Portage of various compounds into bacteria by attachment to glycine residues in peptides

Rational design of a bacterial import system for new-to-nature molecules

Integration of novel compounds into biological processes holds significant potential for modifying or expanding existing cellular functions. However, the cellular uptake of these compounds is often hindered by selectively permeable membranes. We present a novel bacterial transport system that has been rationally designed to address this challenge. Our approach utilizes a highly promiscuous sulfonate membrane transporter, which allows the passage of cargo molecules attached as amides to a sulfobutanoate transport vector molecule into the cytoplasm of the cell. These cargoes can then be unloaded from the sulfobutanoyl amides using an engineered variant of the enzyme γ-glutamyl transferase, which hydrolyzes the amide bond and releases the cargo molecule within the cell. Here, we provide evidence for the broad substrate specificity of both components of the system by evaluating a panel of structurally diverse sulfobutanoyl amides. Furthermore, we successfully implement the synthetic uptake system in vivo and showcase its functionality by importing an impermeant non-canonical amino acid.

Iron-catalyzed C–O bond functionalization of butyrolactam derivatives with various N-/C-nucleophiles

An iron-catalyzed C–O bond functionalization of butyrolactam derivatives with N-/C-nucleophiles to enable the synthesis of butyrolactam derivatives has been developed.

Peptide-Cleavable Self-immolative Maytansinoid Antibody-Drug Conjugates Designed To Provide Improved Bystander Killing

A new type of antibody–drug conjugate (ADC) has been prepared that contains a sulfur-bearing maytansinoid attached to an antibody via a highly stable tripeptide linker. Once internalized by cells, proteases in catabolic vesicles cleave the peptide of the ADC’s linker causing self-immolation that releases a thiol-bearing metabolite, which is then S-methylated. Conjugates were prepared with peptide linkers containing only alanyl residues, which were all l isomers or had a single d residue in one of the three positions. A d-alanyl residue in the linker did not significantly impair a conjugate’s cytotoxicity or bystander killing unless it was directly attached to the immolative moiety. Increasing the number of methylene units in the maytansinoid side chain of a conjugate did not typically affect an ADC’s cytotoxicity to targeted cells but did increase bystander killing activity. ADCs with the highest in vitro bystander killing were then evaluated in vivo in mice, where they displayed improved efficacy compared to previously described types of maytansinoid conjugates.

Mutant Variants of the Substrate-Binding Protein DppA from Escherichia coli Enhance Growth on Nonstandard γ-Glutamyl Amide-Containing Peptides

The import of nonnatural molecules is a recurring problem in fundamental and applied aspects of microbiology. The dipeptide permease (Dpp) of Escherichia coli is an ABC-type multicomponent transporter system located in the cytoplasmic membrane, which is capable of transporting a wide range of di- and tripeptides with structurally and chemically diverse amino acid side chains into the cell. Given this low degree of specificity, Dpp was previously used as an entry gate to deliver natural and nonnatural cargo molecules into the cell by attaching them to amino acid side chains of peptides, in particular, the γ-carboxyl group of glutamate residues. However, the binding affinity of the substrate-binding protein dipeptide permease A (DppA), which is responsible for the initial binding of peptides in the periplasmic space, is significantly higher for peptides consisting of standard amino acids than for peptides containing side-chain modifications. Here, we used adaptive laboratory evolution to identify strains that utilize dipeptides containing γ-substituted glutamate residues more efficiently and linked this phenotype to different mutations in DppA. In vitro characterization of these mutants by thermal denaturation midpoint shift assays and isothermal titration calorimetry revealed significantly higher binding affinities of these variants toward peptides containing γ-glutamyl amides, presumably resulting in improved uptake and therefore faster growth in media supplemented with these nonstandard peptides.IMPORTANCE Fundamental and synthetic biology frequently suffer from insufficient delivery of unnatural building blocks or substrates for metabolic pathways into bacterial cells. The use of peptide-based transport vectors represents an established strategy to enable the uptake of such molecules as a cargo. We expand the scope of peptide-based uptake and characterize in detail the obtained DppA mutant variants. Furthermore, we highlight the potential of adaptive laboratory evolution to identify beneficial insertion mutations that are unlikely to be identified with existing directed evolution strategies.

Photoredox Approach to N-Acyl-N'-aryl-N,N'-aminals Using Enamides and Their Conversion to γ-Lactams

A photoredox catalytic approach to synthetically valuable N-acyl-N'-aryl-N,N'-aminals is described. This method uses the addition of a radical precursor to enamides, with subsequent interception of the cationic iminium intermediate with an arylamine. The reaction has been shown to be compatible with electron-rich and electron-deficient arylamines, and moderate to good levels of diastereoselectivity can be attained using a chiral enamide. Furthermore, the N-acyl-N'-aryl-N,N'-aminal reaction products can be readily cyclized, providing a novel synthetic route to valuable γ-lactams.

