Synthesis of methyl ω-deuterated tetradecanoate and hexadecanoate

Methyl ω-deuterated tetradecanoates have been prepared in high purity by two synthetic routes from methyl hydrogen tetradecanedioate. One method utilizes the selective reducing properties of sodium borodeuteride and sodium cyanoborodeuteride towards, acid chloride, ester, tosyloxy, and iodo groups to introduce the deuterium label at only the carboxyl group of methyl hydrogen tetradecanedioate. The second procedure utilizes a coupling reaction between an organic halide and lithium di-(trideuteriomethyl) cuprate (I). Corresponding ω-deuterated derivatives of methyl hexadecanoate may be prepared by the same methods from methyl hydrogen hexadecanedioate. The two methods should be generally applicable in the synthesis of ω-deuterated alkanoic acids.     

Expression, purification, characterization, and NMR studies of highly deuterated recombinant cytochrome c peroxidase

Two forms of extensively deuterated S. cerevisiae cytochrome c peroxidase (CcP; EC 1.11.1.5) have been overexpressed in E. coli by growth in highly deuterated medium. One of these ferriheme enzyme forms (recDCcP) was produced using >97% deuterated growth medium and was determined to be approximately 84% deuterated. The second form [recD(His)CcP] was grown in the same highly deuterated medium that had been supplemented with excess histidine (at natural hydrogen isotope abundance) and was also approximately 84% deuterated. This resulted in direct histidine incorporation without isotope scrambling. Both of these enzymes along with the corresponding recombinant native CcP (recNATCcP), which was expressed in a standard medium with normal hydrogen isotope abundance, consisted of 294 amino acid polypeptide chains having the identical sequence to the yeast-isolated enzyme, without any N-terminal modifications. Comparative characterizations of all three enzymes have been carried out for the resting-state, high-spin forms and in the cyanide-ligated, low-spin forms. The primary physical methods employed were electrophoresis, UV-visible spectroscopy, hydrogen peroxide reaction kinetics, mass spectrometry, and (1)H NMR spectroscopy. The results indicate that high-level deuteration does not significantly alter CcP's reactivity or spectroscopy. As an example of potential NMR uses, recDCcPCN and recD(His)CcPCN have been used to achieve complete, unambiguous, stereospecific (1)H resonance assignments for the heme hyperfine-shifted protons, which also allows the heme side chain conformations to be assessed. Assigning these important active-site protons has been an elusive goal since the first NMR spectra on this enzyme were reported 18 years ago, due to a combination of the enzyme's comparatively large size, paramagnetism, and limited thermal stability.     

Biosynthetic preparation of selectively deuterated phosphatidylcholine in genetically modified <Emphasis Type="Italic">Escherichia coli</Emphasis>

Phosphatidylcholine (PC) is a major component of eukaryotic cell membranes and one of the most commonly used phospholipids for reconstitution of membrane proteins into carrier systems such as lipid vesicles, micelles and nanodiscs. Selectively deuterated versions of this lipid have many applications, especially in structural studies using techniques such as NMR, neutron reflectivity and small-angle neutron scattering. Here we present a comprehensive study of selective deuteration of phosphatidylcholine through biosynthesis in a genetically modified strain of Escherichia coli. By carefully tuning the deuteration level in E. coli growth media and varying the deuteration of supplemented carbon sources, we show that it is possible to achieve a controlled deuteration for three distinct parts of the PC lipid molecule, namely the (a) lipid head group, (b) glycerol backbone and (c) fatty acyl tail. This biosynthetic approach paves the way for the synthesis of specifically deuterated, physiologically relevant phospholipid species which remain difficult to obtain through standard chemical synthesis.     

Synthesis of esters of saturated and unsaturated sixteen-carbon acids deuterated at the terminal or penultimate carbons

General syntheses of saturated and unsaturated fatty acids, specifically trideuterated at the terminal carbon or dideuterated at the penultimate carbon, from ω-hydroxy esters, have been developed. Methyl [16-²H₃]hexadecanoate was synthesized from methyl 16-hydroxyhexadecanoate. The hydroxyl group was protected as the tetrahydropyranyl ether and the ester group reduced with lithium aluminum deuteride, first to an alcohol and then, by way of the derived mesylate, to a trideuteromethyl group. The new ester group was formed by oxidation of the hydroxyl group. Methyl 16-hydroxy[2-²H₂]hexadecanoate was prepared, from 16-hydroxy-hexadecanoate, by exchange of the α protons and, by the reductive route above, with lithium aluminum hydride, gave methyl [15-²H₂]hexadecanoate. Methyl 16-hydroxy-7-hexadecynoate was synthesized from 6-chlorohexanol and was converted, by means of the above reactions, to methyl [16-²H₃]- and [15-²H₂]-9-hexadecynoates. Lindlar reduction gave methyl [16-²H₃]- and [15-²H₂]cis-9-hexadecenoates. Overall yields ranged from 30% to 38%.     

