Combination of preparative HPLC and HSCCC methods to separate phosphodiesterase inhibitors from Eucommia ulmoides bark guided by ultrafiltration-based ligand screening

Phosphodiesterase (PDE) inhibitors are widely used because of their various pharmacological properties, and natural products are considered the most productive source of PDE inhibitors. In this work, a new ultrafiltration–high-performance liquid chromatography (HPLC)–diode-array detection–mass spectrometry based ligand screening was developed for the first screening of PDE inhibitors from Eucommia ulmoides bark, and then the target bioactive compounds were prepared by combination of stepwise preparative HPLC and high-speed countercurrent chromatography (HSCCC) methods. Experiments were conducted to optimize the parameters in ultrafiltration, stepwise preparative HPLC, and HSCCC to allow rapid and effective screening and isolation of active compounds from complex mixtures. Seven lignans with purity over 97 % were isolated and identified by their UV, electrospray ionization mass spectrometry, and NMR data as (+)-pinoresinol-4,4′-di-O-β-D-glucopyranoside (1), (+)-pinoresinol-4-O-β-D-glucopyranosyl(1?→?6)-β-D-glucopyranoside (2), (+)-medioresinol-4,4′-di-O-β-D-glucopyranoside (3), (+)-syringaresinol-4,4′-di-O- β-D-glucopyranoside (4), (?)-olivil-4′-O-β-D-glucopyranoside (5), (?)-olivil-4-O-β-D- glucopyranoside (6), and (+)-pinoresinol-4-O-β-D-glucopyranoside (7). Compound 2 was first isolated from the genus Eucommia. Lignan diglucopyranosides (compounds 1–4) shower a greater inhibitory effect than lignan monoglucopyranosides (compounds 5–7). The method developed could be widely applied for high-throughput screening and preparative isolation of PDE inhibitors from natural products.     

Rapid Screening of Olefin Polymerization Catalyst Libraries by Electrospray Ionization Tandem Mass Spectrometry

The simultaneous screening of catalysts according to their propensity for catalyzing the polymerization of ethylene (see scheme) can be achieved with the help of electrospray ionization tandem mass spectrometry. A small (eight catalysts) library of Pd^II complexes synthesized simultaneously in a one-pot reaction has demonstrated the efficiency of this new screening technique. This method could be widened to libraries of other olefin polymerization catalysts.     

The structure characterization of dinucleoside and nucleoside glucopyranosides lipophilic phosphotriesters by fast-atom bombardment tandem mass spectrometry

Rules for the gas-phase fragmentation mechanism of the negative ions of lipophilic phosphotriester molecules of biological interest have been established by fast-atom bombardment mass spectrometry/mass spectrometry. The mass-analyzed ion kinetic energy spectra of the [M ? H]^? of dinucleoside (1–4) and nucleoside glucopyranoside (5–9) phosphotriesters show that in the absence of charges on the phosphate bridge, the availability of acidic protons on the 5′-end nucleobase drives a preferred reaction path which leads to 5′-O-nucleotide or 6-O-glucopyranoside monophosphate anions.     

无机磷试剂辅助均环肽库的建立及其电喷雾质谱研究

在无机磷试剂辅助下建立了氨基酸自组装成均环肽的方法, 得到了相应的均环肽库. 均环肽库的建立增加了肽库的多样性, 为药物筛选提供了新的选择性. 采用电喷雾多级质谱技术, 对系列均环多肽 [M＋H]＋离子和[M＋Na]＋离子的质谱裂解规律进行了系统研究, 两种系列的离子具有不同的质谱裂解特征, 分别提出了其可能的质谱裂解机制. 该研究丰富了环多肽化合物的电喷雾多级质谱研究, 结果表明环肽化合物的加钠离子较加氢离子的质谱图可以更容易地用于环多肽的序列测定. 本研究为其它类似环肽化合物结构的分析鉴定及利用电喷雾质谱推测环肽序列提供了有效的质谱方法.     

Novel sesquiterpenoids as tyrosine kinase inhibitors produced by Stachybotrys chortarum

In the course of screening for small-molecule inhibitors to Tyrosine kinase receptor seven novel K-76 derivatives (1-7) have been isolated from the fungal culture of Stachybotrys chortarum. The structures were elucidated by extensive mono- and bi- dimensional spectroscopy and mass spectrometry.     