Syntheses of 5'-Nucleoside Monophosphate Derivatives with Unique Aminal, Hemiaminal, and Hemithioaminal Functionalities: A New Class of 5'-Peptidyl Nucleotides

A number of synthetically useful transformations have been developed to generate novel 5'-peptidyl nucleoside monophosphate analogues that incorporate sensitive phosphoaminal, -hemiaminal or -hemithioaminal functionalities. The strategies adopted entailed the coupling between dipeptides, which enclose a reactive Cα-functionalized glycine residue and phosphate or phosphorothioate moieties. These developments led to potentially powerful and general methodologies for the preparation of α-phosphorylated pseudopeptides as well as nucleoside monophosphate mimics. The resulting conjugates are of interest for a variety of important applications, which range from drug development to synthetic biology, as pronucleotides or artificial building blocks for the enzymatic synthesis of xenobiotic information systems. The potential of all dipeptide-TMP conjugates as pyrophosphate mimics in the DNA polymerization reaction was tested, and the influence of the nature of the linker was evaluated by in vitro chain elongation assay in the presence of wild-type microbial DNA polymerases.

Identification of (S,S)-γ-glutamyl-(cis-S-1-propenyl)thioglycine, a naturally occurring norcysteine derivative, from the Chinese vegetable Toona sinensis

Extracts of Toona sinensis shoots were studied to identify the precursors of volatile sulfur-containing flavor molecules. T. sinensis was found to contain new compounds (S,S)-γ-glutamyl-(cis-S-1-propenyl)thioglycine, 1, (S,S)-γ-glutamyl-(trans-S-1-propenyl)thioglycine, 2, and γ-glutamyl-(cis-S-1-propenyl)-cysteine, 3. The structures of these compounds were determined by interpretation of multistage mass spectrometric (MS(n)), 1D, and 2D NMR data. The absolute configuration of 1 was established by comparison of experimental with computed infrared and vibrational circular dichroism spectra. Because of the flexibility of the molecule and the novelty of the structure, the configuration was further confirmed by X-ray crystallography. Compounds 1 and 2 are the first examples of norcysteine-containing metabolites reported from nature. They may release thiols via cleavage of the amide bond by proteases, followed by spontaneous decomposition of the resulting unstable alk(en)yl norcysteine moiety.

Spectrophotometric determination of peptide transport with chromogenic peptide mimetics

A spectrophotometric assay to determine peptide transport has been developed. Using two chromogenic peptide mimetics, L-phenylalanyl-L-2-sulfanilylglycine (PSG) and L-phenylalanyl-L-3-thiaphenylalanine (PSP), the peptide transport patterns in individual cell species can be evaluated effectively. After the addition of PSG to a HeLa cell suspension, sulfanilic acid accumulated progressively inside, but not outside, the cells, demonstrating that PSG was transported wholly intact. The addition of PSP to the same cell suspension was followed immediately by extracellular thiophenol production. Measurement of the rate of thiophenol release thereby provided direct determination of PSP transport. The thiophenol release was consistent with Michaelis-Menten kinetics, with a K(m) of 0.016 mM and a V(max) of 5.07 nmol/min (1 x 10(6) cells/ml, pH 7.4, 37 degrees C). The resulting kinetic constants estimated were in agreement with values determined by single-substrate enzyme kinetics. Using PSP, transport kinetics of various dipeptides was examined by competitive spectrophotometry. As a result, dipeptides tested could be ranked in order of kinetic power for their transport.

Structure-activity relationship studies of gonadotropin-releasing hormone antagonists containing S-aryl/alkyl norcysteines and their oxidized derivatives

A series of acyline analogues incorporating l- and d-isomers of S-arylated/alkylated norcysteines [Ncy(R), where R is 2-naphthyl, methyl, and isopropyl] at positions 1, 4, 7, and 10 were synthesized. Some of these analogues were mono- and dioxidized to sulfoxides and sulfones. All of the analogues of acyline were screened for the antagonism of the GnRH-induced response in a reporter gene assay in HEK-293 cells expressing the human GnRH receptor. Nine of the analogues (9, 11, 15, 16, 17, 19, 20, 21, and 22) had antagonistic potency (IC50 < 2 nM) similar to that of acyline (IC50 = 0.52 nM) in this assay. Selected analogues (9, 11, 15, 16, 19, and 21) were tested in vitro for their antagonism at the rat GnRH-R in a reporter gene assay as well as in an in vivo intact male rat assay. Analogues 9 and 15 were the most potent in suppressing testosterone levels.