Design,synthesis and biological evaluation of deuterated Vismodegib for improving pharmacokinetic properties

Vismodegib is an oral and high selective hedgehog (Hh) inhibitor used for the treatment of basal cell carcinoma (BCC). In this work, analogs of Vismodegib with deuterium-for-hydrogen replacement at certain metabolically active sites were prepared and found to have a better pharmacokinetic properties in mice. In particular, deuterated compound SKLB-C2211 obviously altered the blood circulation behavior compared to its prototype, which was demonstrated by significantly prolonged blood circulation half-life time (t_1/2) and increased AUC_0→∞. These results suggested SKLB-C2211 had the potential to be a long-acting inhibitor against Hh signaling pathway, and laid the foundation for the further research of its druggability.     

Biosynthesis and characterization of deuterated polyhydroxyoctanoate

The synthesis of a polyhydroxyalkanoate with medium chain length alkyl substituents by Pseudomonas oleovoranswas investigated using protonated and deuterated forms of octanoic acid in a minimal salts medium. Cultivation with deuterated octanoic acid resulted in a reduced rate of polymer accumulation compared to that with its protonated counterpart (107 and 207 mg of polymer L(-1) of medium h(-1) of cultivation, respectively). Nuclear magnetic resonance and gas chromatography coupled mass spectrometry of the derivatized polymer was used to establish the extent and distribution of deuterium in the biopolymer. A partially deuterated heteropolymer with 3-hydroxyoctanoic acid as the main constituent was produced. Deuteration is an important tool for contrast variation studies using neutron scattering, but predicates that the deuterated polymer is otherwise comparable in its physiochemical and material properties to its protonated counterpart. In studies reported here, the deuterated biopolymer exhibited an additional diffraction maximum at 7.55 A and slight differences in its melting point (60 and 55 degrees C) and glass transition temperature (-39 and -36 degrees C) when compared to its protonated equivalent. While significant differences between the protonated and deuterated biopolymers were determined, our results support the use of this deuterated polyhydroxyalkanoate in its application in investigations using analytical neutron scattering techniques.     

Deuterium labeling of diethylstilbestrol and analogues

E-2,2,3',3″,5,5,5',5″-octadeuteriodiethylstilbestrol (DES-d8) and Z-2,3',3″,4,5,5,5',5″-octadeuterio-3,4-bis(p-hydroxyphenyl)-2-hexene (ψ-DES-d8) were synthesized from E-diethylstilbestrol (DES) by hydrogen/ deuterium exchange in a mixture of methanol-d and deuterium chloride in deuterium oxide. The structures, isotopic purity, and positions of up-take of deuterium were determined by nuclear magnetic resonance (NMR) and mass spectrometry (MS). Additional confirmation of the positions of deuterium exchange in stilbestrols was obtained from an analysis of the oxidation of DES-d8 to Z,Z-2,3',3″,5,5',5″-hexadeuteriodienestrol (β-DIES-d6) and of the hydrogen/deuterium exchange reaction of hexestrol (HEX) to 3',3″,5',5″-hexestrol (HEX-d4). Structural analysis and the determination of isotopic purity of the latter two compounds were also carried out by NMR and MS. The uptake of eight deuterium atoms by DES is postulated to proceed via two different reactions occurring simultaneously: 1. acid catalyzed deuteration of all four phenolic ortho-positions (3',3″,5',5″); 2. acid catalyzed deuteration of the olefin bridge with subsequent formation of deuterated ψ-DES (3 or 4). Due to the equilibration between DES, ψ-DES, and Z-diethylstilbestrol (cis-DES) in the acidic reaction mixture at 85°C, the deuterated ψ-DES is thought to rapidly rearrange to deuterated DES. Repeated deuteration will eventually form DES-d8 fully labeled in the 2,2,5,5 methylene positions.     