Synthesis of novel exocyclic amino nucleosides by parallel solid-phase combinatorial strategy

A versatile parallel solid-phase combinatorial strategy was developed for the synthesis of large nucleoside libraries. Twelve libraries L1-12 of 1152 novel exocyclic triazinylamino nucleosides and one library L13 of 82 new substituted clitocine derivatives were synthesized in high quality as natural product mimic nucleosides on the semi-automated synthesizer. The polystyrene MMT-Cl resin was selected and utilized. The key intermediate resins 5 and 9 loaded with the corresponding scaffolds were prepared and validated with various amines before parallel synthesis. After a variety of amino building blocks were validated, 56 primary amines in 12 groups (building block set A) and 24 secondary amines in 3 groups (building block set B) were selected and utilized to combinatorialize the first and the second reactive sites on scaffold 5 for the synthesis of libraries L1-12. Eighty-two amines (building block set C) were utilized for the synthesis of clitocine library L13. Thirteen libraries of 1234 novel exocyclic amino nucleosides were all analyzed and characterized by high throughput LC-MS. 81.3-100% of the library members in 13 libraries show more than 60% purity, and 65.7-92.7% of the library members in these libraries show 80-100% purity. The strategy can be widely used for the synthesis of other diverse nucleoside libraries.     

Confirmatory method for the determination of nandrolone and trenbolone in urine samples using immunoaffinity cleanup and liquid chromatography–tandem mass spectrometry

A confirmatory method for the simultaneous determination of nandrolone (α and β) and trenbolone (α and β) in urine samples by liquid chromatography electrospray mass spectrometry (LC–MS-MS) was developed. After an enzymatic deconjugation, the urine was subjected to a one-step cleanup on a commercially available immunoaffinity chromatography cartridge. The analytes were detected by liquid chromatography–positive ion electrospray tandem mass spectrometry using deuterium labelled internal standards. The analytical procedure was applicable to bovine and swine urine samples. The procedure was validated as a quantitative confirmatory method according to the Commission Decision 2002/657/EC criteria. The results obtained showed that the method was suitable for statutory residues testing regarding the following performance characteristics: instrumental linearity, specificity, precision (repeatability and intra-laboratory reproducibility), recovery, decision limit (CCα), detection capability (CCβ) and ruggedness. The decision limits (CCα) obtained, were between 0.54 and 0.60 μg L⁻¹; the recovery was above 64% for all the analytes. Repeatability was between 1.6% and 5.7% and within-laboratory reproducibility between 1.6% and 6.0% for all the steroids.     

Stereoselective,solid phase-based synthesis of trans 3-alkyl-substituted β-lactams as analogues of cholesterol absorption inhibitors

A straightforward solid phase-based strategy for the rapid generation of two small libraries of trans 3-alkyl-substituted β-lactams is described. For the glycine-derived library, a controlled excess of nonactivated acid chlorides was used to prevent oxazinone formation. The second library involved the attachment of Fmoc-protected p-aminophenol to Wang resin for the preparation of structurally-closed analogues of known cholesterol absorption inhibitors. This strategy allowed us to introduce diversity in the three variable positions of the β-lactam ring.     

Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D

Background: The identification of potent small molecule ligands to receptors and enzymes is one of the major goals of chemical and biological research. Two powerful new tools that can be used in these efforts are combinatorial chemistry and structure-based design. Here we address how to join these methods in a design protocol that produces libraries of compounds that are directed against specific macromolecular targets. The aspartyl class of proteases, which is involved in numerous biological processes, was chosen to demonstrate this effective procedure.Results: Using cathepsin D, a prototypical aspartyl protease, a number of low nanomolar inhibitors were rapidly identified. Although cathepsin D is implicated in a number of therapeutically relevant processes, potent nonpeptide inhibitors have not been reported previously. The libraries, synthesized on solid support, displayed nonpeptide functionality about the (hydroxyethyl)amine isostere. The (hydroxyethyl)amine isostere, which targets the aspartyl protease class, is a stable mimetic of the tetrahedral intermediate of amide hydrolysis. Structure-based design, using the crystal structure of cathepsin D complexed with the peptide-based natural product pepstatin, was used to select the building blocks for the library synthesis. The library yielded a ‘hit rate’ of 6–7% at 1 μM inhibitor concentrations, with the most potent compound having a K_i value of 73 nM. More potent, nonpeptide inhibitors (K_i = 9–15 nM) of cathepsin D were rapidly identified by synthesizing and screening a small second generation library.Conclusions: The success of these studies clearly demonstrates the power of coupling the complementary methods of combinatorial chemistry and structure-based design. We anticipate that the general approaches described here will be successful for other members of the aspartyl protease class and for many other enzyme classes.     

A mass spectrometry screening method for antiaggregatory activity of proteins covalently modified by combinatorial library members: application to sickle hemoglobin

A homogeneous assay, based on electrospray mass spectrometry, is described for identifying compounds in a combinatorial library that covalently modify a protein and thereby enhance its solubility. The technique is based on measuring the distribution of modified proteins in the supernatant versus aggregate. Compounds having the greatest anti-aggregatory activity are those with the highest supernatant/aggregate ratio. Mass is used as a marker to identify which covalent modifier in the library is involved. An exploratory study is presented which demonstrates that the antisickling activity of a family of isothiocyanates, as measured by the standard C(sat) assay, correlates well (r(2) = 0.98) with the mass spectrometry analysis of the supernatant/aggregate distribution. The technique has potential for screening libraries capable of covalently modifying other proteins of clinical interest, e.g., Alzheimer's, Huntington's, and various prion related diseases.     

