Enhanced selectivity for inhibition of analog-sensitive protein kinases through scaffold optimization

The ability to inhibit any protein kinase of interest with a small molecule is enabled by a combination of genetics and chemistry. Genetics is used to modify the active site of a single kinase to render it distinct from all naturally occurring kinases. Next, organic synthesis is used to develop a small molecule, which does not bind to wild-type kinases but is a potent inhibitor of the engineered kinase. This approach, termed chemical genetics, has been used to generate highly potent mutant kinase-specific inhibitors based on a pyrazolopyrimidine scaffold. Here, we asked if the selectivity of the resulting pyrazolopyrimidines could be improved, as they inhibit several wild-type kinases with low-micromolar IC₅₀ values. Our approach to improve the selectivity of allele-specific inhibitors was to explore a second kinase inhibitor scaffold. A series of 6,9-disubstituted purines was designed, synthesized, and evaluated for inhibitory activity against several kinases in vitro and in vivo. Several purines proved to be potent inhibitors against the analog-sensitive kinases and exhibited greater selectivity than the existing pyrazolopyrimidines.     

Sample preparation for metalloprotein analysis: A case study using horse chestnuts

In the present work, 11 different procedures for protein and metalloprotein extraction from horse chestnuts (Aescullus hippocastanum L.) in natura were tested. After each extraction, total protein was determined and, after protein separation through sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), those metals belonging to the protein structure were mapped by synchrotron radiation X-ray fluorescence (SRXRF). After mapping the elements (Cr, Fe and Mn) in the protein bands (ca. 33 and 23.7 kDa), their concentrations were determined using atomic absorption spectrometry (ET AAS).

Good results were obtained for protein extraction using a combination of grinding and sonication. However, this strategy was not suitable to preserve metal ions in the protein structure. In fact, there was 42% decrease on Mn concentration using this procedure, compared to that performed with sample agitation in water (taken as reference). On the other hand, when grinding and agitation with an extracting buffer was used, there was a 530% increase of Mn concentration, when compared to the reference procedure.

These results indicate agreement between metal identification and determination in proteins as well as the great influence of the extraction procedure (i.e., the sample preparation step) for preserving metals in the protein structures.     

Macromolecular crystallography research at Trombay

Neutron diffraction studies of hydrogen positions in small molecules of biological interest at Trombay have provided valuable information that has been used in protein and enzyme structure model-building and in developing hydrogen bond potential functions. The new R-5 reactor is expected to provide higher neutron fluxes and also make possible smallangle neutron scattering studies of large biomolecules and bio-aggregates. In the last few years infrastructure facilities have also been established for macromolecular x-ray crystallography research. Meanwhile, the refinement of carbonic hydrases’ and lysozyme structures have been carried out and interesting results obtained on protein dynamics and structure-function relationships. Some interesting presynaptic toxin phospholipases have also been taken up for study.     

Solubility Measurements of Surfactants and Dissolution of Cytochrome c in 1,1,1,2‐Tetrafluoroethane Modified with Organic Solvents

The solubilities of four surfactants, sodium bis‐2‐ethylhexyl sulfosuccinate (AOT), cetyltrimethylammonium chloride, didodecyldimethylammonium bromide, and n‐dodecyltrimethylammonium chloride in liquid refrigerant 1,1,1,2‐tetrafluoroethane (R134a) modified with methanol, ethanol, and 2‐propanol were measured. The measurements were performed under 25 and 50 bar at 25 °C. The solubility of AOT was as high as 92 mM in R134a with addition of 2% ethanol. Cytochrome c molecules were then verified to be soluble in the AOT‐containing and ethanol‐modified R134a solution. Accordingly, liquid R134a is suggested as a potential extraction solvent for hydrophilic compounds.     

酶的分子仿生研究进展

回顾了近几十年来印迹高分子和有机团簇对酶的仿生发展历程，总结了目前的 研究现状，探讨了电子效应和空间效应（柔性空间效应）对仿对酶在催化过程中实 现类似酶的识别和诱导契合的影响，并展望了酶的仿生发展趋势。     

Unraveling the mystery of efficacy in Chinese medicine formula: New approaches and technologies for research on pharmacodynamic substances

Traditional Chinese medicine (TCM) is the key to unlock treasures of Chinese civilization. TCM and its compound play a beneficial role in medical activities to cure diseases, especially in major public health events such as novel coronavirus epidemics across the globe. The chemical composition in Chinese medicine formula is complex and diverse, but their effective substances resemble “mystery boxes”. Revealing their active ingredients and their mechanisms of action has become focal point and difficulty of research for herbalists. Although the existing research methods are numerous and constantly updated iteratively, there is remain a lack of prospective reviews. Hence, this paper provides a comprehensive account of existing new approaches and technologies based on previous studies with an in vitro to in vivo perspective. In addition, the bottlenecks of studies on Chinese medicine formula effective substances are also revealed. Especially, we look ahead to new perspectives, technologies and applications for its future development. This work reviews based on new perspectives to open horizons for the future research. Consequently, herbal compounding pharmaceutical substances study should carry on the essence of TCM while pursuing innovations in the field.     