A simple protocol for the production of highly deuterated proteins for biophysical studies

Highly deuterated protein samples expand the biophysics and biological tool kit by providing, among other qualities, contrast matching in neutron diffraction experiments and reduction of dipolar spin interactions from normally protonated proteins in magnetic resonance studies, impacting both electron paramagnetic resonance and NMR spectroscopy. In NMR applications, deuteration is often combined with other isotopic labeling patterns to expand the range of conventional NMR spectroscopy research in both solution and solid-state conditions. However, preparation of deuterated proteins is challenging. We present here a simple, effective, and user-friendly protocol to produce highly deuterated proteins in Escherichia coli cells. The protocol utilizes the common shaker flask growth method and the well-known pET system (which provides expression control via the T7 promotor) for large-scale recombinant protein expression. One liter expression typically yields 5 to 50 mg of highly deuterated protein. Our data demonstrate that the optimized procedure produces a comparable quantity of protein in deuterium (²H₂O) oxide M9 medium compared with that in ¹H₂O M9 medium. The protocol will enable a broader utilization of deuterated proteins in a number of biophysical techniques.     

Stereoselective synthesis of chirally deuterated (S)-D-(6-(2)H(1))glucose

Chirally deuterated (S)-D-(6-(2)H(1))glucose has been prepared in good overall yield from d-(6,6'-(2)H(2))glucose by a short, five-step synthesis from D-(6,6-(2)H(2))glucose utilizing (R)-(+)-Alpine-Borane [(R)-9-[(6,6-dimethylbicyclo[3.1.1]hept-2-yl)methyl]-9-borabicyclo[3.3.1]nonane]. Suitably protected methyl 2,3,4-tri-O-benzyl-D-(6,6-(2)H(2))glucopyranoside was prepared and the deuterated O-6 primary alcohol was oxidized to an aldehyde by Swern oxidation. Stereoselective reduction with nondeuterated (R)-(+)-Alpine-Borane gave methyl 2,3,4-tri-O-benzyl-(6S)-D-(6-(2)H(1))glucopyranoside, which was deprotected under standard conditions to afford the title compound. The key stereoselective reduction step was achieved in 90% yield. The preparation uses economical, commercially available starting materials and will be useful for elucidating biosynthetic mechanisms.     

Synthesis of deuterated methyl 6,9,12-octadecatrienoate geometric isomers

Methyl cis-6,cis-9,cis-12-octadecatrienoate-15,15,16,16-d₄ and the corresponding cis,cis,trans isomer were obtained by coupling hexyl-d₄-triphenylphosphonium bromide and methyl 12-oxo-cis-6,cis-9-dodecadienoate by the Wittig reaction. The deuterated phosphonium salt was prepared from 3-hexynol by catalytic deuteration of the corresponding tetrahydropyranyl ether and intermediate formation of the bromide. The dienoic aldehyde ester was obtained through the intermediate dioxanyl and dimethoxy derivatives from the Wittig coupling of methyl 9-oxo-cis-6-nonenoate with [2-(1,3-dioxan-2-yl)ethyl]-triphenylphosphonium bromide. The monoenoic aldehyde ester was prepared in a similar manner by the Wittig reaction between methyl 6-oxohexanoate and the dioxanylphosphonium salt. The saturated aldehyde ester was obtained, through several steps, from the ozonolysis of cyclohexene. Geometric isomers formed during each of the Wittig reactions were separated by silver resin chromatography. ¹³C Nuclear magnetic resonance chemical shifts for the compounds prepared are presented.     

Mixed-metal butterfly acetamidediato clusters derived from a highly reactive ruthenium oxo cluster: synthesis and characterization of [(PPh3)2N][MRu3(CO)12(η-μ3-NC(μ-O)CH3)], (M = Mn or Re)