Synthesis and evaluation of a mechanism-based inhibitor of KDO8P synthase

The enzyme 3-deoxy-D-manno-2-octulosonate-8-phosphate (KDO8P) synthase catalyzes the condensation reaction between phosphoenolpyruvate (PEP) and D-arabinose 5-phosphate (A5P) to produce KDO8P and inorganic phosphate. In attempts to investigate the lack of antibacterial activity of the most potent inhibitor of KDO8P synthase, the amino phosphonophosphate 3, we have synthesized its hydrolytically stable isosteric phosphonate analogue 4 and tested it as an inhibitor of the enzyme. The synthesis of 4 was accomplished in a one step procedure by employing the direct reductive amination in aqueous media between unprotected sugar phosphonate and glyphosate. The analogue 4 proved to be a competitive inhibitor of KDO8P synthase with respect to both substrates A5P and PEP binding. In vitro antibacterial tests against a series of different Gram-negative organisms establish that both inhibitors (3 and 4) lack antibacterial activity probably due to their reduced ability to penetrate the bacterial cell membrane.

New beta-strand macrocyclic peptidomimetic analogues containing alpha-(O-, S- or NH-)aryl substituted glycine residues: synthesis, chemical and enzymatic properties

In so much as bis-macrocyclic peptidomimetics have been recognized as high affinity substrates for HIV-1 protease, we were interested in the design and synthesis of new bis-macrocyclic bioisosteric analogues whose general structure is displayed on Fig. 2. The structures of these new analogues are characterized by the specific replacement of the methylene of the benzyl group directly attached to the N-acyl glycine residue in the original molecule 1, by its main bioisosteres, i.e. O-, S- and NH-aryl groups. Knowing that an intermediate in which an heteroatomic aryl group is directly linked to a free amine glycine residue is not stable, we developed an original synthetic pathway which involved the coupling of a specific side chain to the exocyclic carboxylic acid function, followed by an elegant oxidation-nucleophilic substitution Steglich-type reaction. Analogues 2a-d were then submitted to chemical and enzymatic hydrolysis. We demonstrated that, as expected, the specific cleavage of the exocyclic N-acyl bond led to the release of aryl moieties (phenol, thiophenol and aniline species). These chemical and enzymatic stability studies brought to light the biological potential of such macrocyclic analogues in infected cells.

Use of proline bioisosteres in potential HIV protease inhibitors: phenylalanine-2-thiophenoxy-3-pyrrolidinone: synthesis and anti-HIV evaluation

The synthesis of new phenylalanine-2-thiophenoxy-3-pyrrolidinones is described. Anti-HIV recombinant protease assays and HIV infected cell culture assays (observation of syncytia) demonstrated the potent anti-HIV activity of this new class of pseudopeptides.

Polymeric prodrugs of antibiotics with improved efficiency

Macromolecular prodrugs of the antibiotic norfloxacin were prepared by coupling the drug via a peptide spacer onto a mannosylated dextran. The tetrapeptide gly-phe-gly-gly-gly-OMe was selected as substrate for lysosomal enzymes. The drug was coupled on the alpha-C of the terminal glycine. In vitro degradation studies demonstrated the release of the parent drug in the presence of cathepsin B. In vivo experiments on mice showed a promising therapeutic effect.

Synthesis and anti-HIV activity of alpha-thiophenoxy-hydroxyethylamide derivatives

A series of new anti-HIV derivatives containing a novel alpha-thiophenoxyhydroxyethylamide core have been synthesized, using S-phenylbenzenethiosulfonate as the thiosulfenylating reagent. Some of the new synthesized compounds (1a, 1c, 1g, 1i, 1j and 1l) inhibited HIV replication in cell culture assays (syncytia formation) with effective concentrations (EC(50)) ranging from 0.1-1 microM. Incorporation of thiophenoxy substitution within various pseudomimetic peptide backbones provided a series of highly potent HIV inhibitors.

Synthesis of a selenomethionine peptide and a preliminary study of transport into Escherichia coli monitored by high-performance liquid chromatography

The tripeptide Gly-SeMet-Gly has been synthesized by a combination of solution and solid-phase methods. Increase in weight of the resin was very nearly theoretical, and purification was straightforward. Its absorption was compared to that of the corresponding peptide, Gly-Met-Gly, in E. coli using HPLC ion-exchange separation and fluorometric determination of the disappearance of peptides in the culture medium and the appearance of methionine and selenomethionine in the same culture medium. As E. coli are not known to possess extracellular peptidases, and in fact have been shown to possess transport systems for peptides, this absorption is interpreted as transport of the peptide through the cell wall and membrane into the cytoplasm, endohydrolysis of the peptide, and efflux of the peptides' amino acids. Uptake of both peptides was approximately equal, but was slowed when both peptides were present simultaneously.

