Could chroman-4-one derivative be a better inhibitor of PTR1? – Reason for the identified disparity in its inhibitory potency in Trypanosoma brucei and Leishmania major

Most notable Kinetoplastids are of the genus Trypanosoma and Leishmania, affecting several millions of humans in Africa and Latin America. Current therapeutic options are limited by several drawbacks, hence the need to develop more efficacious inhibitors. An investigation to decipher the mechanism behind greater inhibitory potency of a chroman-4-one derivative (compound 1) in Trypanosoma brucei pteridine reductase 1 (TbPTR1) and Leishmania major pteridine reductase 1 (LmPTR1) was performed. Estimation of ΔG_bind revealed that compound 1 had a greater binding affinity in TbPTR1 with a ΔG_bind value of −49.0507 Kcal/mol than −29.2292 Kcal/mol in LmPTR1. The ΔGbind in TbPTR1 were predominantly contributed by “strong” electrostatic energy compared to the “weak” van der Waals in LmPTR1. In addition to this, the NADPH cofactor contributed significantly to the total energy of TbPTR1. A characteristic weak aromatic π interaction common in PTR1 was more prominent in TbPTR1 than LmPTR1. The consistent occurrence of high-affinity conventional hydrogen bond interactions as well as a steady interaction of crucial active site residues like Arg14/Arg17, Ser95/Ser111, Phe97/Phe113 in TbPTR1/LmPTR1 with chroman-4-one moiety equally revealed the important role the moiety played in the activity of compound 1. Overall, the structural and conformational analysis of the active site residues in TbPTR1 revealed them to be more rigid than LmPTR1. This could be the mechanism of interaction TbPTR1 employs in exerting a greater potency than LmPTR1. These findings will further give insight that will be assistive in modifying compound 1 for better potency and the design of novel inhibitors of PTR1.     

Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2'-azido-2'-deoxyribonucleoside 5'-diphosphates

2'-azido-2'-deoxyribonucleoside 5'-diphosphates are mechanism-based inhibitors of Ribonucleotide Reductase. Considerable effort has been made to elucidate their mechanism of inhibition, which is still controversial and not fully understood. Previous studies have detected the formation of a radical intermediate when the inhibitors interact with the enzyme, and several authors have proposed possible structures for this radical. We have conducted a theoretical study of the possible reactions involved, which allowed us to identify the structure of the new radical among the several proposals. A new reactional path is also proposed that is the most kinetically favored to yield this radical and ultimately inactivate the enzyme. The energetic involved in this mechanism, both for radical formation and radical decay, as well as the calculated Hyperfine Coupling Constants for the radical intermediate, are in agreement with the correspondent experimental values. This mechanistic alternative is fully coherent with remaining experimental data.     

Synthesis of 8-vinyladenosine 5′-di- and 5′-triphosphate: evaluation of the diphosphate compound on ribonucleotide reductase

The synthesis of 5′-di- and 5′-triphosphate of 8-vinyladenosine to be tested on ribonucleotide reductases requires the modification of known methods. The phosphate group was introduced by treatment with an in situ generated chlorophosphite. Protection of the 2′,3′ diol with acetyl groups suppressed depurination during acid removal of the phosphotriester protecting groups. The di- and triphosphate compounds were obtained by treatment of the activated adenylic acid with phosphate or pyrophosphate anions followed by removal of the acetate protecting groups. Preliminary studies were conducted on Escherichia coli ribonucleotide reductase and have shown that the diphosphate compound is efficiently reduced.     

Synthesis and biological activity of fluorinated 2-amino-4-aryl-3,4-dihydro[1,3,5]triazino[1,2-a]benzimidazoles

The heterocyclic nucleus s-triazino[1,2-a]benzimidazole has been reported to exhibit antibacterial activity. In this study, seven new 3,4-dihydro[1,3,5]triazino[1,2-a]benzimidazole derivatives were prepared via cyclocondensation between 2-guanidinobenzimidazole and fluorine substituted (including trifluoromethyl) benzaldehydes. The structures of all the compounds were confirmed by ¹H, ¹³C NMR and IR spectral data. Spectral data also suggested the existence of various tautomeric forms of the fluorine-containing s-triazino[1,2-a]benzimidazole compounds. The synthesized compounds were also screened for antibacterial and bovine dihydrofolate reductase (DHFR) inhibitory activities. The compound 3g substituted with a 3′,5′-bis(trifluoromethyl)phenyl moiety demonstrated the best antibacterial activity in the series. None of the tested compounds significantly inhibited bovine DHFR.     

Synthesis of phosphonocinnamic thioesters, substrate analogues of cinnamoyl-CoA reductase, a key enzyme in the lignification process

The one-pot transesterification of diethylarylvinylphosphonates with N-acetylcysteamine has been achieved using phosphonochloridates as intermediates. Reaction of phosphonodiesters with (COCl)₂ gave the corresponding chlorinated compounds, which were coupled with N-acetylcysteamine in presence of Et₃N.     

