Proving and Probing the Presence of the Elusive C-H⋠⋠⋠O Hydrogen Bond in Liquid Solutions at Room Temperature.

Hydrogen bonds (H bonds) play a major role in defining the structure and properties of many substances, as well as phenomena and processes. Traditional H bonds are ubiquitous in nature, yet the demonstration of weak H bonds that occur between a highly polarized C-H group and an electron-rich oxygen atom, has proven elusive. Detailed here are linear and nonlinear IR spectroscopy experiments that reveal the presence of H bonds between the chloroform C-H group and an amide carbonyl oxygen atom in solution at room temperature. Evidence is provided for an amide solvation shell featuring two clearly distinguishable chloroform arrangements that undergo chemical exchange with a time scale of about 2 ps. Furthermore, the enthalpy of breaking the hydrogen bond is found to be 6-20 kJ mol-1 . Ab-initio computations support the findings of two distinct solvation shells formed by three chloroform molecules, where one thermally undergoes hydrogen-bond making and breaking.

Synthesis of the Aminovinylcysteine-Containing C-Terminal Macrocycle of the Linaridins.

N-Phthalimido-d-cysteine allyl ester was S-alkylated with 2-iodoethanol. The derived ß-thioaldehyde was condensed with Nα-tetrachlorophthalimidovalinamide to afford a Z-thioenamide. Removal of the tetrachlorophthalimido protecting group and homologation with N-Boc-l-leucine afforded the linear tripeptide. Removal of the Boc and allyl protecting groups, followed by carbodiimide-mediated cyclization, led to the 13-membered ring with the aminovinylcysteine moiety embedded. This constitutes the C-terminal macrocycle of all known members of the linardin family of peptides, including the antileukemia agent, cypemycin.

Total Synthesis of Alloviroidin.

Alloviroidin is a cyclic heptapeptide, produced by several species of Amanita mushrooms, that demonstrates high affinity for F-actin as is characteristic of virotoxins and phallotoxins. Alloviroidin was synthesized via a [3 + 4] fragment condensation of Fmoc-d-Thr(OTBS)-d-Ser(OTBS)-(2 S,3 R,4 R)-DHPro(OTBS)2-OH and H-Ala-Trp(2-SO2Me)-(2 S,4 S)-DHLeu(5-OTBS)-Val-OMe to form bond A. The linear heptapeptide favored a turn conformation, facilitating cyclization between Val1 and d-Thr2 (position B). Global deprotection and HPLC purification afforded alloviroidin with NMR spectra in excellent agreement with the natural product.

Structural modification of the tripeptide KPV by reductive "glycoalkylation" of the lysine residue.

Peptides that exhibit enzymatic or hormonal activities are regulatory factors and desirable therapeutic drugs because of their high target specificity and minimal side effects. Unfortunately, these drugs are susceptible to enzymatic degradation, leading to their rapid elimination and thereby demanding frequent dosage. Structurally modified forms of some peptide drugs have shown enhanced pharmacokinetics, improving their oral bioavailability. Here, we discuss a novel glycomimetic approach to modify lysine residues in peptides. In a model system, the ε-amine of Ts-Lys-OMe was reductively alkylated with a glucose derivative to afford a dihydroxylated piperidine in place of the amine. A similar modification was applied to H-KPV-NH2, a tripeptide derived from the α-melanocyte stimulating hormone (α-MSH) reported to have antimicrobial and anti-inflammatory properties. Antimicrobial assays, under a variety of conditions, showed no activity for Ac-KPV-NH2 or the α- or ε-glycoalkylated analogs. Glycoalkylated peptides did, however, show stability toward proteolytic enzymes.

Influence of Sulfur on Acid-Mediated Enamide Formation.

The acid-mediated condensation of acetamide with butanal dimethylacetal and EtSCH2CH(OMe)2, followed by dehydration, was investigated by electronic structure calculations that supported the prediction that the Z-geometry would be favored in the product. The reaction was investigated experimentally using suitably functionalized cysteine building blocks. Some side reactions and optimization of reaction conditions are reported, en route to identifying a mild, inexpensive Lewis acid that achieves a reasonable yield of (Z)-thioenamide 21 with high stereoselectivity.

Crystal Structure of Carboxyltransferase from Staphylococcus aureus Bound to the Antibacterial Agent Moiramide B.

