Alexandre A. M. Lapis

Recent Developments in the Chemistry of Deoxyribonucleic Acid (DNA) Intercalators: Principles, Design, Synthesis, Applications and Trends

In the present overview, we describe the bases of intercalation of small molecules (cationic and polar neutral compounds) in DNA. We briefly describe the importance of DNA structure and principles of intercalation. Selected syntheses, possibilities and applications are shown to exemplify the importance, drawbacks and challenges in this pertinent, new, and exciting research area. Additionally, some clinical applications (molecular processes, cancer therapy and others) and trends are described.

Ionic Liquid Supported Acid/Base-Catalyzed Production of Biodiesel

The transesterification (alcoholysis) reaction was successfully applied to synthesize biodiesel from vegetable oils using imidazolium-based ionic liquids under multiphase acidic and basic conditions. Under basic conditions, the combination of the ionic liquid 1-n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BMINTf2), alcohols, and K2CO3 (40 mol %) results in the production of biodiesel from soybean oil in high yields (>98%) and purity. H2SO4 immobilized in BMINTf2 efficiently promotes the transesterification reaction of soybean oil and various primary and secondary alcohols. In this multiphase process the acid is almost completely retained in the ionic liquid phase, while the biodiesel forms a separate phase. The recovered ionic liquid containing the acid could be reused at least six times without any significant loss in the biodiesel yield or selectivity. In both catalytic processes (acid and base), the reactions proceed as typical multiphasic systems in which the formed biodiesel accumulates as the upper phase and the glycerol by-product is selectively captured by the alcohol-ionic liquid-acid/base phase. Classical ionic liquids such as 1-n-butyl-3-methylimidazolium tetrafluoroborate and hexafluorophosphate are not stable under these acidic or basic conditions and decompose.

On the use of 2,1,3-benzothiadiazole derivatives as selective live cell fluorescence imaging probes

Newly designed 2,1,3-benzothiadiazole-containing fluorescent probes with four excited state intramolecular proton transfer (ESIPT) sites were successfully tested in live cell-imaging assays using a confluent monolayer of human stem-cells (tissue). All tested dyes were compared with the commercially available DAPI and gave far better results.

Charge-tagged acetate ligands as mass spectrometry probes for metal complexes investigations: applications in Suzuki and Heck phosphine-free reactions.

An acetate anion bearing an imidazolium cation as its charge tag was reacted with M(OAc)(2) complexes (where M = Ni, Cu, and Pd; in situ reaction) to form members of a new class of charge-tagged metal complexes. The formation of these unprecedented precatalysts with potential for cross-coupling reactions was confirmed by electrospray ionization (and tandem) mass spectrometry. The catalytic performance of the palladium complex was tested in Heck and Suzuki cross-coupling reactions, often with superior activity and yields as compared with Pd(OAc)(2).

On the selective detection of duplex deoxyribonucleic acids by 2,1,3-benzothiadiazole fluorophores

A series of 4,7-pi-extended 2,1,3-benzothiadiazoles (BTDs) with different molecular architectures, in particular, the organic dyes based on the 4-(arylethynyl)-7-(4-methoxy)-2,1,3-benzothiazole skeleton, can be used at very low concentrations (down to 10 microM) to detect DNA at 1 ppm in phosphate buffer solutions. Upon binding to DNA, these dyes showed an exponential increase in the fluorescence intensity (hyperchromic effect) and a red shift (1-5 nm) in the long-wavelength emission maxima. Pre-steady state kinetic experiments (stopped-flow) demonstrated the fast dye interaction with the biomacromolecules of DNA with an increase in fluorescence, especially with non-symmetrical BTDs containing an ethynyl spacer. An intercalation model could be proposed based on the photophysical properties, X-ray analysis, and theoretical calculations (ab initio). In this model, the intercalation occurs on the ethynyl side of the BTD, and as a consequence, the PhOMe portion is free to perform the ICT process with the BTD core and stabilizes it in the excited state.

An efficient synthesis of enantiopure (+)- and (−)-3-exo-amino-7,7-dimethoxynorbornan-2-exo-ols

Abstract We describe the synthesis of new amino alcohols (+)- and (−)-3- exo -amino-7,7-dimethoxynorbonan-2- exo -ols. The (+)- or (−)-7,7-dimethoxy-1,4,5,6-tetrachlorobicyclo[2.2.1]hept-5-en-2- endo -ol, obtained from the enzyme catalysed transesterification of the racemate, was reduced and dechlorinated (Na/NH 3 ; ethanol), followed by pyridinium chlorochromate oxidation of the resultant alcohols to the corresponding ketones. After treatment with t -BuOK/BuONO, in a nitrosation reaction, α-keto oximes were obtained. Reduction over two steps with NaBH 4 and NaBH 4 /NiCl 2 ·6H 2 O followed by in situ acetylation furnished the corresponding acetamido esters, which were hydrolysed with CH 3 OH/Na to produce the enantiopure amino alcohols in good yields.