Competitive Binding Sites of a Ruthenium Arene Anticancer Complex on Oligonucleotides Studied by Mass Spectrometry: Ladder-Sequencing versus Top-Down

We report identification of the binding sites for an organometallic ruthenium anticancer complex [(η ⁶-biphenyl)Ru(en)Cl][PF₆] (1; en = ethylenediamine) on the 15-mer single-stranded oligodeoxynucleotides (ODNs), 5′-CTCTCTX₇G₈Y₉CTTCTC-3′ [X = Y = T (I); X = C and Y = A (II); X = A and Y = T (III); X = T and Y = A (IV)] by electrospray ionization mass spectrometry (ESI-MS) in conjunction with enzymatic digestion or tandem mass spectrometry (top-down MS). ESI-MS combined with enzymatic digestion (termed MS-based ladder-sequencing), is effective for identification of the thermodynamically-favored G-binding sites, but not applicable to determine the thermodynamically unstable T-binding sites because the T-bound adducts dissociate during enzymatic digestion. In contrast, top-down MS is efficient for localization of the T binding sites, but not suitable for mapping ruthenated G bases, due to the facile fragmentation of G bases from ODN backbones prior to the dissociation of the phosphodiester bonds. The combination of the two MS approaches reveals that G₈ in each ODN is the preferred binding site for 1, and that the T binding sites of 1 are either T₇ or T₁₁ on I and IV, and either T₆ or T₁₁ on II and III, respectively. These findings not only demonstrate for the first time that T-bases in single-stranded oligonucleotides are kinetically competitive with guanine for such organoruthenium complexes, but also illustrate the relative merits of the combination of ladder-sequencing and top-down MS approaches to elucidate the interactions of metal anticancer complexes with DNA.      

A study on the formation of N-tosyl-1,3,2-oxazaborolidin-5-one by electrospray mass spectrometry

The crude product generated in a reaction between N-tosyl valine and borane was studied by electrospray mass spectrometry (ESIMS). Intermediates in the formation of N-tosyl-1,3,2-oxazaborolidin-5-one 1a and further reactions of 1a were studied with negative ion mode. According to the results 1a may, as soon as it is generated, react with the starting amino acid.     

Convenient preparation of pinometostat and related 5′-deoxy-5′-amino adenosine derivatives as well as their activity against DOT1L

From adenosine and 2′-C-Me adenosine, a 3-step route towards nucleoside DOT1L inhibitors, including pinometostat, EPZ5677, and FED1, was established. With useful structural-activity relationship information, the newly prepared 2′-C-Me adenosine derivatives contribute to the limited repertoire of ribose-modified nucleoside DOT1L inhibitors. In general, this new synthetic method will facilitate not only the study of nucleoside DOT1L inhibitors, but also the synthetic and medicinal chemistry research of 5′-deoxy-5′-amino adenosine derivatives.     

Unconventional nucleotide analogues—XVIII: Ring expansion of uridine halocarbene adducts. Synthesis of diazepine nucleosides

The diastereomeric adducts of dichlorocarbene and dibromocarbene with (protected) uridine react with alcohols to give diazepine nucleosides (4a–c). The endo-chloro-exo-fluorocarbene adducts (1d and 2d) also react analogously to yield diazepine nucleoside 4d. On the other hand, the corresponding exo-chloro-endo-fluoro isomers (1e and 2e) are totally inert under the same reaction conditions. The adducts 1b and 2b yield, besides the ring-expanded product (4b), uridine-5-aldehyde (6a) in varying amounts which depend upon the conformation of the diastereomer. These results are explained on the basis of a possible role of the ring-oxygen of the ribose moiety.     

Furanoside phosphite–phosphoroamidite and diphosphoroamidite ligands for Cu-catalyzed asymmetric 1,4-addition reactions

A sugar-based phosphite–phosphoroamidite and diphosphoroamidite ligand library L1–L5a–g was tested in the asymmetric Cu-catalyzed 1,4-conjugate addition reactions of β-substituted and β,β′-disubstituted enones. Our results indicated that the selectivity was strongly dependent on the ligand parameters and on the substrate structure. Moderate-to-good enantioselectivities (ees up to 84%) were obtained in the 1,4-addition of several types of β-substituted cyclic and linear substrates. Of particular note is the high enantioselectivity (ees up to 90%) obtained for the more challenging β,β′-disubstituted 3-methyl-cyclohexenone.     