The dramatic increase in the prevalence of antibiotic-resistant bacteria has necessitated a search for new antibacterial agents against novel targets. Moiramide B is a natural product, broad-spectrum antibiotic that inhibits the carboxyltransferase component of acetyl-CoA carboxylase, which catalyzes the first committed step in fatty acid synthesis. Herein, we report the 2.6 Å resolution crystal structure of moiramide B bound to carboxyltransferase. An unanticipated but significant finding was that moiramide B bound as the enol/enolate. Crystallographic studies demonstrate that the (4S)-methyl succinimide moiety interacts with the oxyanion holes of the enzyme, supporting the notion that an anionic enolate is the active form of the antibacterial agent. Structure-activity studies demonstrate that the unsaturated fatty acid tail of moiramide B is needed only for entry into the bacterial cell. These results will allow the design of new antibacterial agents against the bacterial form of carboxyltransferase.

Design, synthesis, and antibacterial properties of dual-ligand inhibitors of acetyl-CoA carboxylase.

There is an urgent demand for the development of new antibiotics due to the increase in drug-resistant pathogenic bacteria. A novel target is the multifunctional enzyme acetyl-CoA carboxylase (ACC), which catalyzes the first committed step in fatty acid synthesis and consists of two enzymes: biotin carboxylase and carboxyltransferase. Covalently attaching known inhibitors against these enzymes with saturated hydrocarbon linkers of different lengths generated dual-ligand inhibitors. Kinetic results revealed that the dual-ligands inhibited the ACC complex in the nanomolar range. Microbiology assays showed that the dual-ligand with a 15-carbon linker did not exhibit any antibacterial activity, while the dual-ligand with a 7-carbon linker displayed broad-spectrum antibacterial activity as well as a decreased susceptibility in the development of bacterial resistance. These results suggest that the properties of the linker are vital for antibacterial activity and show how inhibiting two different enzymes with the same compound increases the overall potency while also impeding the development of resistance.

Conformational changes associated with post-translational modifications of Pro(143) in Skp1 of Dictyostelium--a dipeptide model system.

Prolyl hydroxylation and subsequent glycosylation of the E3(SCF) ubiquitin ligase subunit Skp1 affects its conformation and its interaction with F-box proteins and, ultimately, O2-sensing in the organism. Taking a reductionist approach to understand the molecular basis for these effects, a series of end-capped Thr-Pro dipeptides was synthesized, tracking the sequential post-translational modifications that occur in the protein. The conformation of the pyrrolidine ring in each compound was gauged via coupling constants ((3)JHα,Hß) and the electronegativity of the Cγ-substituents by chemical shifts ((13)C). The equilibrium between the cis-trans conformations about the central prolyl peptide bond was investigated by integration of signals corresponding to the two species in the (1)H NMR spectra over a range of temperatures. These studies revealed an increasing preference for the trans-conformation in the order Pro < Hyp < [α-(1,4)GlcNAc]Hyp. Rates for the forward and reverse reactions, determined by magnetization transfer experiments, demonstrated a reduced rate for the trans-to-cis conversion and a significant increase in the cis-to-trans conversion upon hydroxylation of the proline residue in the dipeptide. NOE experiments suggest that the Thr side chain pushes the sugar away from the pyrrolidine ring. These effects, which depended on the presence of the N-terminal Thr residue, offer a mechanism to explain altered properties of the corresponding full-length proteins.

Synthesis of oligomers of ß-l-arabinofuranosides of (4R)-4-hydroxy-l-proline relevant to the mugwort pollen allergen, Art v 1.

An efficient, convergent solution phase synthesis of monomer, dimer, trimer and tetramer of the ß-l-arabinofuranosylated hydroxyproline (ß-l-Araf-Hyp) glycocluster is described. This motif constitutes the carbohydrate-specific epitope of Art v 1, the major allergen of mugwort pollen. While a single monomeric unit was proposed at the outset, poor yields for the seemingly trivial steps of end-capping to replace protecting groups with N-terminal acetamides and C-terminal methyl amides led to the introduction of N-terminal, central and C-terminal ß-l-Araf-Hyp building blocks. Dimer 2 was obtained in 60% yield by coupling of two monomers, followed by hydrogenolysis of benzyl ether protecting groups. Trimer 3 was obtained in 35% yield via a [2 + 1] coupling and tetramer 4 in 15% yield via a [2 + 2] fragment condensation. Circular dichroism spectra show that monomer 1 displays no organized structure, whereas compounds 2-4 show a strong negative band at 200 nm and a weak positive band at ∼220 mn, as is characteristic of the polyproline II helix.

