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.     

Direct Addition of Amides to Glycals Enabled by Solvation‐Insusceptible 2‐Haloazolium Salt Catalysis

The direct 2‐deoxyglycosylation of nucleophiles with glycals leads to biologically and pharmacologically important 2‐deoxysugar compounds. Although the direct addition of hydroxyl and sulfonamide groups have been well developed, the direct 2‐deoxyglycosylation of amide groups has not been reported to date. Herein, we show the first direct 2‐deoxyglycosylation of amide groups using a newly designed Brønsted acid catalyst under mild conditions. Through mechanistic investigations, we discovered that the amide group can inhibit acid catalysts, and the inhibition has made the 2‐deoxyglycosylation reaction difficult. Diffusion‐ordered two‐dimensional NMR spectroscopy analysis implied that the 2‐chloroazolium salt catalyst was less likely to form aggregates with amides in comparison to other acid catalysts. The chlorine atom and the extended π‐scaffold of the catalyst played a crucial role for this phenomenon. This relative insusceptibility to inhibition by amides is more responsible for the catalytic activity than the strength of the acidity.     

The 1H and 13C NMR chemical shifts of Strychnos alkaloids revisited at the DFT level

The density functional theory calculation of ¹H and ¹³C NMR chemical shifts in a series of ten 10 classically known Strychnos alkaloids with a strychnine skeleton was performed at the PBE0/pcSseg-2//pcseg-2 level. It was found that calculated ¹H and ¹³C NMR chemical shifts provided a markedly good correlation with experiment characterized by a mean absolute error of 0.08 ppm in the range of 7 ppm for protons and 1.67 ppm in the range of 150 ppm for carbons, so that a mean absolute percentage error was as small as ~1% in both cases.     

Identifying aspirin polymorphs from combined DFT-based crystal structure prediction and solid-state NMR

A combined experimental and computational approach was used to distinguish between different polymorphs of the pharmaceutical drug aspirin. This method involves the use of ab initio random structure searching (AIRSS), a density functional theory (DFT)-based crystal structure prediction method for the high-accuracy prediction of polymorphic structures, with DFT calculations of nuclear magnetic resonance (NMR) parameters and solid-state NMR experiments at natural abundance. AIRSS was used to predict the crystal structures of form-I and form-II of aspirin. The root-mean-square deviation between experimental and calculated ¹H chemical shifts was used to identify form-I as the polymorph present in the experimental sample, the selection being successful despite the large similarities between the molecular environments in the crystals of the two polymorphs.     

Nano-sized Cu(II) and Zn(II) complexes and their use as a precursor for synthesis of CuO and ZnO nanoparticles: A study on their sonochemical synthesis,characterization, and DNA-binding/cleavage,anticancer, and antimicrobial activities

Two new divalent copper (C1) and zinc (C2) chelates having the formulae [M(PIMC)₂] (where M = Cu(II), Zn(II) and PIMC = Ligand [(E)-3-(((3-hydroxypyridin-2-yl)imino)methyl)-4H-chromen-4-one] were obtained and characterized by several techniques. Structures and geometries of the synthesized complexes were judged based on the results of alternative analytical and spectral tools supporting the proposed formulae. IR spectral data confirmed the coordination of the ligands to the copper and zinc centers as monobasic tridentate in the enol form. Thermal analysis, UV-Vis spectra and magnetic moment confirmed the geometry around the copper center to be tetrahedral, square pyramidal and octahedral. Study of the binding ability of the synthesized compounds with Circulating tumor DNA (CT-DNA) bas been evaluated applying UV-Vis spectral titration and viscosity measurements. The copper and zinc oxides were achieved from the copper and zinc nano-particles structures Schiff base complexes as the raw material after calcination for 5 hr at 600°C. On the other hand, synthesized of C1 and C2 NPs were used as suitable precursors to the preparation of CuO and ZnO NPs. Finally, the synthesized of the two complexes exhibited enhanced activity against the tested bacterial (Staphylococcus aureus and Escherichia Coli) and fungal strains (Candida albicans and Aspergillus fumigatus) as compared to HPIMC. Among all these synthesized compounds, C1 exhibits good cleaving ability compared to other newly synthesized C2.     

Development and validation of a reversed‐phase HPLC method for CYP1A2 phenotyping by use of a caffeine metabolite ratio in saliva

CYP1A2 is important for metabolizing various clinically used drugs. Phenotyping of CYP1A2 may prove helpful for drug individualization therapy. Several HPLC methods have been developed for quantification of caffeine metabolites in plasma and urine. Aim of the present study was to develop a valid and simple HPLC method for evaluating CYP1A2 activity during exposure in xenobiotics by the use of human saliva. Caffeine and paraxanthine were isolated from saliva by liquid‐liquid extraction (chlorophorm/isopropanol 85/15v/v). Extracts were analyzed by reversed‐phase HPLC on a C₁₈ column with mobile phase 0.1% acetic acid/methanol/acetonitrile (80/20/2 v/v) and detected at 273nm. Caffeine and paraxanthine elution times were <13min with no interferences from impurities or caffeine metabolites. Detector response was linear (0.10–8.00µg/ml, R²>0.99), recovery was >93% and bias <4.47%. Intra‐ and inter‐day precision was <5.14% (n=6). The limit of quantitation was 0.10µg/ml and the limit of detection was 0.018±0.002µg/mL for paraxanthine and 0.032±0.002µg/ml for caffeine. Paraxanthine/caffeine ratio of 34 healthy volunteers was significantly higher in smokers (p<0.001). Saliva paraxanthine/caffeine ratios and urine metabolite ratios were highly correlated (r=0.85, p<0.001). The method can be used for the monitoring of CYP1A2 activity in clinical practice and in studies relevant to exposure to environmental and pharmacological xenobiotics. Copyright © 2015 John Wiley & Sons, Ltd.     

Study of Endogen Substrates,Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.     

Spectral estimates for saddle point matrices arising in weak constraint four‐dimensional variational data assimilation

We consider the large sparse symmetric linear systems of equations that arise in the solution of weak constraint four‐dimensional variational data assimilation, a method of high interest for numerical weather prediction. These systems can be written as saddle point systems with a 3 × 3 block structure but block eliminations can be performed to reduce them to saddle point systems with a 2 × 2 block structure, or further to symmetric positive definite systems. In this article, we analyse how sensitive the spectra of these matrices are to the number of observations of the underlying dynamical system. We also obtain bounds on the eigenvalues of the matrices. Numerical experiments are used to confirm the theoretical analysis and bounds.