Jung-Keun Suh

Photodegradation mechanism and reaction kinetics of recombinant human interferon-α2a

The photodegradation mechanism of recombinant human interferon-alpha2a (IFNalpha2a) has been investigated using absorption, fluorescence, and circular dichroism (CD) spectroscopies, and fluorescence photobleaching kinetics measurements under various conditions. After photobleaching, the absorption profile of aromatic amino acid residues in IFNalpha2a was almost absent, and an absorption profile showing a monotonic increase toward short wavelengths was observed. According to the CD spectrum analysis, partial unfolding of IFNalpha2a was accompanied by a complete loss of fluorescence. This unfolding was attributed to tryptophan-mediated photoinduced disulfide bond cleavage. Photooxygenation and photoionization of tryptophan (Trp) residues followed by subsequent radical reactions were the main photodegradation pathways of IFNalpha2a. Photobleaching kinetics was faster in acidic solution (pH 2.5) than in neutral solution (pH 7.4). The variation of photobleaching kinetics seemed to be caused by the structural differences in IFNalpha2a according to the solution pH. The relationship between the protein conformation and photobleaching rate could be explained based on the competition between excited state energy transfer and the photoionization process in Trp residues.

Novel chemical scaffolds of the tumor marker AKR1B10 inhibitors discovered by 3D QSAR pharmacophore modeling

Aim:Recent evidence suggests that aldo-keto reductase family 1 B10 (AKR1B10) may be a potential diagnostic or prognostic marker of human tumors, and that AKR1B10 inhibitors offer a promising choice for treatment of many types of human cancers. The aim of this study was to identify novel chemical scaffolds of AKR1B10 inhibitors using in silico approaches.Methods:The 3D QSAR pharmacophore models were generated using HypoGen. A validated pharmacophore model was selected for virtual screening of 4 chemical databases. The best mapped compounds were assessed for their drug-like properties. The binding orientations of the resulting compounds were predicted by molecular docking. Density functional theory calculations were carried out using B3LYP. The stability of the protein-ligand complexes and the final binding modes of the hit compounds were analyzed using 10 ns molecular dynamics (MD) simulations.Results:The best pharmacophore model (Hypo 1) showed the highest correlation coefficient (0.979), lowest total cost (102.89) and least RMSD value (0.59). Hypo 1 consisted of one hydrogen-bond acceptor, one hydrogen-bond donor, one ring aromatic and one hydrophobic feature. This model was validated by Fischers randomization and 40 test set compounds. Virtual screening of chemical databases and the docking studies resulted in 30 representative compounds. Frontier orbital analysis confirmed that only 3 compounds had sufficiently low energy band gaps. MD simulations revealed the binding modes of the 3 hit compounds: all of them showed a large number of hydrogen bonds and hydrophobic interactions with the active site and specificity pocket residues of AKR1B10.Conclusion:Three compounds with new structural scaffolds have been identified, which have stronger binding affinities for AKR1B10 than known inhibitors.

Role of yeast flavin-containing monooxygenase in maintenance of thiol-disulfide redox potential.

Publisher Summary Yeast flavin-containing monooxygenase (yFMO) is localized on the cytoplasmic surface of the endoplasmic reticulum (ER) membrane and uses NADPH and oxygen to oxidize the cellular thiols glutathione (GSH), cysteamine, and cysteine. Although the concentration of the latter two thiols required to half-saturate yFMO far exceeds their cellular concentrations, the redox potential for GSH is close to its concentration in yeast. The disulphide form of GSH (GSSG) can permeate into the lumen of isolated microsomal fragments. The oxidizing equivalents generated by yFMO influence the redox potential of the ER. yFMO is required for the correct folding of disulfide bond-containing proteins, as seen by the use of a gene deletion yeast strain. Proper refolding can be restored by expression yFMO on a plasmid. This chapter describes the components required to determine the redox status in the cells in the context of yFMO activity.

A lazy learning-based QSAR classification study for screening potential histone deacetylase 8 (HDAC8) inhibitors

Histone deacetylases 8 (HDAC8) is an enzyme repressing the transcription of various genes including tumour suppressor gene and has already become a target of human cancer treatment. In an effort to facilitate the discovery of HDAC8 inhibitors, two quantitative structure–activity relationship (QSAR) classification models were developed using K nearest neighbours (KNN) and neighbourhood classifier (NEC). Molecular descriptors were calculated for the data set and database compounds using ADRIANA.Code of Molecular Networks. Principal components analysis (PCA) was used to select the descriptors. The developed models were validated by leave-one-out cross validation (LOO CV). The performances of the developed models were evaluated with an external test set. Highly predictive models were used for database virtual screening. Furthermore, hit compounds were subsequently subject to molecular docking. Five hits were obtained based on consensus scoring function and binding affinity as potential HDAC8 inhibitors. Finally, HDAC8 structures in complex with five hits were also subjected to 5 ns molecular dynamics (MD) simulations to evaluate the complex structure stability. To the best of our knowledge, the NEC classification model used in this study is the first application of NEC to virtual screening for drug discovery.