Synthesis of orthogonally protected (2S)-2-amino-adipic acid (α-AAA) and (2S,4R)-2-amino-4-hydroxyadipic acid (Ahad).

(2S,4R)-2-amino-4-hydroxyadipic acid (Ahad) building block 45 was synthesized in 11 steps and 6.5% overall yield from commercially available materials. Key steps in stereocontrol were an asymmetric conjugate addition employing a proline-based catalyst and a syn-selective intramolecular-conjugate addition of an oxygen nucleophile to an α,ß-unsaturated ester. To enable incorporation of α-amino-adipic acid (α-AAA) and Ahad into peptides, a truly orthogonal protecting group scheme was developed, encompassing an allyloxycarbonyl (Alloc) carbamate for Nα, a tert-butyl ester for the δ-COOH, an acetol ester for the α-COOH, and a tert-butyldimethylsilyl ether for the γ-hydroxy group of Ahad.

Evidence that thaxtomin C is a pathogenicity determinant of Streptomyces ipomoeae, the causative agent of Streptomyces soil rot disease of sweet potato.

Streptomyces ipomoeae is the causal agent of Streptomyces soil rot of sweet potato, a disease marked by highly necrotic destruction of adventitious roots, including the development of necrotic lesions on the fleshy storage roots. Streptomyces potato scab pathogens produce a phytotoxin (thaxtomin A) that appears to facilitate their entrance into host plants. S. ipomoeae produces a less-modified thaxtomin derivative (thaxtomin C) whose role in pathogenicity has not been examined. Here, we cloned and sequenced the thaxtomin gene cluster (txt) of S. ipomoeae, and we then constructed targeted txt mutants that no longer produced thaxtomin C. The mutants were unable to penetrate intact adventitious roots but still caused necrosis on storage-root tissue. These results, taken in context with previous histopathological study of S. ipomoeae infection, suggest that thaxtomin C plays an essential role in inter- and intracellular penetration of adventitious sweet potato roots by S. ipomoeae. Once inside the plant host, the pathogen uses one or more yet-to-be-determined factors to necrotize root tissue, including that of any storage roots it encounters.

Glycosides of hydroxyproline: some recent, unusual discoveries.

Glycosides of hydroxyproline (Hyp) in the plant cell wall matrix were discovered by Lamport and co-workers in the 1960s. Since then, much has been learned about these Hyp-rich glycoproteins. The intent of this review was to compare and contrast some less common structural motifs, in nontraditional roles, to uncover themes. Arabinosylation of short-peptide plant hormones is essential for growth, cell differentiation and defense. In a very recent development, prolyl hydroxylase and arabinosyltransferase activity has been shown to have a direct impact on the growth of root hairs in Arabidopsis thaliana. Pollen allergens of mugwort and ragweed contain proline-rich domains that are hydroxylated and glycosylated and play a structural role. In the case of mugwort, this domain also presents a significant immunogenic epitope. Major crops, including tobacco and maize, have been used to express and produce recombinant proteins of mammalian origin. The risks of plant-imposed glycosylation are discussed. In unicellular eukaryotes, Skp1 (a subunit of the E3(SCF) ubiquitin ligase complex) harbors a key Hyp residue that is modified by a linear pentasaccharide. These modifications may be involved in sensing oxygen levels. A few studies have probed the impact of glycosylation on the structure of Hyp-containing peptides. These have necessarily looked at small, synthetic molecules, since natural peptides and proteins are often isolable in only minuscule amounts and/or are heterogeneous in nature. The characterization of native structural motifs, together with the determination of glycopeptide conformation and properties, holds the key to rationalizing nature's architectural design.

Synthesis of histidinoalanine: a comparison of ß-lactone and sulfamidate electrophiles.

