Mapping allostery through equilibrium perturbation NMR spectroscopy

The understanding of allostery relies on the comparative analysis of macromolecules in their free and bound states. However, the direct free versus bound comparison is often challenging due to the instability of one of the two forms. This problem is effectively circumvented by using minor free/bound equilibrium perturbations which are tolerated without compromising sample stability. The subtle equilibrium perturbations are still able to reveal significant apo/holo differences if monitored by NMR experiments that are sensitive to minor populations within dynamic equilibria, such as NMR relaxation dispersion (NMRD) and hydrogen exchange (H/D and H/H) rates. These measurements are complementary to each other as they unmask how a ligand affects both the stable and the excited states of the free energy landscape for its protein receptor. The proposed equilibrium perturbation approach therefore significantly expands the scope of applicability of NMRD and hydrogen exchange experiments to the investigation of ligand-protein interactions, in general, unveiling allosteric "hot spot" maps for systems that have been traditionally elusive to direct free/bound comparisons.     

Quantification of tamoxifen and metabolites and soy isoflavones in human plasma using liquid chromatography with electrospray ionization tandem mass spectrometry

Tamoxifen is an important estrogen receptor antagonist used successfully for the treatment and prevention of breast cancer. The use of complementary and alternative medicines is an increasingly popular means for patients to participate in their own health care, and soy products, which contain phytoestrogens, have been widely promoted for possible beneficial effects on menopausal symptoms. The possibility that soy isoflavones could reduce tamoxifen efficacy has been demonstrated in animal models of post-menopausal breast cancer, but the occurrence of such an effect in women has not been explored. This paper describes the development and validation of a sensitive method using solid-phase extraction and isotope dilution liquid chromatography/tandem mass spectrometry with multiple reaction monitoring for the concurrent analysis of the major soy isoflavones (genistein and daidzein), an important metabolite of daidzein (equol), tamoxifen, and its important metabolites (4-hydroxytamoxifen, N-desmethyltamoxifen, and 4-hydroxy-N-desmethyltamoxifen or "endoxifen") in the serum of rats and women. The limits of quantification achieved are sufficient to determine accurately and precisely the concentrations of all of these analytes in women consuming soy foods and/or therapeutic doses of tamoxifen at levels consistent with modulation of estrogen receptor-mediated functions. These procedures enable future investigations of the possible impact of diet on the outcome of breast cancer therapy.     

Quantification of Paraquat, MPTP, and MPP+ in brain tissue using microwave-assisted solvent extraction (MASE) and high-performance liquid chromatography–mass spectrometry

Animal models, consistent with the hypothesis of direct interaction of paraquat (PQ) and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) with specific areas of the central nervous system have been developed to study Parkinson’s disease (PD) in mice. These models have necessitated the creation of an analytical method for unambiguous identification and quantitation of PQ and structurally similar MPTP and 1-methyl-4-phenylpyridinium ion (MPP⁺) in brain tissue. A method for determination of these compounds was developed using microwave-assisted solvent extraction (MASE) and liquid chromatography–mass spectrometry. Extraction solvent and microwave conditions such as power and time were optimized to produce recoveries of 90% for PQ 78% for MPTP and 97% for its metabolite MPP⁺. The chromatographic separation was performed on a C8, column and detection was carried out using an ion trap as an analyzer with electrospray ionization. Mass spectrometer parameters such as heated capillary temperature, spray voltage, capillary voltage and others were also optimized for each analyte. Analysis was done in selective ion-monitoring (SIM) mode using m/z 186 for PQ, m/z 174 for MPTP, and m/z 170 for MPP⁺. The method detection limit for paraquat in matrix was 100 pg, 40 pg for MPTP, and 20 pg MPP⁺.     

Thickness measurement of a thin hetero-oxide film with an interfacial oxide layer by X-ray photoelectron spectroscopy

The general equation T_ove = L cos  θ ln(R_exp/R₀ + 1) for the thickness measurement of thin oxide films by X-ray photoelectron spectroscopy (XPS) was applied to a HfO₂/SiO₂/Si(1 0 0) as a thin hetero-oxide film system with an interfacial oxide layer. The contribution of the thick interfacial SiO₂ layer to the thickness of the HfO₂ overlayer was counterbalanced by multiplying the ratio between the intensity of Si⁴⁺ from a thick SiO₂ film and that of Si⁰ from a Si(1 0 0) substrate to the intensity of Si⁴⁺ from the HfO₂/SiO₂/Si(1 0 0) film. With this approximation, the thickness levels of the HfO₂ overlayers showed a small standard deviation of 0.03 nm in a series of HfO₂ (2 nm)/SiO₂ (2-6 nm)/Si(1 0 0) films. Mutual calibration with XPS and transmission electron microscopy (TEM) was used to verify the thickness of HfO₂ overlayers in a series of HfO₂ (1-4 nm)/SiO₂ (3 nm)/Si(1 0 0) films. From the linear relation between the thickness values derived from XPS and TEM, the effective attenuation length of the photoelectrons and the thickness of the HfO₂ overlayer could be determined.     

