Development,validation and application of a UHPLC–MS/MS method for quantification of the adiponectin-derived active peptide ADP355 in rat plasma

A UHPLC–MS/MS method for the quantification of ADP355, an adiponectin-derived active peptide, was developed and validated. The extraction method employed simple protein precipitation using methanol and chromatographic separation was achieved on anAccucore™ RP-MS C₁₈ column (100 × 2.1 mm, 2.6 μm, 80 Å), using 0.1% formic acid in both water and acetonitrile with gradient elution at the flow rate of 400 μl/min within 4.0 min. Detections were performed under positive ion mode with multiple reaction monitoring ion transitions m/z 1109.2 → 309.8 and 871.4 → 310.1 for ADP355 and Jt003 respectively at unit resolution. The linearity range of the calibration curve was 2–1,000 ng/ml with a lower limit detection of 0.5 ng/ml. The selectivity, linearity, precision, accuracy, recovery, matrix effect and stability were validated, and all items met the requirement of US Food and Drug Administration guidance. This method was successfully applied to an intravenous pharmacokinetic study of ADP355 in rats and the in-vitro stability in rat serum, plasma and whole blood was also assessed.     

Chemical analysis of Gothic mortar from a bridge pier in Roudnice nad Labem (Czech Republic)

In this paper, a Gothic mortar originating from the remains of a bridge pier in Roudnice nad Labem (Czech Republic) was analyzed. The inorganic composition of the mortar showing special mechanical properties was studied using polarizing light microscopy, scanning electron microscopy coupled with energy dispersive X-ray spectrometry, and X-ray diffraction, while the protein content was analyzed by peptide mass mapping using matrix-assisted laser desorption/ionization—time of flight mass spectrometry and nanoliquid chromatography coupled to tandem mass spectrometry. Two types of inorganic binders having a composition similar to mineral wollastonite and hydraulic lime and milk protein additive were detected. We believe that organic and inorganic binders added together to the mortar increase its hardness and firmness in the aquatic environment.     

Study of peptide conformation in terms of the ABEEM/MM method

The ABEEM/MM model (atom-bond electronegativity equalization method fused into molecular mechanics) is applied to study of the polypeptide conformations. The Lennard-Jones and torsional parameters were optimized to be consistent with the ABEEM/MM fluctuating charge electrostatic potential. The hydrogen bond was specially treated with an electrostatic fitting function. Molecular dipole moments, dimerization energies, and hydrogen bond lengths of complexes are reasonably achieved by our model, compared to ab initio results. The ABEEM/MM fluctuating charge model reproduces both the peptide conformational energies and structures with satisfactory accuracy with low computer cost. The transferability is tested by applying the parameters of our model to the tetrapeptide of alanine and another four dipeptides. The overall RMS deviations in conformational energies and key dihedral angles for four di- or tetrapeptide, is 0.39 kcal/mol and 7.7 degrees . The current results agree well with those by the accurate ab initio method, and are comparable to those from the best existing force fields. The results make us believe that our fluctuating charge model can obtain more promising results in protein and macromolecular modeling with good accuracy but less computer cost.     

Investigation of the interaction between HⅣ-1 DNA and cyclic peptides by electrospray ionization mass spectrometry

The interaction between HⅣ-1 DNA and five cyclic peptides (CP1-CP5) was investigated using electrospray ionization mass spectrometry (ESI-MS). It revealed that CP1 [c(Ala-Tyr-Leu-Ala-Gly)] and CP4 [c(Pro-D-Tyr-Leu-D-Ala-Gly)] have the higher binding affinity with the duplex DNA among the five cyclic peptides.     

一种基于遗传算法的肽/蛋白质结合模式虚拟筛选建模技术

“合理”QSAR模型是指在了解配体与受体相互作用模式的前提下建立定量构效关系, 这样避开了传统做法仅仅依靠样本集分子自身信息来构建预测模型的诸多弊端. 本文将此思想应用于肽/蛋白质亲和活性的研究当中, 借助于遗传算法作为虚拟受体结合靶点及相互作用模式的筛选手段得到了一种新的建模技术: 肽/蛋白质结合模式遗传虚拟筛选(genetic virtual screening of combinative mode for peptide/protein, GVSC). 该法成功解决了“合理”QSAR研究中的难题, 即大多数情况下受体结构未知而难以了解配基与之发生的结合方式. 分别使用58个血管紧张素转化酶, 18个Camel抗体蛋白cAb-lys3双位点突变残基对GVSC加以检验, 其结果表明GVSC能够较好地阐明配基与受体之间的作用机理, 并能得到优于传统方法的QSAR模型.     

