Jochen Junker | Fundação Oswaldo Cruz (original) (raw)

Papers by Jochen Junker

Social Science Research Network, 2023

Journal of Analytical Methods in Chemistry

As has been documented numerous times over the years, nuclear magnetic resonance (NMR) experiment... more As has been documented numerous times over the years, nuclear magnetic resonance (NMR) experiments are intrinsically quantitative. Still, quantitative NMR methods have not been widely adopted or largely introduced into pharmacopoeias. Here, we describe the quantitative interpretation of the 1D proton NMR experiment using only absolute signal intensities with the variation of common experimental parameters and their application.

Molecules, 2021

Structure elucidation with NMR correlation data is dicey, as there is no way to tell how ambiguou... more Structure elucidation with NMR correlation data is dicey, as there is no way to tell how ambiguous the data set is and how reliably it will define a constitution. Many different software tools for computer assisted structure elucidation (CASE) have become available over the past decades, all of which could ensure a better quality of the elucidation process, but their use is still not common. Since 2011, WebCocon has integrated the possibility to generate theoretical NMR correlation data, starting from an existing structural proposal, allowing this theoretical data then to be used for CASE. Now, WebCocon can also read the recently presented NMReDATA format, allowing for uncomplicated access to CASE with experimental data. With these capabilities, WebCocon presents itself as an easily accessible Web-Tool for the quality control of proposed new natural products. Results of this application to several molecules from literature are shown and demonstrate how CASE can contribute to improve...

Magnetic Resonance in Chemistry, 2021

The nuclear magnetic resonance extracted data (NMReDATA) format has been proposed as a way to sto... more The nuclear magnetic resonance extracted data (NMReDATA) format has been proposed as a way to store, exchange, and disseminate nuclear magnetic resonance (NMR) data and physical and chemical metadata of chemical compounds. In this paper, we report on analytical workflows that take advantage of the uniform and standardized NMReDATA format. We also give access to a repository of sample data, which can serve for validating software packages that encode or decode files in NMReDATA format.

Copyright information:Taken from "TAR-RNA recognition by a novel cyclic a... more Copyright information:Taken from "TAR-RNA recognition by a novel cyclic aminoglycoside analogue"Nucleic Acids Research 2006;34(12):3599-3608.Published online 19 Jul 2006PMCID:PMC1524922.© 2006 The Author(s) () View of the best energy structure of the family of . The aminoglycoside analogue (color coded by atom: dark gray, red and blue sticks) is placed in the major groove of the upper stem of the HIV-2 TAR-RNA. A22 and U40, depicted in orange, clearly show that the hydrogen bonds between 22 and 40 are disrupted and that A22 tilts away from the major groove to accommodate the ligand. Besides A22 and G26, U23 (magenta), U25 (turquoise) and A35 (pink) have direct contacts with the aminoglycoside analogue. The positively charged amino group of the ligand sugar- interacts with the π-orbital of the A35 base, the amino group of sugar- interacts electrostatically with the major groove edge of G28 (dashed yellow line), while the amino group of sugar- contacts the phosphate of A22 (dashed yellow line). G34 (yellow sticks) stacks on the top of G36. The backbone of the loop is shown as yellow lines. A similar intermolecular interaction pattern is observed also for the other structures of the ensemble. () Same as in (A) after 90° rotation around the vertical axis.

Copyright information:Taken from "TAR-RNA recognition by a novel cyclic a... more Copyright information:Taken from "TAR-RNA recognition by a novel cyclic aminoglycoside analogue"Nucleic Acids Research 2006;34(12):3599-3608.Published online 19 Jul 2006PMCID:PMC1524922.© 2006 The Author(s) The function ( − )/( − ) is plotted versus the concentration of the aminoglycoside analogue in each lane of the PACE gel. is the retardation distance in each lane, is the retardation distance of the TAR-RNA without and is the retardation distance of the TAR-RNA completely bound to (concentration of = 500 µM). The function ( − )/( − ) can be expressed in terms of molar fractions of bound and free RNA, according to the procedure described by Cilley and Williamson (). Different binding models were assumed and the theoretical dependence of ( − )/( − ) on the concentration of was calculated in each case from the molar fractions assuming constant concentration of in each lane. The experimental data (red dots) were fitted to the theoretical functions using IgorPro to derive the binding stoichiometry for the TAR/ complex. Six different models were considered: (i) one molecule of the TAR-RNA binds one molecule of (yellow line); (ii) one molecule of the TAR-RNA binds two molecules of with the same (green line); (iii) two molecules of the RNA bind one molecule of (magenta); (iv) one molecule of the TAR-RNA binds two molecules of with different (blue line); (v) one molecule of the TAR-RNA binds one molecule of (); subsequently the TAR/ complex dimerizes () (close to the yellow line, not shown); (vi) two molecules of the RNA bind one molecule of (2 ); subsequently two molecules of are recruited by the RNA dimer for a total of two RNA molecules and three molecules of () (red line; ≈ 20 µM; ≈ 3 mM). The best fit is obtained for case (f), which supports the stoichiometry inferred from the NMR data.