Synthesis of optically active β′-hydroxy-β-enaminoketones via enzymatic resolution of carbinols derived from 3,5-disubstituted isoxazoles

The preparation of several enantiomerically pure β′-hydroxy-β-enaminoketones from the corresponding isoxazolic carbinols, which have been obtained by enzymatic kinetic resolution of the racemic β-hydroxyisoxazoles catalyzed by lipases, is described. The enzymatic transesterification of racemic (±)-5-(2-hydroxypropyl)-3-methylisoxazole 3a, and racemic (±)-5-(2-hydroxy-2-p-tolylethyl)-3-methylisoxazole 3d, has been studied with respect to the influence of experimental variables such as the used enzyme, the acylating agent or the solvent on the enantioselectivity of the reaction. After the reductive cleavage of the isoxazolic ring of the enantiopure carbinols, (R)- and (S)-2-amino-4-oxo-2-hepten-6-ol, (R)- and (S)-5, and (R)-2-amino-6-p-tolyl-4-oxo-2-hexen-6-ol, (R)-7 with an enantiomeric excess >98% were obtained.     

Triazolyl C-nucleosides via the intermediacy of β-1′-ethynyl-2′-deoxyribose derived from a Nicholas reaction: Synthesis,photophysical properties and interaction with BSA

We report the design and synthesis of triazolyl donor/acceptor unnatural C-nucleosides via alkyne (sugar)—azide (aromatic) 1, 3-dipolar cyclo-addition reaction as a key step and studies on their photophysical properties. We have chosen β-1′-ethynyl-2′-deoxyribose as a precursor to synthesize triazolyl-C-nucleosides. Overcoming the difficulties, we obtain β-1′-ethynyl-2′-deoxyribose as a major product following a Co₂(CO)₈ catalyzed intramolecular Nicholas reaction. The 1,3-diaxial interaction is the driving force for the α to β-anomeric conversion while performing cobalt complexation followed by oxidation to afford β-1′- ethynyl-2′-deoxyribose as the major product. A Cu(I)-catalyzed click reaction between different aromatic donor/acceptor azides and β-1′- ethynyl-2′-deoxyribose generates the desired unnatural triazolyl donor-acceptor aromatic C-nucleosides (^cTB_Do/Ac) within 30 min. Single crystal X-ray structure shows the puckered conformation of sugar as C3′-exo. Studies on the photophysical properties suggests good fluorophoric as well as solvatochromic characteristics of these nucleosides. Two of the synthesised nucleosides, ^cTAnthB_Do and ^cTPyB_Do, are found to interact with BSA as the only tested protein with quenching of fluorescence signal. The designed bases, thus, might find applications in stabilizing a DNA and in the biophysical study thereof, if a pair of such donor acceptor C-nucleosides could be incorporated into a DNA sequence.     

Screening DNA Adducts by LC–ESI–MS–MS: Application to Screening New Adducts Formed from Acrylamide

A method for screening DNA adducts with unknown chemical structures was developed; it involves the use of liquid chromatography–electrospray ionization-tandem mass spectrometry (LC–ESI–MS–MS). In electrospray ionization (ESI) product ion mass spectra of guanine adducts, fragment ions were observed at m/z 152 and 135. Precursor ion scan analysis of these fragment ions indicated that the screening of DNA adducts would be possible. The developed method was used for the analysis of DNA adducts derived from acrylamide, which is not only a constituent of many commonly consumed foods but also a carcinogenic compound. We successfully discovered new guanine adducts. The results of this study indicate that the developed method is useful for screening new DNA adducts.     

Chemoenzymatic synthesis of 4-diphosphocytidyl-2-C-methyl-d-erythritol: a substrate for IspE

Enantiomerically pure 2-C-methyl-d-erythritol 4-phosphate 1 (MEP) is synthesized from 1,2-O-isopropylidene-α-d-xylofuranose via facile benzylation in good yield. Subsequently, 1 is used for enzymatic synthesis of 4-diphosphocytidyl-2-C-methyl-d-erythritol 2 (CDP-ME) using 4-diphosphocytidyl-2-C-methyl-d-erythritol synthase (IspD). The chemoenzymatically synthesized 2 can be used as substrate for assay of IspE and for high throughput screening to identify IspE inhibitors.     

Novel ester linked glycosyl amino acids: convenient building blocks for the synthesis of glycopeptide libraries

The completely orthogonally protected aspartic acid derivative FmocAsp(OBn)O^tBu is readily synthesized on a large scale. Deprotection of the β-carboxylic acid allows coupling to various sugar derivatives via free hydroxyl groups to produce novel glycosyl amino acids. Subsequent deprotection of either the α-acid or nitrogen is achieved cleanly to allow elaboration into an oligopeptide, whilst selective deprotection of PMB protected sugar hydroxyls is also readily achievable. Such novel glycosyl amino acid building blocks may be useful for the combinatorial synthesis of novel glycopeptide libraries.