Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases

Target identification is a critical step following the discovery of small molecules that elicit a biological phenotype. The present work seeks to provide an in silico correlate of experimental target fishing technologies in order to rapidly fish out potential targets for compounds on the basis of chemical structure alone. A multiple-category Laplacian-modified na?ve Bayesian model was trained on extended-connectivity fingerprints of compounds from 964 target classes in the WOMBAT (World Of Molecular BioAcTivity) chemogenomics database. The model was employed to predict the top three most likely protein targets for all MDDR (MDL Drug Database Report) database compounds. On average, the correct target was found 77% of the time for compounds from 10 MDDR activity classes with known targets. For MDDR compounds annotated with only therapeutic or generic activities such as "antineoplastic", "kinase inhibitor", or "anti-inflammatory", the model was able to systematically deconvolute the generic activities to specific targets associated with the therapeutic effect. Examples of successful deconvolution are given, demonstrating the usefulness of the tool for improving knowledge in chemogenomics databases and for predicting new targets for orphan compounds.     

Spectropolarimetric Assay of R(-)-Epinephrine

Abstract

A rapid, simple and specific procedure for the simultaneous assay and determination of enantiomeric purity of pharmaceutical grade 1-epinephrine solution is described. The procedure is faster, more precise and more specific for the levoisomer than the U.S.P. XXI method. It can also be used for 1-epine-phrine inhalation solution and 1-epinephrine injection solution.     

Multiple inverse isotope dilution assay for the stereospecific quantitative determination of R(-) and S(+)-oxaprotiline in biological fluids

An isotope dilution assay for the determination of both oxaprotiline enantiomers in biological samples after administration of the racemic mixture has been developed. The enantiomers were reacted with synthetically prepared, optically pure N-trifluoroacetyl-S(-)-prolyl chloride, followed by high-performance liquid chromatographic separation of the diastereoisomers formed. Quantitation was performed by on-line UV detection at 260 nm and off-line radiometry by liquid scintillation counting. Endogenous compounds and metabolites do not interfere in the assay. Analysis of water and the blood and urine of rats spiked with [14C]oxaprotiline X HCl showed recoveries for S(+)-oxaprotiline X HCl (mean +/- coefficient of variation, n = 4-6) of 98.0 +/- 1.0% (water), 100.5 +/- 0.6% (blood) and 101.5 +/- 2.0% (urine), and for R(-)-oxaprotiline X HCl of 101.3 +/- 2.0% (water), 102.2 +/- 2.1% (blood) and 103.2 +/- 0.2% (urine). A pilot study to determine blood levels of the two enantiomers in two rats dosed with racemic [14C]oxaprotiline X HCl (10 mg/kg i.v.) was carried out to test the method. The results indicated stereoselective disposition of oxaprotiline enantiomers in the rat. The ratio of the areas under the blood concentration curves for R(-)-to S(+)-oxaprotiline X HCl was 1.14.     

A stoichiometric approach to quantitative structure-property relationships (QSPR)

An unusual analogy between the quantitative structure-property relationships (QSPR), stoichiometry, chemical thermodynamics, and kinetics is presented. Namely, the conventional ordinary least-squares (OLS) QSPR analysis is modified so as to explicitly minimize the residuals of the species subject to a set of linear relations among the residuals. The ways the linear relations among the residuals are visualized and defined totally resemble the formalism of chemical stoichiometry and, therefore, were called isostructural reactions. It is further proved that the residuals may be uniquely partitioned into a sum of contributions associated with a set of isostructural reactions that have the same properties as the response reactions (RERs) previously deduced by us from chemical thermodynamics and kinetics. This finding is shown to be a useful tool for a deeper understanding of the QSPR. In particular, the isostructural RERs approach may be effectively used to detect the outliers.     