Química Nova, 2021

SYNTHESIS OF NOVEL 1,2,3-TRIAZOLES INSPIRED ON THE SRPIN340 AND EVALUATION OF THEIR EFFECTS ON HU... more SYNTHESIS OF NOVEL 1,2,3-TRIAZOLES INSPIRED ON THE SRPIN340 AND EVALUATION OF THEIR EFFECTS ON HUMAN GLIOBLASTOMA CELL LINE. It is herein described the synthesis of a series of thirty novel 1,2,3-triazole1,4-disubstituted compounds inspired on the known SRPKs inhibitor N-(2-(piperidin-1-yl)-5-(trifluoromethyl)phenyl)isonicotinamide (SRPIN340) and biological evaluation of them against human glioblastoma multiforme cell line U87MG. Starting with 1-fluoro2-nitro-4- (trifluoromethyl)benzene (1), the substances were prepared via a five-step synthetic route. The crucial step corresponded to the copper-catalyzed cycloaddition reaction between trifluoromethyl phenyl azides and different alkynes. In general, the compounds were obtained with good yields and they were characterized utilizing spectroscopic (IR and NMR) and spectrometric (HRMS) techniques. The evaluation of the synthesized compounds at three different treatment time (24 h, 48 h, and 72 h) and concentrations (50, 100, and 150 µmo...

Molecules, 2021

Over the past decades, different software programs have been developed for the Computer-Assisted ... more Over the past decades, different software programs have been developed for the Computer-Assisted Structure Elucidation (CASE) with NMR data using with various approaches. WebCocon is one of them that has been continuously improved over the past 20 years. Here, we present the inclusion of 4JCH correlations (4J-HMBC) in the HMBC interpretation of Cocon and NOE data in WebCocon. The 4J-HMBC data is used during the structure generation process, while the NOE data is used in post-processing of the results. The marine natural product oxocyclostylidol was selected to demonstrate WebCocon’s enhanced HMBC data processing capabilities. A systematic study of the 4JCH correlations of oxocyclostylidol was performed. The application of NOEs in CASE is demonstrated using the NOE correlations of the diterpene pyrone asperginol A known from the literature. As a result, we obtained a conformation that corresponds very well to the existing X-ray structure.

Zeitschrift fur Naturforschung. C, Journal of biosciences, Jan 4, 2018

The endophytic fungus Mycosphaerella sp. (UFMGCB2032) was isolated from the healthy leaves of Eug... more The endophytic fungus Mycosphaerella sp. (UFMGCB2032) was isolated from the healthy leaves of Eugenia bimarginata, a plant from the Brazilian savanna. Two novel usnic acid derivatives, mycousfuranine (1) and mycousnicdiol (2), were isolated from the ethyl acetate extract, and their structure was elucidated by NMR and MS analyses. Compounds 1 and 2 exhibited moderate antifungal activities against Cryptococcus neoformans and Cryptococcus gattii, each with minimum inhibitory concentration values of 50.0 μg/mL and 250.0 μg/mL, respectively.

Journal of Analytical & Bioanalytical Techniques, 2012

Dengue is a very common viral disease in tropical countries. From time to time it has become epid... more Dengue is a very common viral disease in tropical countries. From time to time it has become epidemic, hindering economics and affecting the social system. Early starting treatment reduces recovery time and suffering of the patients. But, the usual diagnostics is done by detection of the antibodies, which can only be done after five days. Other parts of the metabolomics might change much faster and therefore the small molecule content in the blood might change much faster than that. By using NMR spectroscopy we attempted to differentiate blood plasma from infected patients from healthy subjects and afterwards identify the consistent changes. Several of these were found and are discussed.

Social Science Research Network, 2023

Journal of Analytical Methods in Chemistry

Molecules, 2021

Magnetic Resonance in Chemistry, 2021

Copyright information:Taken from "TAR-RNA recognition by a novel cyclic a... more Copyright information:Taken from "TAR-RNA recognition by a novel cyclic aminoglycoside analogue"Nucleic Acids Research 2006;34(12):3599-3608.Published online 19 Jul 2006PMCID:PMC1524922.© 2006 The Author(s) The function ( − )/( − ) is plotted versus the concentration of the aminoglycoside analogue in each lane of the PACE gel. is the retardation distance in each lane, is the retardation distance of the TAR-RNA without and is the retardation distance of the TAR-RNA completely bound to (concentration of = 500 µM). The function ( − )/( − ) can be expressed in terms of molar fractions of bound and free RNA, according to the procedure described by Cilley and Williamson (). Different binding models were assumed and the theoretical dependence of ( − )/( − ) on the concentration of was calculated in each case from the molar fractions assuming constant concentration of in each lane. The experimental data (red dots) were fitted to the theoretical functions using IgorPro to derive the binding stoichiometry for the TAR/ complex. Six different models were considered: (i) one molecule of the TAR-RNA binds one molecule of (yellow line); (ii) one molecule of the TAR-RNA binds two molecules of with the same (green line); (iii) two molecules of the RNA bind one molecule of (magenta); (iv) one molecule of the TAR-RNA binds two molecules of with different (blue line); (v) one molecule of the TAR-RNA binds one molecule of (); subsequently the TAR/ complex dimerizes () (close to the yellow line, not shown); (vi) two molecules of the RNA bind one molecule of (2 ); subsequently two molecules of are recruited by the RNA dimer for a total of two RNA molecules and three molecules of () (red line; ≈ 20 µM; ≈ 3 mM). The best fit is obtained for case (f), which supports the stoichiometry inferred from the NMR data.

Química Nova, 2021

Molecules, 2021

Zeitschrift fur Naturforschung. C, Journal of biosciences, Jan 4, 2018

Journal of Analytical & Bioanalytical Techniques, 2012