Reduction of nitrates,the no donors,by hemoglobin in the presence of cysteine

Hemoglobin (Hb) reduces 3,3-bis(nitroxymethyl)oxetane (NMO) only in the presence of cysteine (Cys) via intermediate cysteine thionitrate. The kinetics of the reaction of NMO with Cys and the kinetics and mechanism of formation of NO in the ternary system Hb-NMO-Cys were studied. The formation rate of Hb-NO in the ternary system is higher than that of Hb-NO in the reaction of Hb only with NO ₂ ⁻ generated in the binary system NMO-Cys. The second-order rate constants of the main reaction steps in the system Hb-NMO-Cys were estimated by simulating the kinetics of the reactions with a system of equations taking into account equilibria between all components of the reaction mixture. Hemoglobin reduces cysteine thionitrate, the intermediate in the reaction of NMO with Cys, to NO. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 725–731, April, 2007.     

Protein identification by peptide mass fingerprinting and peptide sequence tagging with alternating scans of nano-liquid chromatography/infrared multiphoton dissociation Fourier transform ion cyclotron resonance mass spectrometry

We have developed a method for protein identification with peptide mass fingerprinting and sequence tagging using nano liquid chromatography (LC)/Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). To achieve greater sensitivity, a nanoelectrospray (nano-ES) needle packed with reversed-phase medium was used and connected to the nano-ES ion source of the FTICR mass spectrometer. To obtain peptide sequence tag information, infrared multiphoton dissociation (IRMPD) was carried out in nano-LC/FTICR-MS analysis. The analysis involves alternating nano-ES/FTICR-MS and nano-ES/IRMPD-FTICR-MS scans during a single LC run, which provides sets of parent and fragment ion masses of the proteolytic digest. The utility of this alternating-scan nano-LC/IRMPD-FTICR-MS approach was evaluated by using bovine serum albumin as a standard protein. We applied this approach to the protein identification of rat liver diacetyl-reducing enzyme. It was demonstrated that this enzyme was correctly identified as 3-alpha-hydroxysteroid dehydrogenase by the alternating-scan nano-LC/IRMPD-FTICR-MS approach with accurate peptide mass fingerprinting and peptide sequence tagging.     

Modeling,stability and the activity assessment of glutathione reductase from Streptococcus Thermophilus; Insights from the in-silico simulation study

Antioxidant enzymes (AEs) are the main parts of the natural barriers of the body which deactivate the oxidant factors. To discover and understand their structures and function will deserve a deeper investigation. Accordingly, as an AE of probiotic strains, glutathione reductase of Streptococcus thermophilus (GRst), is characterized and modeled by in-silico methods. The investigation indicated the physicochemical properties of the enzyme and estimated its half-life of being more than 10 h. The analysis revealed that the enzyme is composed of 86 strands, 123 helices, and 241 random coils. Homology modeling of the GRst led to the construction of the enzyme’s 3D model that 62% of which is analogous to the glutathione reductase of Escherichia Coli (GRec), and which is qualitatively high in terms of Molpdf, ERRAT, Verify-3D and Ramachandran scores. Moreover, the structural stability of the model was substantiated within 10 and 20 ns at 400 and 300 K, respectively. Interestingly, these data showed that the enzyme is more stable than GRec at 400 K. In other words, the active cavity of the constructed model is characteristic of 38 amino acid residues within 4 Å around the NADPH and GSSG as corresponding ligands of GRst. Noteworthy, herein is the fact that, CYS40 and CYS45 are specified as the active site residues of this enzyme. Furthermore, the interaction assays of the model support its antioxidant capability which is even more than that of GRec.In general, these data provide a new model of AEs being inclusive of high antioxidant capacity and thermostability.     

Determination of triapine,a ribonucleotide reductase inhibitor,in human plasma by liquid chromatography tandem mass spectrometry

Triapine is an inhibitor of ribonucleotide reductase (RNR). Studies have shown that triapine significantly decreases the activity of RNR and enhanced the radiation‐mediated cytotoxicity in cervical and colon cancer. In this work, we have developed and validated a selective and sensitive LC‐MS/MS method for the determination of triapine in human plasma. In this method, 2‐[(3‐fluoro‐2‐pyridinyl)methylene] hydrazinecarbothioamide (NSC 266749) was used as the internal standard (IS); plasma samples were prepared by deproteinization with acetonitrile; tripaine and the IS were separated on a Waters Xbridge Shield RP₁₈ column (3.5 µm; 2.1 × 50 mm) using a mobile phase containing 25.0% methanol and 75.0% ammonium bicarbonate buffer (10.0 mm , pH 8.50; v/v); column eluate was monitored by positive turbo‐ionspray tandem mass spectrometry; and quantitation of triapine was carried out in multiple‐reaction‐monitoring mode. The method developed had a linear calibration range of 0.250–50.0 ng/mL with correlation coefficient of 0.999 for triapine in human plasma. The IS‐normalized recovery and the IS‐normalized matrix factor of triapine were 101–104% and 0.89–1.05, respectively. The accuracy expressed as percentage error and precision expressed as coefficient of variation were ≤±6 and ≤8%, respectively. The validated LC‐MS/MS method was applied to the measurement of triapine in patient samples from a phase I clinical trial. Copyright © 2015 John Wiley & Sons, Ltd.