Mass spectrometry and n-in-one analytics in early drug discovery : combinatorial chemistry libraries, lipophilicity and absorption screening

This thesis describes current and past n-in-one methods and presents three early experimental studies using mass spectrometry and the triple quadrupole instrument on the application of n-in-one in drug discovery. N-in-one strategy pools and mix samples in drug discovery prior to measurement or analysis. This allows the most promising compounds to be rapidly identified and then analysed. Nowadays properties of drugs are characterised earlier and in parallel with pharmacological efficacy. Studies presented here use in vitro methods as caco-2 cells and immobilized artificial membrane chromatography for drug absorption and lipophilicity measurements. The high sensitivity and selectivity of liquid chromatography mass spectrometry are especially important for new analytical methods using n-in-one. In the first study, the fragmentation patterns of ten nitrophenoxy benzoate compounds, serial homology, were characterised and the presence of the compounds was determined in a combinatorial library. The influence of one or two nitro substituents and the alkyl chain length of methyl to pentyl on collision-induced fragmentation was studied, and interesting structurefragmentation relationships were detected. Two nitro group compounds increased fragmentation compared to one nitro group, whereas less fragmentation was noted in molecules with a longer alkyl chain. The most abundant product ions were nitrophenoxy ions, which were also tested in the precursor ion screening of the combinatorial library. In the second study, the immobilized artificial membrane chromatographic method was transferred from ultraviolet detection to mass spectrometric analysis and a new method was developed. Mass spectra were scanned and the chromatographic retention of compounds was analysed using extract ion chromatograms. When changing detectors and buffers and including n-in-one in the method, the results showed good correlation. Finally, the results demonstrated that mass spectrometric detection with gradient elution can provide a rapid and convenient n-in-one method for ranking the lipophilic properties of several structurally diverse compounds simultaneously. In the final study, a new method was developed for caco-2 samples. Compounds were separated by liquid chromatography and quantified by selected reaction monitoring using mass spectrometry. This method was used for caco-2 samples, where absorption of ten chemically and physiologically different compounds was screened using both single and nin- one approaches. These three studies used mass spectrometry for compound identification, method transfer and quantitation in the area of mixture analysis. Different mass spectrometric scanning modes for the triple quadrupole instrument were used in each method. Early drug discovery with n-in-one is area where mass spectrometric analysis, its possibilities and proper use, is especially important.Tämä tutkielma kertoo vanhoista sekä uusista seosanalytiikan muodoista lääkkeen keksimisessä ja kehittämisessä sekä esittelee kolme varhaista kokeellista tutkimusta käyttäen kolmoiskvadrupoli massa spektrometri -laitteistoa. Lääkekehityksen seosanalytiikka, n-in-one, yhdistää tutkittavia kemikaaleja ja niiden näytteitä sekä ennen kokeellista määritystä että analysointia, ja siten mahdollistaa uusien yhdisteiden löytämisen ja tunnistamisen nopeasti. Aikaisessa vaiheessa, samanaikaisesti farmakologisten vaikutusten seulonnan kanssa, määritetään myös yhdisteiden ominaisuuksia. Työssä esitetyt in vitro menetelmät, kuten caco-2 solut ja kromatografiset lipidikalvot, mallintavat lääkeaineiden imeytymistä ja lipofiilisyyttä. Nestekromatografia massa spektrometria on herkkä ja erittäin erottelukykyinen tekniikka ja siksi se on erityisen tärkeä uusissa seosanalytiikan menetelmissä. Ensimmäisessä työssä tutkittiin kymmenen nitrofenoksibentsoaatti -rakenteisen molekyylin massaspektrometrinen hajoaminen. Tämä homologisarja myös yhdistettiin ja määritettiin kuin kombinatorinen kirjasto. Nitro ja di-nitro substituointi sekä molekyylien eripituiset alkyyliketjut aiheuttivat massaspektrometrisesti mielenkiintoisia rakenne/hajoaminen -suhteita. Kaksi nitro-ryhmää lisäsi hajoamista verrattuna yhteen, kun taas pidemmillä alkyyliketjuilla oli rakennetta stabiloiva vaikutus. Nitrofenoksi-ioni oli vallitsevin hajoamistuote, ja tätä hyödynnettiin myös kombinatorisen kirjaston seulonnassa. Seuraavassa työssä kehitettiin uusi menetelmä kromatografiselle lipidikalvolle, IAM – kolonnille, jossa vanhan menetelmän ultravioletti detektori vaihdettiin massa spektrometriksi. Yhdisteiden retentioajat määritettiin skannaamalla massaspektrejä ja suodattamalla spektreistä ionikromatogrammit. Tulokset osoittivat hyvää korrelaatiota vanhan menetelmän tuloksiin, vaikka menetelmässä vaihdettiin detektoria, puskuria ja lisättiin mahdollisuus seosanalytiikkaan. Lisäksi työssä esiteltiin nopea n-in-one menetelmä erilaisten yhdisteiden samanaikaiseen lipofiilisyyden luokitteluun käyttäen massaspektrometriä sekä gradienttia. Viimeisessä tutkimuksessa kehitettiin uusi menetelmä caco-2 näytteille. Yhdisteet erotettiin nestekromatografisesti ja pitoisuudet määritettiin massaspektrometrisesti valittujen reaktioiden avulla. Tätä menetelmää käytettiin caco-2 näytteille, jossa kymmenen kemiallisesti ja fysiologisesti erilaisen yhdisteen imeytyminen tutkittiin yksittäin sekä käyttäen seosanalyysejä. Nämä kolme tutkimusta käyttivät massaspektrometriaa ja seosanalytiikkaa yhdisteiden tunnistamisessa, menetelmän siirrossa sekä pitoisuuden määrityksessä. Jokaisessa tutkimuksessa käytettiin kolmoiskvadrupoli massaspektrometrin eri määritystapoja. Massaspektrometrisen analytiikan mahdollisuudet ja oikeanlainen käyttö ovat erityisen tärkeitä kun määritetään seoksia lääkkeen keksimisen varhaisessa vaiheessa