Characterization of proteins separated by displacement chromatography using low angle laser light scattering photometry

Summary -Lactoglobulin A and B (-LACT) were separated by displacement chromatography (DSC) on an ionexchange column using dextran sulfate as the displacer. A LALLS photometer and a UV detector, in series, were used to determine the molecular weight (MW) of the proteins, on-line. The results indicate that both, -LACT A and B, were present as dimers in the buffer used for the mobile phase. The MWs of the proteins were about 6–8% higher than the theoretical MW of a dimer (37,000). Additional control studies have shown the presence of a high molecular weight species in both the proteins, which could possibly be an aggregate. This species was observed in the LALLS signal but was nearly absent in the UV signal. Our work has demonstrated the feasibility of interfacing LALLS with displacement chromatography for detecting impurities or aggregates which may be difficult to detect by conventional detectors used for chromatography.     

Selectivity features of molecularly imprinted polymers recognising the carbamate group

The molecular recognition properties of molecular imprinted polymers which bind the carbamate function were studied. Functional monomers potentially able to form non-covalent interactions with the model molecule N,O-dibenzylcarbamate were selected on the basis of a computational approach describing possible interactions between the template and a small library of vinylic monomers. These results were in accordance with N,O-dibenzylcarbamate batch-rebinding measurements performed on several miniMIPs prepared with the same library. From these preliminary results, four polymers were prepared by thermoinduced radical polymerization, using ethylene dimethacrylate as a cross-linker, chloroform (MIP1, MIP3) or acetonitrile (MIP2, MIP4) as porogens and methacrylic acid (MIP1, MIP2) or acrylamide (MIP3, MIP4) as functional monomers. Molecular recognition features of these materials were studied by high-performance liquid chromatography. In this manner selectivity was evaluated by considering the column retention of a library of sixteen structural analogues of dibenzylcarbamate, characterized by the transformation of the carbamate into a related function, or by the alteration of the molecular structure.The experimental results show that methacrylic acid is more efficient than acrylamide as a functional monomer (imprinting factors: MIP1 = 24.1, MIP2 = 25.6, MIP3 = 13.3, MIP4 = 2.44), and that chloroform enhances polymer selectivity. As regards structural motifs which conditionate the selectivity, the carbamate function strictly controls the presence/absence of molecular recognition, while shape and dimension of the substituents modulate the recognition itself. In particular, a marked recognition for analogs which were slightly bigger than the template was observed (N-benzyl-O-phenethylcarbamate: MIP1 α = 1.13, MIP2 α = 1.41, MIP3 α = 0.97; N-phenethyl-N-benzylcarbamate: MIP1 α = 1.61, MIP2 α = 1.17, MIP3 α = 0.81; N,O-diphenethylcarbamate: MIP1 α = 0.89, MIP2 α = 1.20, MIP3 α = 0.55).     

A comparison of the adsorption of saliva proteins and some typical proteins onto the surface of hydroxyapatite

Adsorption of protein from saliva on hydroxyapatite was compared with adsorption of several typical proteins with different electric charges, i.e. lysozyme, human serum albumin, β-lactoglobulin and ovalbumin. Adsorbed amounts of these proteins were determined and electrophoretic mobilities of protein-covered hydroxyapatite particles were measured, at different values for the adsorbed mass and, therefore, at various degrees of surface coverage. Also, adsorption kinetics were investigated by streaming potential measurements of a hydroxyapatite surface in contact with a protein solution, allowing monitoring of changes in the zeta-potential of the protein-covered hydroxyapatite surface in real time. The adsorbed amounts show that, as compared to most of the other proteins, the saliva proteins have remarkably low adsorption affinity. The measured values for the electrophoretic mobilities indicate that the positively charged proteins in the saliva mixture preferentially adsorb onto the negatively charged hydroxyapatite surface; this is most pronounced at low protein concentration in solution (i.e. at low coverage of the surface by the protein). Preferential uptake of the positively charged saliva proteins during the initial stages of the adsorption process is also concluded from the results of the kinetics experiments. Preferential adsorption of positive proteins is somewhat suppressed by the presence of Ca²⁺ ions in the medium. The results suggest that an acquired pellicle on a tooth in an oral environment contains a significant fraction of positively charged proteins. The positively charged proteins in the pellicle reduce the zeta-potential at the tooth surface to low values; consequently, electrostatic forces are expected to play only a minor role in the interaction with other components (e.g. bacterial cells).     

Functional characterization of two-dimensional gel-separated proteins using sequential staining

Proteins separated by two-dimensional (2-D) gel electrophoresis can be visualized using various protein staining methods. This is followed by downstream procedures, such as image analysis, gel spot cutting, protein digestion, and mass spectrometry (MS), to characterize protein expression profiles within cells, tissues, organisms, or body fluids. Characterizing specific post-translational modifications on proteins using MS of peptide fragments is difficult and labor-intensive. Recently, specific staining methods have been developed and merged into the 2-D gel platform so that not only general protein patterns but also patterns of phosphorylated and glycosylated proteins can be obtained. We used the new Pro-Q Diamond phosphoprotein dye technology for the fluorescent detection of phosphoproteins directly in 2-D gels of mouse leukocyte proteins, and Pro-Q Emerald 488 glycoprotein dye to detect glycoproteins. These two fluorescent stains are compatible with general protein stains, such as SYPRO Ruby stain. We devised a sequential procedure using Pro-Q Diamond (phosphoprotein), followed by Pro-Q Emerald 488 (glycoprotein), followed by SYPRO Ruby stain (general protein stain), and finally silver stain for total protein profile. This multiple staining of the proteins in a single gel provided parallel determination of protein expression and preliminary characterization of post-translational modifications of proteins in individual spots on 2-D gels. Although this method does not provide the same degree of certainty as traditional MS methods of characterizing post-translational modifications, it is much simpler, faster, and does not require sophisticated equipment and expertise in MS.