Analogy with the isolable oxo cluster [Fe₃(CO)₉(μ₃-O)]²⁻, which is structurally interesting and synthetically useful, prompted the present attempt to synthesize its ruthenium analog. Although the high reactivity of [Ru₃(CO)₉(μ₃-O)]²⁻ (I) prevented its isolation, the reaction of this species with [M(CO)₃(NCCH₃)]⁺, where M = Mn or Re, yields [PPN][MRu₃(CO)₁₂(η²-μ₃-NC(μ-O)CH₃]⁻. The high nucleophilicity of the oxo ligand in [Ru₃(CO)₉(μ₃-O)]²⁻ (I) appears to be responsible for the conversion of acetonitrile to an acetamidediato ligand and for the instability of I. The crystal structure of [PPN][MnRu₃(CO)₁₂(η²-μ₃-NC(μ-O)CH₃)]] reveals a hinged butterfly array of metal atoms in which the acetamidediato ligand bridges the two wings with μ₃-N bonding to an Mn and two Ru atoms, and μ-O bonding to an Ru atom.     

Synthesis of 2-(2,3-dimethoxyphenyl)-4-(aminomethyl)imidazole analogues and their binding affinities for dopamine D(2) and D(3) receptors.

A series of 2-(2,3-dimethoxyphenyl)-4-(aminomethyl)imidazole derivatives was prepared and their affinity for dopamine D₂ and D₃ receptors was measured using in vitro binding assays. Several oxadiazole analogues were also prepared and tested for their affinity for dopamine D₂ and D₃ receptors. The results of receptor binding studies indicated that the incorporation of an imidazole moiety between the phenyl ring and the basic nitrogen did not significantly increase the selectivity for dopamine D₃ receptors, whereas the incorporation of an oxadiazole at the same region resulted in a total loss of affinity for both dopamine receptor subtype binding sites. The most selective compound in this series is 2-(5-bromo-2,3-dimethoxyphenyl)-4-(6,7-dimethoxy-1,2,3,4-tetrahydroisoquinolinomethyl)imidazole (5i), which has a D₃ receptor affinity of 21 nM and a 7-fold selectivity for D₃ versus D₂ receptors. The binding affinity for σ₁ and σ₂ receptors was also measured, and the results showed that several analogues were selective σ₁ receptor ligands.     

Thermal phase transitions in deuterated lecithin bilayers.

Differential Thermal Analyses and Optical Density measurements show that perdeuteration of the fatty acid residues in phosphatidylcholines causes a 4–5°C decrease in the phase transition temperatures of bilayer dispersions prepared from these deuterated phospholipids. The implications of these findings on the use of deuterated phospholipids in membrane research will be briefly discussed.     

Neutron structure factors of in-vivo deuterated amorphous protein C-phycocyanin

Neutron powder diffraction measurements of fully deuterated protein C-phycocyanin have been made at three temperatures, 295, 200, and 77 K, using dry and partially hydrated samples. The average coherent structure factors and the corresponding radial distribution functions d(r) are determined. The changes in d(r) functions observed in hydrated samples depend strongly on the level of hydration and most of these changes are due to water-protein interactions. At 0.365 gram D₂O per gram of protein, the water crystallized into hexagonal ice at 200 K and below, but at 0.175 gram D₂O per gram of protein, no crystallization of water was observed. At the higher hydration a peak appears in the radial distribution function which indicates that the average distance of the water molecule in the first hydration shell from the amino acid residues is 3.5 Å.     

1H NMR studies of deuterated ribonuclease HI selectively labeled with protonated amino acids

Summary Two-dimensional (2D)¹H NMR experiments using deuterium labeling have been carried out to investigate the solution structure of ribonuclease HI (RNase HI) fromEscherichia coli (E. coli), which consists of 155 amino acids. To simplify the¹H NMR spectra, two fully deuterated enzymes bearing several prototed amino acids were prepared from an RNase HI overproducing strain ofE. coli grown in an almost fully deuterated medium. One enzyme was selectively labeled by protonated His, He. Val. and Leu. The other was labeled by only protonated His and Ile. The 2D¹H NMR spectra of these deuterated R Nase H1 proteins, selectively labeled with protonated amino acids, were much more simple than those of the normally protonated enzyme. The simplified spectra allowed unambiguous assignments of the resonance peaks and connectivities in COSY and NOESY for the side-chain protons. The spin-lattice relaxation times of the side-chain protons of the buried His residue of the deuterated enzyme became remarkably longer than that of the protonated enzyme. In contrast, the relaxation times of the side-chain protons of exposed His residues remained essentially unchanged.     