Structural Identification of a Non-Glycosylated Variant at Ser126 for O-Glycosylation Site from EPO BRP, Human Recombinant Erythropoietin by LC/MS Analysis

A variant peak was detected in the analysis of RP-HPLC of rHu-EPO, which has about 7% relative content. Fractions of the main and the variant peaks were pooled separately and further analyzed to identify the molecular structure of the variant peak. Total mass analysis for each peak fraction using ESI-TOF MS shows differences in molecular mass. The fraction of the main peak tends to result in higher molecular masses than the fraction of the variant. The detected masses for the variant are about 600–1000 Da smaller than those for the main peak. Peptide mapping analysis for each peak fraction using Asp-N and Glu-C shows differences in O-glycopeptide profiles at Ser126. The O-glycopeptides were not detected in the fraction of the variant. It is concluded that the variant peak is non-O-glycosylated rHu-EPO and the main peak is fully O-glycosylated rHu-EPO at Ser126.

Assessment for quantification of biopharmaceutical protein using a microvolume spectrometer on microfluidic slides

Spectrophotometric procedure is a traditional method for quantifying protein concentration in solution. The benefit of this method is simple and direct, not requiring standard materials, sample incubation, and exogenous chromophore addition. There are also some drawbacks, low detection limits and high amounts of protein needed. The recent advances in fiber optics and nano-technology enable to overcome those drawbacks by using microvolume sampling and extremely short pathlengths. In this study, the utility of the microvolume system with microfluidic carriers was assessed for concentration measurement of biopharmaceutical protein using absorbance at 280 nm and also compared to a traditional instrument. The results show a high correlation of estimation by Cohen’s d effect size and Pearson correlation coefficient between two different spectrometers. For UV spectral analysis, there are no statistically significant difference between those spectra from a microvolume spectrometer and a traditional one. For the extinction coefficient determination, two different spectrometers also give quite comparable and similar values. Thus a microvolume spectrometer can be used as an alternative over a traditional one to determine the concentration of biopharmaceutical protein. Moreover, the dynamic range for protein quantification by a microvolume spectrometer is over 10-fold higher than that of a traditional one.

Sulfonanilide Derivatives in Identifying Novel Aromatase Inhibitors by Applying Docking, Virtual Screening, and MD Simulations Studies

Breast cancer is one of the leading causes of death noticed in women across the world. Of late the most successful treatments rendered are the use of aromatase inhibitors (AIs). In the current study, a two-way approach for the identification of novel leads has been adapted. 81 chemical compounds were assessed to understand their potentiality against aromatase along with the four known drugs. Docking was performed employing the CDOCKER protocol available on the Discovery Studio (DS v4.5). Exemestane has displayed a higher dock score among the known drug candidates and is labeled as reference. Out of 81 ligands 14 have exhibited higher dock scores than the reference. In the second approach, these 14 compounds were utilized for the generation of the pharmacophore. The validated four-featured pharmacophore was then allowed to screen Chembridge database and the potential Hits were obtained after subjecting them to Lipinskis rule of five and the ADMET properties. Subsequently, the acquired 3,050 Hits were escalated to molecular docking utilizing GOLD v5.0. Finally, the obtained Hits were consequently represented to be ideal lead candidates that were escalated to the MD simulations and binding free energy calculations. Additionally, the gene-disease association was performed to delineate the associated disease caused by CYP19A1.

Subject Test Using Electroencephalogram According to Variation of Autostereoscopic Image Quality

There have been many studies on subject tests for 3D contents using 3D glasses, but there is a limited research for 3D contents using autostereoscopic display. In this study, we investigated to assess usability of electroencephalogram (EEG) as an objective evaluation for 3D contents with different quality using autosteroscopic display, especially for lenticular lens type. The image with optimal quality and the image with distorted quality were separately generated for autostereosopic display with lenticular lens type and displayed sequentially through lenticular lens for 26 subjects. EEG signals of 8 channels from 26 subjects exposed to those images were detected and correlation between EEG signal and the quality of 3D images were statistically evaluated to check differences between optimal and distorted 3D contents. What we found was that there was no statistical significance for a wave vibration, however b wave vibration shows statistically significant between optimal and distorted 3D contents. b wave vibration observed for the distorted 3D image was stronger than that for the optimal 3D image. This results suggest that subjects viewing the distorted 3D contents through lenticular lens experience more discomfort or fatigue than those for the optimum 3D contents, which resulting in the greater b wave activity for those watching the distorted 3D contents. In conclusion, these results confirm that electroencephalogram (EEG) analysis can be used as a tool for objective evaluation of 3D contents using autosteroscopic display with lenticular lens type.