The Participation of 3,3,3-Trichloro-1-nitroprop-1-ene in the [3+2] Cycloaddition Reaction with Selected Nitrile N-Oxides in the Light of the Experimental and MEDT Quantum Chemical Study

The regioselective zw-type [3 + 2] cycloaddition (32CA) reactions of a series of aryl-substituted nitrile N-oxides (NOs) with trichloronitropropene (TNP) have been both experimentally and theoretically studied within the Molecular Electron Density Theory (MEDT). Zwitterionic NOs behave as moderate nucleophiles while TNP acts as a very strong electrophile in these polar 32CA reactions of forward electron density flux, which present moderate activation Gibbs free energies of 22.8-25.6 kcal·mol−1 and an exergonic character of 28.4 kcal·mol−1 that makes them irreversible and kinetically controlled. The most favorable reaction is that involving the most nucleophilic MeO-substituted NO. Despite Parr functions correctly predicting the experimental regioselectivity with the most favorable O-CCCl3 interaction, these reactions follow a two-stage one-step mechanism in which formation of the O-C(CCl3) bond takes place once the C-C(NO2) bond is already formed. The present MEDT concludes that the reactivity differences in the series of NOs come from their different nucleophilic activation and polar character of the reactions, rather than any mechanistic feature

Part I: Nitroalkane Transformations: Synthesis of Vicinal Diamines and Arylnitromethanes Part II: Quantification of Electrophile Lumo-Lowering via Colorimetric Probes

Part I of this dissertation focuses on the synthetic chemistry of arylnitromethanes as both products and reactants. Use of these compounds as key building blocks in the synthesis of vicinal diamines was explored via a catalytic aza-Henry strategy. These studies resulted in the identification of simple cinchonidinium acetate as an effective catalyst for the asymmetric synthesis of syn-1,2-diarylethylenediamines with excellent diastereocontrol. Difficulties in synthesizing arylnitromethanes from existing techniques provided impetus for the development of an improved method of greater generality. Ultimately, successful conditions were identified for the palladium-catalyzed cross coupling of nitromethane with readily available aryl halide partners, providing facile access to an array of functionalized arylnitromethanes. A tandem reductive Nef process was incorporated to provide a one-pot transformation directly to aryl aldehyde or oxime, thereby exploiting the use of nitromethane as a formylation equivalent. Application of the nitromethylation conditions to vinyl halides resulted in the discovery of a unique tandem cross-coupling/π-allylation nitroethylation reaction. Part II of this dissertation focuses on the use of colorimetric sensors for the quantitative measurement of catalyst strength via LUMO-lowering of electrophiles. Despite rampant growth in catalyst synthesis and application, understanding of controlling factors of catalyst activity, particularly for those functioning through hydrogen-bonding, remains limited. A simple pyrazinone chromophore was found to exhibit hypsochromic shifts upon binding to an array of known hydrogen-bond catalysts. These wavelength shifts showed high correlation to relative rate enhancement of the catalysts in Diels Alder and Friedel Crafts reactions. Acidity values, often used to estimate hydrogen-bond strength, were illustrated to be poor indicators of catalytic activity, in contrast to that of the wavelength shifts. The results establish the catalyst-sensor wavelength is a useful tool with which to gauge catalyst strength and also reveal catalyst structure-activity relationships. Current efforts for measuring stronger Brønsted and Lewis Acid catalysts with an alternate colorimetric sensor are also described

Electrostatic Discharge and Energetic Materials

In this short review, excerptions from the literature on electrostatic discharge  which includes  physics of electric spark, charging of organic molecules, sensitivity measurements, some theory and predictions, and electrostatic discharge   values of some group of explosives, including nitro compounds, nitramines, composites thermites, etc., have been presented

Quantitative toxicity prediction using topology based multi-task deep neural networks

The understanding of toxicity is of paramount importance to human health and environmental protection. Quantitative toxicity analysis has become a new standard in the field. This work introduces element specific persistent homology (ESPH), an algebraic topology approach, for quantitative toxicity prediction. ESPH retains crucial chemical information during the topological abstraction of geometric complexity and provides a representation of small molecules that cannot be obtained by any other method. To investigate the representability and predictive power of ESPH for small molecules, ancillary descriptors have also been developed based on physical models. Topological and physical descriptors are paired with advanced machine learning algorithms, such as deep neural network (DNN), random forest (RF) and gradient boosting decision tree (GBDT), to facilitate their applications to quantitative toxicity predictions. A topology based multi-task strategy is proposed to take the advantage of the availability of large data sets while dealing with small data sets. Four benchmark toxicity data sets that involve quantitative measurements are used to validate the proposed approaches. Extensive numerical studies indicate that the proposed topological learning methods are able to outperform the state-of-the-art methods in the literature for quantitative toxicity analysis. Our online server for computing element-specific topological descriptors (ESTDs) is available at http://weilab.math.msu.edu/TopTox/Comment: arXiv admin note: substantial text overlap with arXiv:1703.1095