Evaluation of TILI-2 as an Anti-Tyrosinase,Anti-Oxidative Agent and Its Role in Preventing Melanogenesis Using a Proteomics Approach

There is a desire to develop new molecules that can combat hyperpigmentation. To this end, the N-terminal cysteine-containing heptapeptide TILI-2 has shown promising preliminary results. In this work, the mechanism by which it works was evaluated using a series of biochemical assays focusing on known biochemical pathways, followed by LC-MS/MS proteomics to discover pathways that have not been considered before. We demonstrate that TILI-2 is a competitive inhibitor of tyrosinase’s monophenolase activity and it could potentially scavenge ABTS and DPPH radicals. It has a very low cytotoxicity up to 1400 µM against human fibroblast NFDH cells and macrophage-like RAW 264.7 cells. Our proteomics study revealed that another putative mechanism by which TILI-2 may reduce melanin production involves the disruption of the TGF-β signaling pathway in mouse B16F1 cells. This result suggests that TILI-2 has potential scope to be used as a depigmenting agent.     

DFT study and vibrational spectra of the phoshorus-containing G0 generation dendrimer

The Raman (10–3500 cm⁻¹) and infrared (150–3500 cm⁻¹) spectra have been recorded for tris(4-oxibenzaldehyde)thiophosphate. This compound includes structural parts of elementoorganic dendrimers: a core and terminal aldehyde groups. The structural optimization and normal mode analysis are performed for elementoorganic dendrimer on the basis of the ab initio density functional theory. It is found that the dendrimer exist in a single stable conformation with planar C₆H₄CHO fragments. Our calculations show that conformer with one trans and two gauche 4-oxibenzaldehyde groups is realized. All these observations suggest that steric congestion does not disturb the construction of dendrimers even for the highest generations, and that terminal groups are readily available for further reactions. Relying on DFT calculations a complete vibrational assignment is proposed for different parts of the studied dendrimers.     

High-level expression of soluble human β-defensin-2 fused with green fluorescent protein in Escherichia coli cell-free system

Human β-defensin-2 (hBD2), a small cationic peptide, exhibits a broad range of antimicrobial activity and does not acquire any microbial resistance. To produce this uneasily detectable, degradable, and toxic polypeptide efficiently, an alternative approach based on the Escherichia coli cell-free biosynthesis system was proposed. The approach implies that a polypeptide of interest is synthesized as a fusion protein linked to a green fluorescent protein (GFP) through a cleavable spacer. With batch-mode operation, a significant amount of hBD2 fused with GFP (0.25 mg/mL) can be expressed in this cell-free system. The productivity of the fusion protein can be improved up to 1.2 mg/mL by employing a continuous-exchange cell-free system. Furthermore, the GFP moiety provides directly visible and quantitative monitoring of the polypeptide synthesis, and the product is soluble and stable. This work will be helpful in allowing the rapid and visible expression of other similar defensins using an in vitro cell-free system.     

Target-Directed Azide-Alkyne Cycloaddition for Assembling HIV-1 TAR RNA Binding Ligands

The highly conserved HIV-1 transactivation response element (TAR) binds to the trans-activator protein Tat and facilitates viral replication in its latent state. The inhibition of Tat–TAR interactions by selectively targeting TAR RNA has been used as a strategy to develop potent antiviral agents. Therefore, HIV-1 TAR RNA represents a paradigmatic system for therapeutic intervention. Herein, we have employed biotin-tagged TAR RNA to assemble its own ligands from a pool of reactive azide and alkyne building blocks. To identify the binding sites and selectivity of the ligands, the in situ cycloaddition has been further performed using control nucleotide (TAR DNA and TAR RNA without bulge) templates. The hit triazole-linked thiazole peptidomimetic products have been isolated from the biotin-tagged target templates using streptavidin beads. The major triazole lead generated by the TAR RNA presumably binds in the bulge region, shows specificity for TAR RNA over TAR DNA, and inhibits Tat–TAR interactions.