HPLC Assay for S-2-(3-Aminopropylamino)ethyl Phosphorothioate (WR 2721) in Plasma

Abstract

A specific HPLC assay has been developed for determination of the radioprotective drug WR 2721. The method is based on precolumn derivatization of plasma with fluorescamine, separation with a C-18 cartridge and detection by fluorescence. An external standard was used for calibration, and values were adjusted based upon recovery of added ¹⁴C-labeled WR 2721. WR 2721 had a retention time of about 13 minutes using a mobile phase of acetonitrile/water (22:78), 0.01 M in dibutylammonium phosphate, at a flow rate of 2 mL/min. Sensitivity of the assay was characterized to 2 μg/mL, and detector response was linear over the range of 2 to 1100 μg/mL. The assay requires 90 μL of plasma and has a total chromatography time of about 45 minutes. 2-(3-Aminopropylamino)ethanethiol (WR 1065) and bis- [2- (3-aminopropylamino)ethyl]disulfide (WR 33278), metabolites of the drug, and a variety of primary amines were shown not to interfere with the assay. Suitability of this assay for pharmacokinetic studies was demonstrated in preliminary experiments with a beagle dog.     

High-Pressure Liquid Chromatography Assay for Dane Salt Potassium (-)-N-(1-Methoxycarbonylpropene-2yl)-p-hydroxyphenylglycine

Abstract

A rapid, ion-pair, high-pressure liquid chromatographic method for analysis of Dane Salt Potassium (-)-N-(1-Methoxycarbonylpropene-2-yl)-p-Hydroxy-phenylglycine was developed. Tetrabutylammonium hydroxide was used as a counter-ion in the mobile phase. A fixed wavelength detector (λ = 280 nm) and a μ-Bondapak C-18 column were employed. The percent relative range of the method (precision) was 0.6% (n = 3).     

Synthesis and biological evaluation of (-)-16-normethyldictyostatin: a potent analogue of (-)-dictyostatin

[structure: see text] (-)-16-Normethyldictyostatin has been made by total synthesis and is a potent antitumor agent in cells expressing wild-type tubulin and in one mutant cell line that is resistant to paclitaxel, but it is much less active than dictyostatin in another paclitaxel-resistant cell line where Val is substituted for Phe270. This provides strong evidence that the C16 methyl group of the dictyostatins is oriented toward Phe270 in the paclitaxel-binding site on beta-tubulin.     

4-(9-fluorenylmethyloxycarbonyl)phenylhydrazine (FmPH): a new chromophoric reagent for quantitative monitoring of solid-phase aldehydes(1-3)

A direct method for quantifying solid-phase aldehydes has been developed, using a new reagent, 4-(9-fluorenylmethyloxycarbonyl)phenylhydrazine (FmPH). The FmPH reagent was synthesized in three steps (24% overall yield) from commercially available p-hydrazinobenzoic acid. Resin-bound aldehydes reacted quantitatively with FmPH, in the presence of trimethylorthoformate (TMOF) as a dehydrating agent, to form a highly conjugated, immobilized FmPH-hydrazone. Next, mild treatment of the hydrazone with an excess of piperidine-N,N-dimethylformamide (1:1) released the piperidine-dibenzofulvene adduct chromophore (epsilon(301nm) = 7800 M(-1) cm(-1)) from the support. FmPH quantitation of aldehydes proved to be a straightforward, sensitive, and reproducible technique for monitoring resin-bound aldehydes [albeit insufficiently reactive to allow reliable quantification of ketones]. The FmPH aldehyde assay is applicable to a range of solid supports, as demonstrated specifically for poly(ethylene glycol)-polystyrene (PEG-PS), aminomethylpolystyrene (AMP), and cross-linked ethoxylate acrylate resin (CLEAR).     