Synthesis,characterization and antimicrobial activity of cobalt(II), nickel(II)and copper(II) complexes with new asymmetrical Schiff base ligands derived from 7-formyanil-substituted diamine-sulphoxine and acetylacetone

Asymmetric 7-formyanil-substituted-imino-4-(4-methyl-2-butanone)-8-hydroxyquinoline-5-sulphonic acid (Schiff bases), react with Co^II, Ni^II and Cu^II ions to give 1:2, 1:1 and 2:1 complexes as established by conductometric titrations in 1:1 DMF:H₂O. The complexes were investigated by elemental analyses, molecular weight determinations, molar conductance, magnetic moments, thermal analysis, i.r., u.v.–vis. and e.s.r. spectra. The complexes have an octahedral crystal structure and general formula [ML·(OH₂)₂], where M^II = Co, Ni and Cu, and L = Na[7—X—HL], (—X— = (CH₂)₂, (CH₂)₃, p-C₆H₄, o-C₆H₄). Antimicrobial activity of these new ligands and their transition metal complexes has been screened in vitro on common fungi and bacteria.     

Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach

Before entering the cell, the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. Hence, this RBD is a critical target for the development of antiviral agents. Recent studies have discovered that SARS-CoV-2 variants with mutations in the RBD have spread globally. The purpose of this in silico study was to determine the potential of a fruit bromelain-derived peptide. DYGAVNEVK. to inhibit the entry of various SARS-CoV-2 variants into human cells by targeting the hACE binding site within the RBD. Molecular docking analysis revealed that DYGAVNEVK interacts with several critical RBD binding residues responsible for the adhesion of the RBD to hACE2. Moreover, 100 ns MD simulations revealed stable interactions between DYGAVNEVK and RBD variants derived from the trajectory of root-mean-square deviation (RMSD), radius of gyration (Rg), and root-mean-square fluctuation (RMSF) analysis, as well as free binding energy calculations. Overall, our computational results indicate that DYGAVNEVK warrants further investigation as a candidate for preventing SARS-CoV-2 due to its interaction with the RBD of SARS-CoV-2 variants.     

The behavior of 2‐thioxo‐4‐thiazolidinones toward organophosphorus reagents

The reaction of 2‐thioxo‐4‐thiazolidinone ( 1a ) with phosphorus ylides 2a and 2b afforded compounds 5 and 6. On the other hand, formylmethylenetriphenylphosphorane (2c) reacts with 1a and its N‐methyl derivative 1b to give the new complicated phosphonium ylides 7a,b, respectively. Reactions of 1b with ylides 2a and 2d gave rise to the olefinic compound 8 and the new phosphorane product 9. Moreover, dialkyl phosphites 3a,b and trialkyl phosphites 4a–c react with 1a to give both the alkylated products 10a–c and the dimeric compounds 11,12. A mechanism is proposed to explain the formation of the new products.© 1999 John Wiley & Sons, Inc. Heteroatom Chem 10: 337–341, 1999     

Reaction of 2‐amino‐3‐cyano‐4,5,6,7‐tetrahydrobenzo‐[b]thiophene with ethyl acetoacetate: Novel syntheses of pyridines,pyrazoles, and their fused derivatives

The reaction of 2‐amino‐3‐cyano‐4,5,6,7‐tetrahydrobenzo[b]thiophene 1 with ethyl acetoacetate 2 gave compound 3 . The reactivity of the latter product toward a variety of chemical reagents was studied to give fused thiophene derivatives of potential pharmaceutical interest. © 2001 John Wiley & Sons, Inc. Heteroatom Chem 12:518–527, 2001     

Activated nitriles in heterocyclic synthesis: Novel syntheses of 3H-1,2,4-triazolo-[1,5-a]pyridine derivatives

A new route for the synthesis of 3H-1,2,4-triazolo[1,5-a]pyridines 7a–j , 12a , b , and 17a , b utilizing the reaction of the hydrazones of cyanoethanoic acid hydrazide 3a , b with ylidene malononitriles 2a–e , malononitrile, and 3-aminocrotononitrile is described.