Structure-activity relationships of cyclic β-casomorphin-5 analogues

Cyclic analogues of the β-casein-derived opioid peptide β-casomorphin-5 (H-Tyr-Pro-Phe-Pro-Gly-OH) were prepared through substitution of the Pro² residue with various ,ω-diamino acid residues (lysine, ornithine, 2,4-diaminobutyric acid) and cyclization of the ω-amino group to the C-terminal carboxyl function. Compounds of this type, with D-configuration at the 2-position residue, showed high opioid receptor affinity with some preference for μ receptors over δ receptors, high potency in the guinea pig ileum assay and considerable activity in the mouse vas deferens assay. Configurational inversion at the 4-position in these cyclic analogues resulted in enhanced affinity for both μ and δ receptors, whereas N-methylation of the Phe³ residue produced a potency decrease.     

An Unprecedented Combination of Serine and Cysteine Nucleophiles in a Split Intein with an Atypical Split Site

Protein splicing mediated by inteins is a self-processive reaction leading to the excision of the internal intein domain from a precursor protein and the concomitant ligation of the flanking sequences, the extein-N and extein-C parts, thereby reconstituting the host protein. Most inteins employ a splicing pathway in which the upstream scissile peptide bond is consecutively rearranged into two thioester or oxoester intermediates before intein excision and rearrangement into the new peptide bond occurs. The catalytically critical amino acids involved at the two splice junctions are cysteine, serine, or threonine. Notably, the only potential combination not observed so far in any of the known or engineered inteins corresponds to the transesterification from an oxoester to a thioester, which suggested that this formal uphill reaction with regard to the thermodynamic stability might be incompatible with intein-mediated catalysis. We show that corresponding mutations also led to inactive gp41-1 and AceL-TerL inteins. We report the novel GOS-TerL split intein identified from metagenomic databases as the first intein harboring the combination of Ser1 and Cys+1 residues. Mutational analysis showed that its efficient splicing reaction indeed follows the shift from oxoester to thioester and thus represents a rare diversion from the canonical pathway. Furthermore, the GOS-TerL intein has an atypical split site close to the N terminus. The Int^N fragment could be shortened from 37 to 28 amino acids and exchanged with the 25-amino acid Int^N fragment from the AceL-TerL intein, indicating a high degree of promiscuity of the Int^C fragment of the GOS-TerL intein.     

Optimized N-phenyl-N'-(2-chloroethyl)ureas as potential antineoplastic agents: synthesis and growth inhibition activity

In our ongoing research program aimed at the optimization of microtubule-self-assembly disrupting agents, we have prepared three series of phenylurea analogues (CEU), derived from N-(3-ω-hydroxyalkyl or 4-ω-hydroxyalkyl or 3-ω-hydroxyalkynyl)-phenyl-N′-(2-chloroethyl)ureas. Most compounds exhibit potent growth inhibitory activity on human colon carcinoma HT-29, human skin melanoma M21, and human breast carcinoma MCF-7 tumor cell lines, with a GI₅₀ ranging from 250 nM to 8 μM. Among these new molecules, three CEUs exhibit GI₅₀ in the nanomolar range. They are more potent by approximately an order of magnitude than previously described CEU analogues. As such, they are attractive hit compounds for the development of potent new alkylating antitubulin drugs.     

New syntheses of deuterated protoporphyrin-IX derivatives for heme protein nmr studies

An efficient total synthesis of 1,5-di(trideuteromethyl)protoporphyrin-IX (3) dimethyl ester from monopyrrole precursors is described, the synthesis proceeding through crystalline tripyrrene and a,c-biladiene salt intermediates. The 2- and 4-vinyl groups in (3) are formed from the corresponding (2-chloroethyl) substituents by way of base-promoted dehydrochlorination. In protio solvents, this synthetic step is shown to exchange out preferentially deuterons in the 1-methyl group, and this observation is exploited in an efficient synthesis of the 1,3-di(trideuteromethyl)protoporphyrin-IX (22) dimethyl ester from 2,4-diacetyldeuteroporphyrin-IX (20) dimethyl ester (which is in turn accessible from commercially available protoporphyrin-IX (5)). Thus, basic exchange in deuterated solvent of (20) gives the deuterated analog, which after reduction and dehydration gives the 1,3-di(trideuteromethyl)protoporphyrin-IX analog (22), in which the vinyl H₂ and propionic CH₂·CO functions have also become deuterated.