Synthesis and biological evaluation of (-)-laulimalide analogues

[reaction: see text] The syntheses of five laulimalide analogues are described, incorporating modifications at the C(16)-C(17)-epoxide, the C(20)-alcohol, as well as the C(1)-C(3)-enoate of the parent natural product. The resultant analogues are active in drug-sensitive HeLa and MDA-MB-435 cell lines. Significantly, like laulimalide, these analogues are poor substrates for the drug transport protein P-glycoprotein (Pgp) and are thus effective against Taxol-resistant cell lines.     

Total synthesis and biological evaluation of (-)-9-deoxy-englerin A

An effective total synthesis of (-)-9-deoxy-englerin (4), an analogue of the natural guaiane sesquiterpene englerin A (1), has been achieved. The synthesis features a transannular epoxide opening to construct the 5,7-fused ring system followed by transannular ether formation with mercury(II) trifluoroacetate.     

A Liquid Chromatographic Electrochemical Assay for S-2-(3-Aminopropylamino) Ethylphosphorothioate (WR2721) in Human Plasma

Abstract

A liquid chromatographic electrochemical method for the determination of the radioprotective drug WR2721 in human plasma has been developed. This method includes the use of a Hg/Au electrochemical detector for the direct measurement of WR2721 concentration. An analog of WR2721, S-3-{4-aminobutylamino} propylphosphorothioate (WR80855) is the internal standard. The retention times for WR2721 and WR80855 are approximately 4.5 and 9 minutes, respectively. WR1065, the free sulfhydryl metabolite of WR2721, is retained on the column under the described chromatographic conditions and therefore does not interefere with the determination of the parent drug. With modification of the mobile phase WR1065 is eluted from the column at a retention time of approximately 20 minutes. This method has good linearity, precision and accuracy, and is free from interference from endogenous plasma substances. Preliminary results showing the applicability of this method to human pharmacokinetic studies and to investigating the enzymatic hydrolysis of WR2721 are presented.     

Synthesis and biological activity of some 3-(4-(substituted)-piperazin-1-yl)cinnolines

A new series of 6-substituted-4-methyl-3-(4-arylpiperazin-1-yl)cinnolines 8-10 were synthesized as potential antifungal agents via intramolecular cyclization of the respective 1-(2-arylhydrazono)-1-(4-arylpiperazin-1-yl)propan-2-ones 5-7, mediated by polyphosphoric acid (PPA). The amidrazones themselves were synthesized via direct interaction of the appropriate hydrazonoyl chlorides 4a-d with the corresponding N-substituted piperazine in the presence of triethylamine. The structures of the new prepared compounds were confirmed by elemental analyses, (1)H-NMR, (13)C-NMR, and ESI-HRMS spectral data. The antitumor, antibacterial, and antifungal activity of the newly synthesized compounds was evaluated.     

Synthesis and biological evaluation of (-)-dictyostatin and stereoisomers

Total syntheses of (−)-dictyostatin, 6,16-bis-epi-dictyostatin, 6,14,19-tris-epi-dictyostatin, and a number of other isomers and analogs are reported. Three main fragments—top, middle, and bottom—were first assembled and then joined by olefination or anionic addition reactions. After appending the two dienes at either end of the molecule, macrolactonization and deprotection completed the syntheses. The work proves both the relative and absolute configurations of (−)-dictyostatin. The compounds were evaluated by cell-based measurements of increased microtubule mass and antiproliferative activity, and in vitro tubulin polymerization assays as well as competitive assays with paclitaxel for its binding site on microtubules. These assays showed dictyostatin to be the most potent of the agents and further showed that the structural alterations caused from 20- to >1000-fold decreases in activity.     