Previous syntheses of histidinoalanine (HAL) have led to mixtures of regioisomers and/or stereoisomers. For example, opening of N-Cbz-D-serine-ß-lactone (6) with Boc-L-His-OMe (5) gave a 2:1 mixture of τ- and π-regioisomers. The sulfamidate 10, derived from N-benzyl-D-serine methyl ester (11), was reacted with Boc-L-His-OMe (5) to give the τ-HAL derivative 17 as a single isomer in 57% yield. A similarly prepared τ-HAL 19, bearing protecting groups that were all hydrogenolytically labile, led to the free bis-amino acid, τ-L-histidinyl-D-alanine (τ-4), as a salt-free standard for amino acid analysis.

Requirements for Skp1 processing by cytosolic prolyl 4(trans)-hydroxylase and α-N-acetylglucosaminyltransferase enzymes involved in O2 signaling in dictyostelium.

The social amoeba Dictyostelium expresses a hypoxia inducible factor-α (HIFα) type prolyl 4-hydroxylase (P4H1) and an α-N-acetylglucosaminyltransferase (Gnt1) that sequentially modify proline-143 of Skp1, a subunit of the SCF (Skp1/Cullin/F-box protein) class of E3 ubiquitin ligases. Prior genetic studies have implicated Skp1 and its modification by these enzymes in O(2) regulation of development, suggesting the existence of an ancient O(2)-sensing mechanism related to modification of the transcription factor HIFα by animal prolyl 4-hydroxylases (PHDs). To better understand the role of Skp1 in P4H1-dependent O(2) signaling, biochemical and biophysical studies were conducted to characterize the reaction product and the basis of Skp1 substrate selection by P4H1 and Gnt1. (1)H NMR demonstrated formation of 4(trans)-hydroxyproline as previously found for HIFα, and highly purified P4H1 was inhibited by Krebs cycle intermediates and other compounds that affect animal P4Hs. However, in contrast to hydroxylation of HIFα by PHDs, P4H1 depended on features of full-length Skp1, based on truncation, mutagenesis, and competitive inhibition studies. These features are conserved during animal evolution, as even mammalian Skp1, which lacks the target proline, became a good substrate upon its restoration. P4H1 recognition may depend on features conserved for SCF complex formation as heterodimerization with an F-box protein blocked Skp1 hydroxylation. The hydroxyproline-capping enzyme Gnt1 exhibited similar requirements for Skp1 as a substrate. These and other findings support a model in which the protist P4H1 conditionally hydroxylates Skp1 of E3(SCF)ubiquitin ligases to control half-lives of multiple targets, rather than the mechanism of animal PHDs where individual proteins are hydroxylated leading to ubiquitination by the evolutionarily related E3(VBC)ubiquitin ligases.

Synthesis of a dimer of ß-(1,4)-L-arabinosyl-(2S,4R)-4-hydroxyproline inspired by Art v 1, the major allergen of mugwort.

Nα-tert-Butoxycarbonyl-L-trans-4-hydroxyproline allyl ester (Boc-Hyp-OAll) was glycosylated with 2,3,5-tri-O-benzyl-L-arabinose p-cresylthioglycoside in 60% yield with 4:1 ß:α stereoselectivity. Deprotection of N- and C-terminii independently gave a prolyl amine and prolyl carboxylate respectively that were coupled under standard conditions with 1-[bis-(dimethylamino)methylene]-1H-1,2,3-triazolo-[4,5,b]-pyridininium hexafluorophosphate 3-oxide (N-HATU) to give the dimer 1 in 46% yield. These results represent the first steps toward the production of homogeneous oligomers to determine the minimal epitope of the Art v 1 allergen.

Peptides containing gamma,delta-dihydroxy-L-leucine.

(+/-)-Dehydroleucine was prepared and resolved by porcine kidney acylase. Under the conditions of the Sharpless asymmetric dihydroxylation (SAD), employing AD-mix-alpha, N alpha-carbobenzyloxy-(2S)-4,5-dehydroleucine methyl ester (16) gave rise to a 6.5:1.0 mixture of gamma-lactones 17, favoring the 4R configuration. Such carbamate-protected alpha-amino-gamma-hydroxylactones are not recommended as intermediates for peptide synthesis, since model studies showed that lactone 13 was unreactive toward amines. Moreover, the lactone ring could not be opened hydrolytically without epimerization at C alpha. N alpha-carbobenzyloxy-(2S)-4,5-dehydroleucine (22) was condensed with valine ethyl ester (19) to give dipeptide 23. Treatment of 23 with AD-mix-beta, under the SAD conditions, converted the dehydroleucine residue to gamma,delta-dihydroxyleucine with 4S configuration, as occurs in alloviroidin (3), a natural product isolated from Amanita suballiacea.

