat liver ribosomes. 2.dl-Cyclohexylpuromycin was active in reacting with N-[3H]acetylphenylalanyl-tRNA on rat liver ribosomes to form N-E13H]lacetylphenylalanycyclohexypuromycin. 3. The reaction product N-acetylphenylalanylcyclohexylpuromycin and the corresponding analogue N-acetylphenylalanylpuromycin were chemically synthesized for evaluation of the structure of the released N-acetylphenylalanyl-containing material. 4. The results obtained suggest that the model of Raacke (1971) for purmycin reactivity needs further examination with regard to the role played by the aromatic ring system of the Lphenylalanyl moiety of the nucleoside

Substrates for ribosomal peptidyl transferase: synthesis of 3'-N-aminoacyl and 5'-O-nucleotidyl analogues of puromycin

The chemical synthesis, on a 10–30 μmol scale, of two series of puromycin analogues is described: the first is the type 3′-N-aminoacyl-puromycin aminonucleoside (e.g. 3′-N-glycyl-PANS or PANS-Gly) in which the O-methyl-L-tyrosyl residue of puromycin is replaced by various aminoacyl residues, and the second is the type NpPANS-Gly in which the 5′-hydroxyl of PANS-Gly is substituted with phosphate, 3′-AMP, 3′-CMP, 3′-GMP, or 3′-UMP. The 3′-N-aminoacyl-PANS derivatives were synthesized either by coupling N-protected amino acids via their N-hydroxysuccinimide esters to PANS in 70% aqueous pyridine or by direct coupling in ethanol or methanol of N-protected amino acids to PANS using N-ethoxycarbonyl-2-ethoxy-1,2-dihydroquinoline (EEDQ) as condensing agent After removal of the protecting groups, reaction mixtures were purified by preparative thin-layer chromatography on silicic acid, paper chromatography, and paper electrophoresis to give the 3′-N-aminoacyl-PANS derivatives in yields of 40–80%.The 5′-O-nucleotidyl derivatives of PANS-Gly were synthesized by three methods: (i) by the coupling of fully acetylated 3′-mononucleotides to 3′-N-(Boc-glycyl)-PANS, (ii) by the coupling of N4-acetyl-2′,5′-di-O-tetrahydropyranylcytidine or N2,O2′,O5′-tritetrahydropyranylguanosine to 5′-O-phosphoryl-(Boc-glycyl)-PANS, and (iii) by the coupling of N4-acetyl-2′,5′-di-O-tetrahydropyranyl-3′-CMP or N2,O2′,O5′-tritetrahydropyranyl-3′-GMP to 3′-N-Boc-PANS or 3′-N-trifluoroacetyl-PANS followed by aminoacylation of the CpPANS or GpPANS produced with Boc-glycine and EEDQ. Coupling reactions were carried out using either N,N′-dicyclohexylcarbodiimide or 2,4,6-triisopropylbenzenesulfonyl chloride as condensing agents in anhydrous pyridine. After removal of protecting groups, reaction mixtures were purified by paper chromatography and paper electrophoresis to give the NpPANS-Gly derivatives in 3–30% yield.