Simultaneous exploitation of different peptide permeases by combinations of synthetic peptide smugglins can lead to enhanced antibacterial activity

Various synthetic, peptide prodrugs (smugglins) were tested alone and in combination for activity against Escherichia coli. The smugglins may be transported through any of three peptide permeases, and once inside the bacteria are activated by intracellular peptidase action to release their intrinsically impermeant, antibacterial moieties. When each such antibiotic peptide present in a mixture was accumulated via a different permease, synergistic effects could be observed. Synergy was also found when smugglins were combined with other non-peptide antibiotics. The principle of using smugglin combinations could extend the scope of their application, and should minimise the potential problem that can arise from the occurrence of resistant, transport mutants. The smugglin interactions were studied using a modified microtitre plate assay.

Relative rates of transport of peptidyl drugs by Candida albicans

A variety of peptide drugs are known to be active against Candida albicans; however, little is known about the transport of such agents into the target organism. To provide further information concerning transport of this type, we studied the uptake of two classes of small linear peptides: polyoxins which act intact within the cell and the m-fluorophenylalanyl (m-F-Phe) peptides which require peptidase cleavage to release m-F-Phe. Competition studies with a specific dipeptide detector (alanyl-alpha-thiophenylglycine) enabled us to determine Ki values of 2.6 microM for nikkomycin Z and 350 microM for polyoxin D. Rates of uptake of the peptidyl-nucleosides are approximately 30 times lower than those of the m-F-Phe peptides (apparent maximal velocities: nikkomycin Z, 62 pmol min-1 mg (dry weight) of cells-1; M-F-Phe alanine 1.3 nmol min-1 mg (dry weight) of cells-1). For both the m-F-Phe peptides and the peptidyl-nucleosides, the affinity of the drug for the transport system is an important determinant of its whole-cell activity.

Multiplicity of peptide permeases in Candida albicans: evidence from novel chromophoric peptides

Evidence is presented for the presence of multiple peptide permeases in the eucaryotic organism Candida albicans. Instrumental in these studies were the peptides L-alanyl-L-2-thiophenylglycine (Ala-alpha-TPG) and L-alanyl-L-2-thiophenylglycyl-L-alanine (Ala-alpha-TPG-Ala), which contain thiophenol attached to the alpha-carbon of glycine. Subsequent to transport into the fungal cell, enzymatic hydrolysis of these peptides resulted in the release of free thiophenol, which was quantified by using Ellman reagent. Thiophenol release was shown to be directly correlated to peptide transport and hydrolysis, with transport being the rate-limiting step in intact cells. These peptides, whose uptake showed Michaelis-Menten kinetics, have been used to determine peptide uptake in C. albicans. In addition, we found that the intracellular peptidases can readily be assayed in permeabilized cells and that bestatin, an aminopeptidase inhibitor, inhibits all detectable peptidase activity. C. albicans 124 was able to transport and hydrolyze both Ala-alpha-TPG and Ala-alpha-TPG-Ala, whereas the mutant (124NIK5) was able to transport only the tripeptide. The intracellular peptidases of this mutant were unaffected. In wild-type C. albicans 124, oligopeptides were able to compete with uptake of Ala-alpha-TPG-Ala to a far greater extent than with that of Ala-alpha-TPG; dipeptides inhibited uptake of both Ala-alpha-TPG and Ala-alpha-TPG-Ala. These results provide complementary evidence for the existence of distinct transport systems.

Spectrophotometric determination of affinities of peptides for their transport systems in Escherichia coli

The use of novel synthetic peptides to measure peptide transport by spectrophotometric means is described. These peptides contain glycine residues alpha-substituted with thiophenol and are recognized as substrates by both peptide transport systems and intracellular peptidases of Escherichia coli (Kingsbury et al., Gilvarg, C., Proc. Natl. Acad. Sci. U.S.A. 81:4573-4576, 1984). Transport and peptidase cleavage results in the intracellular release of thiophenol, which exits rapidly from the cell. The release of thiophenol from these peptides by cell suspensions can be measured with Ellman sulfhydryl reagent [5,5'-dithiobis(2-nitrobenzoic acid)] and provides a direct determination of the rate of peptide transport. The reductions in thiophenol release from these peptides resulting from the addition of peptide competitors enable the affinities of the competitors for their transport systems to be determined. By this method, it is shown that the dipeptide transport system is more restrictive with respect to changes in the amino acid sidechains of its substrates than those of the oligopeptide transport system.