Beta-glycosides of hydroxyproline via an umpolung approach.

Reaction of 1,2-O-dibutylstannylene-3,4-6-tri-O-benzyl-beta-D-mannopyranose with Nalpha-fluorenylmethoxycarbonyl-cis-4-trifluoromethanesulfonyloxyproline allyl ester led to formation of a beta-mannoside of trans-4-hydroxyproline. Subsequent manipulation of the C2 hydroxy group gave rise to beta-D-Glc and beta-D-GlcNAc derivatives.

The impact of pyrrolidine hydroxylation on the conformation of proline-containing peptides.

[structure: see text] A series of eight dipeptides of the general formula Ac-Phe-Pro-NHMe was synthesized and the thermodynamics of the cis --> trans isomerization about the central amide bond were studied by NMR. Pro* represents the following prolines: l-proline (Pro), l-trans-4-hydroxyproline (Hyp), l-cis-4-hydroxyproline (hyp), l-cis-4-methoxyproline (hyp[OMe]), l-trans-3-hydroxyproline (3-Hyp), l-cis-3-hydroxyproline (3-hyp), l-2,3-trans-3,4-cis-3,4-dihydroxyproline (DHP), and l-2,3-cis-3,4-trans-3,4-dihydroxyproline (dhp). The conformation of the pyrrolidine ring in each case is discussed in light of previous structural studies, analysis of potential stereoelectronic effects, and NMR data. Hydroxy substituents at C-4 have a greater impact on cis --> trans isomerization than analogous substituents at C-3 as a result of the intervening bond distances and bridging groups. The position of the equilibrium and its dependence on temperature are a reflection of both enthalpic and entropic factors, the latter being complicated in this study by an Ar-Pro interaction in the cis conformation. The substituents on the pyrrolidine ring determine the conformation of the five-membered ring, which in turn influences the strength of the Ar-Pro interaction, backbone dihedral angles, and the relative energy of the cis and trans species. The ultimate position of the equilibrium depends on a complex blend of steric, electronic, and conformational factors.

Factors affecting conformation in proline-containing peptides.

[reaction: see text] NMR was used to study the thermodynamics of the cis --> trans isomerization for prolyl amide bonds in the compounds shown. The magnitude of K(t/c) for C-terminal esters is greater than for the corresponding amides, signifying stronger backbone stereoelectronic effects in esters. Increasing the steric bulk of the N-terminal residue from Ac- to Ac-Gly- favors the trans conformation. Incorporation of a Phe residue N-terminal to Pro, however, shifts the equilibrium in favor of the cis conformation, via a stabilizing aromatic-proline interaction.

Design, preparation, and characterization of mixed dimers of inducible nitric oxide synthase oxygenase domains.

A limitation of site-directed mutagenesis of homodimeric proteins is that both subunits will carry the same mutation. We have devised a way to prepare mixed dimers, in which only one chain bears a desired mutation, or each chain can bear a different mutation. Using the inducible nitric oxide oxygenase domain as a model, our strategy focused on the co-expression of two differentially tagged versions of the oxygenase domain, with isolation of the desired mixed dimer in two chromatography steps. We evaluated expression vectors encoding polyhistidine (His(6)), cellulose binding domain, glutathione-S-transferase, and polyglutamate (Glu(7))-tagged versions of the oxygenase domain for satisfactory levels of soluble protein expression and for their ability to form mixed dimers. The combination of His(6)- and Glu(7)-tagged subunits was successful in both respects, and the mixed dimers could be separated from either form of homodimer by sequential immobilized metal affinity chromatography and anion exchange chromatography. The UV-Vis spectrum, substrate binding properties, and enzymatic activity were not altered in the mixed dimer wild-type (His(6)/Glu(7)) compared to the two homodimers (His(6)/His(6) and Glu(7)/Glu(7)). We then characterized a mixed dimer variant in which one chain contained an E371A substitution (which prevents binding of the substrate L-arginine) while the other subunit was left unaltered. This species binds L-arginine and has about one-half the activity of the wild-type homodimer. Mutants known to destabilize the iNOS dimer (E411A, D454A, and W188F) were also investigated; in these cases co-expression with the wild-type subunit did not lead to the formation of stable mixed dimers.