Synthesis, structural elucidation and biological activities of organotin(IV) derivatives of (E)-3-(4-methoxyphenyl)-2-(4-chlorophenyl)-2-propenoic acid

A new series of di- and tri-organotin(IV) compounds with the general formula R_4?n SnL _n , where R?=?Me (1,2), Et (3), n-Bu (4,5), n-Oct (6), Ph (7) and L?=?(E)-3-(4-methoxyphenyl)-2-(4-chlorophenyl)-2-propenoate, were synthesized by reaction of silver salt of ligand or ligand acid with diorganotin dichloride/oxide and triorganotin chloride in 2:1 and 1:1 molar ratio, respectively. These compounds were characterized by elemental analyses, FT-IR, multinuclear (¹H, ¹³C, ¹¹⁹Sn) NMR and mass spectrometry. The spectroscopic results revealed that all the diorganotin(IV) compounds possess trigonal bipyramidal structures in solution and octahedral geometry in the solid state around the tin atom. A linear polymeric trigonal bipyramidal structure in the solid state and a tetrahedral environment around the tin atom in non-coordinating solvents has been proposed for the triorganotin(IV) compounds. All synthesized compounds were tested in vitro against a number of microorganisms to assess their biocidal activity. These studies revealed that ligand acid and some of its organotin compounds show promising activity against different strains of bacteria and fungi but lowered than reference drugs.     

Target grafting of poly(2-(dimethylamino)ethyl methacrylate) to biodegradable block copolymers

A series of copolymers composed of methoxy poly(ethylene glycol) and a hydrophobic block of poly(ɛ-caprolactone-co-propargyl carbonate) grafted with poly(2-[dimethylamino]ethyl methacrylate) was synthesized by combining ring opening polymerization, azide-alkyne click reaction, and atom transfer radical polymerization (ATRP). Well-defined copolymers with a target composition and a tailored structure were achieved via the grafting from approach by using a single catalytic system for both click reaction and ATRP. Kinetic studies demonstrated the controlled/living character of the employed polymerization methods. The thermal properties and self-assembly in aqueous medium of the graft copolymers were dependent on their composition. The resulting polymeric materials showed low cytotoxicity toward L929 cells, demonstrating their potential for biomedical applications. This type of materials containing cationic side chains tethered to biocompatible and biodegradable segments could be the basis for promising candidates as drug and gene delivery systems.     

Asymmetric total synthesis of (-)-callystatin A and (-)-20-epi-callystatin A employing chemical and biological methods

An efficient asymmetric total synthesis of the potent cytotoxic marine natural product (-)-callystatin A and its 20-epi analogue has been achieved. The synthetic pathway involved the preparation of three fragments to be coupled with each other at the end of the route. The first fragment 3 was obtained using a biocatalytic enantioselective reduction of a 3,5-dioxocarboxylate as the key step. For the second intermediate 4 the asymmetric alpha-alkylation of an O-protected derivative of 4-hydroxybutanal was performed exploiting the SAMP/RAMP hydrazone alkylation methodology, and followed by a highly Z-selective Horner-Wadsworth-Emmons reaction under modified conditions. For the synthesis of the polypropionate fragment 5 a diastereoselective syn-aldol reaction was employed between a chiral ethyl ketone and an alpha-substituted chiral aldehyde, both prepared in enantiopure form again by means of the asymmetric alkylation of their corresponding RAMP hydrazones. Finally, these three building blocks were coupled using highly E-selective Wittig reactions via allyltributylphosphonium ylides to afford the target compounds after a final oxidation/deprotection sequence.     

General diastereoselective synthetic approach toward isospongian diterpenes. Synthesis of (-)-marginatafuran, (-)-marginatone, and (-)-20-acetoxymarginatone

This work describes a synthetic approach to the carbocyclic skeleton of isospongian diterpenes that uses the commercially available monoterpene (S)-carvone as a C-ring synthon, which is incorporated into the tetracyclic isospongian framework via a C→ABC→ABCD ring annulation strategy using intramolecular Diels-Alder and ring-closing metathesis reactions. This approach has been successfully used to prepare both the title natural isospongians and several nonnatural oxygenated analogues. A preliminary evaluation of the inhibitory activity of the small collection of synthesized isospongians on the mammalian mitochondrial respiratory chain revealed that most were able to inhibit the integrated electron transfer chain (NADH oxidase activity) in the micromolar range.