Steady-state kinetics of indole-3-glycerol phosphate synthase from Mycobacterium tuberculosis

Indole-3-glycerol phosphate synthase (IGPS) catalyzes the irreversible ring closure of 1-(o-carboxyphenylamino)-1-deoxyribulose 5-phosphate (CdRP), through decarboxylation and dehydration steps, releasing indole-3-glycerol phosphate (IGP), the fourth step in the biosynthesis of tryptophan. This pathway is essential for Mycobacterium tuberculosis virulence. Here we describe the cloning, expression, purification, and kinetic characterization of IGPS from M. tuberculosis. To perform kinetic studies, CdRP was chemically synthesized, purified, and spectroscopically and spectrometrically characterized. CdRP fluorescence was pH-dependent, probably owing to excited-state intramolecular proton transfer. The activation energy was calculated, and solvent isotope effects and proton inventory studies were performed. pH-rate profiles were carried out to probe for acid/base catalysis, showing that a deprotonated residue is necessary for CdRP binding and conversion to IGP. A model to describe a steady-state kinetic sequence for MtIGPS-catalized chemical reaction is proposed.

Synthesis and Enzymatic Evaluation of the Guanosine Analogue 2-Amino-6-mercapto- 7-methylpurine Ribonucleoside (MESG). Insights into the Phosphorolysis Reaction Mechanism based on the Blueprint Transition State: S N 1 or S N 2?

A modificacao experimental para a sintese do MESG (2-amino-6-mercapto-7-metilpurina ribonucleosideo) 1 foi realizada com sucesso e sua caracterizacao total apresentada. ESI(+)-MSMS em alta resolucao foram realizados indicando que a clivagem nucleosidica como principal e um possivel mecanismo S N 1. Calculos ab initio baseados em estados de transicao blueprint corroboram com a proposta de um mecanismo S N 1 e descartam a possibilidade de um mecanismo S N 2. Ensaios com a enzima purina nucleosidica fosforilase (PNP, tanto humana como de M. tuberculosis) indicam a eficiencia do substrato na reacao de fosforilacao do MESG e permitem a determinacao de fosfato inorgânico em tempo real em ensaios biologicos. A modified experimental procedure for the synthesis of MESG (2-amino-6-mercapto-7methylpurine ribonucleoside) 1 has been successfully performed and its full characterization is presented. High resolution ESI(+)-MSMS indicates both the nucleoside bond cleavage as the main fragmentation in the gas phase and a possible S N 1 mechanism. Ab initio transition state calculations based on the blue print transition state support this mechanistic rationale and discard an alternative S N 2 mechanism. Assays using purine nucleoside phosphorylase (PNP) enzyme (human and M. tuberculosis sources) indicate its efficiency in the phosphorolysis of MESG and allow the quantitative determination of inorganic phosphate in real time assay.

On the mechanism of skeletal rearrangements in the acid catalysed acetylation of isodrin

1,8,9,10,11,11-Hexachlorotetracyclo[6.2.1.13,6.02,7]dodec-9-en-4-exo-yl acetate, tetracyclic1; 1,2,2,3,10,11-hexachloropentacyclo[5.4.1.03,10.04,12.05,9]dodecan-8-exo-yl acetate, half-cage2; 1,2,2,3,10,11-hexachloropentacyclo[5.4.1.03,10.04,12.05,9]dodecan-8-endo-yl acetate, half-cage3 and 1,9,10,11,11,12-hexachlorohexacyclo[5.4.1.02,6.03,10.04,8.09,12]dodecane, birdcage4 were obtained from acid catalysed acetylation of isodrin. It was observed that the intramolecular rearrangement control is highly dependent on reaction time. The equilibria involved in these rearrangements were determined by gas chromatography. Semiempirical calculations at the PM3-MNDO, AM1 and MNDO levels have been performed to obtain the optimized geometry of the reagent, products, intermediates and transition states for the rearrangement mechanism. The results of the calculations are in good agreement with the experimental data. On the basis of the theoretical and experimental investigations we propose a revised mechanism which involves a new transition state and a new non-classical reaction intermediate.