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RISS 인기검색어
- 검색키워드
- 저자 : Jung Hum Park (검색결과 83 건)
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Toward the Virtual Screening of α-Glucosidase Inhibitors with the Homology-Modeled Protein Structure
Park, Jung-Hum,Ko, Sung-Min,Park, Hwang-Seo Korean Chemical Society 2008 Bulletin of the Korean Chemical Society Vol.29 No.5
Discovery of $\alpha$-glucosidase inhibitors has been actively pursued with the aim to develop therapeutics for the treatment of diabetes and the other carbohydrate mediated diseases. As a method for the discovery of new novel inhibitors of $\alpha$-glucosidase, we have addressed the performance of the computer-aided drug design protocol involving the homology modeling of $\alpha$-glucosidase and the structure-based virtual screening with the two docking tools: FlexX and the automated and improved AutoDock implementing the effects of ligand solvation in the scoring function. The homology modeling of $\alpha$-glucosidase from baker’s yeast provides a high-quality 3-D structure enabling the structure-based inhibitor design. Of the two docking programs under consideration, AutoDock is found to be more accurate than FlexX in terms of scoring putative ligands to the extent of 5-fold enhancement of hit rate in database screening when 1% of database coverage is used as a cutoff. A detailed binding mode analysis of the known inhibitors shows that they can be stabilized in the active site of $\alpha$- glucosidase through the simultaneous establishment of the multiple hydrogen bond and hydrophobic interactions. The present study demonstrates the usefulness of the automated AutoDock program with the improved scoring function as a docking tool for virtual screening of new $\alpha$-glucosidase inhibitors as well as for binding mode analysis to elucidate the activities of known inhibitors.
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Computational Prediction of Solvation Free Energies of Amino Acids with Genetic Algorithm
Park, Jung-Hum,Lee, Jin-Won,Park, Hwang-Seo Korean Chemical Society 2010 Bulletin of the Korean Chemical Society Vol.31 No.5
We propose an improved solvent contact model to estimate the solvation free energies of amino acids from individual atomic contributions. The modification of the solvation model involves the optimization of three kinds of parameters in the solvation free energy function: atomic fragmental volume, maximum atomic occupancy, and atomic solvation parameters. All of these atomic parameters for 17 atom types are developed by the operation of a standard genetic algorithm in such a way to minimize the difference between experimental and calculated solvation free energies. The present solvation model is able to predict the experimental solvation free energies of amino acids with the squared correlation coefficients of 0.94 and 0.93 for the parameterization with Gaussian and screened Coulomb potential as the envelope functions, respectively. This result indicates that the improved solvent contact model with the newly developed atomic parameters would be a useful tool for the estimation of the molecular solvation free energy of a protein in aqueous solution.
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Computational Prediction of Solvation Free Energies of Amino Acids with Genetic Algorithm
Jung-Hum Park,이진원,박황서 대한화학회 2010 Bulletin of the Korean Chemical Society Vol.31 No.5
We propose an improved solvent contact model to estimate the solvation free energies of amino acids from individual atomic contributions. The modification of the solvation model involves the optimization of three kinds of parameters in the solvation free energy function: atomic fragmental volume, maximum atomic occupancy, and atomic solvation parameters. All of these atomic parameters for 17 atom types are developed by the operation of a standard genetic algorithm in such a way to minimize the difference between experimental and calculated solvation free energies. The present solvation model is able to predict the experimental solvation free energies of amino acids with the squared correlation coefficients of 0.94 and 0.93 for the parameterization with Gaussian and screened Coulomb potential as the envelope functions, respectively. This result indicates that the improved solvent contact model with the newly developed atomic parameters would be a useful tool for the estimation of the molecular solvation free energy of a protein in aqueous solution.
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Toward the Virtual Screening of α-Glucosidase Inhibitors with the Homology-Modeled Protein Structure
Jung-Hum Park,박황서,Sungmin Ko 대한화학회 2008 Bulletin of the Korean Chemical Society Vol.29 No.5
Discovery of a-glucosidase inhibitors has been actively pursued with the aim to develop therapeutics for the treatment of diabetes and the other carbohydrate mediated diseases. As a method for the discovery of new novel inhibitors of a-glucosidase, we have addressed the performance of the computer-aided drug design protocol involving the homology modeling of a-glucosidase and the structure-based virtual screening with the two docking tools: FlexX and the automated and improved AutoDock implementing the effects of ligand solvation in the scoring function. The homology modeling of a-glucosidase from bakers yeast provides a high-quality 3-D structure enabling the structure-based inhibitor design. Of the two docking programs under consideration, AutoDock is found to be more accurate than FlexX in terms of scoring putative ligands to the extent of 5-fold enhancement of hit rate in database screening when 1% of database coverage is used as a cutoff. A detailed binding mode analysis of the known inhibitors shows that they can be stabilized in the active site of a-glucosidase through the simultaneous establishment of the multiple hydrogen bond and hydrophobic interactions. The present study demonstrates the usefulness of the automated AutoDock program with the improved scoring function as a docking tool for virtual screening of new a-glucosidase inhibitors as well as for binding mode analysis to elucidate the activities of known inhibitors.
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NF-κB signaling is key in the wound healing processes of silk fibroin
Park, Ye Ri,Sultan, Md. Tipu,Park, Hyun Jung,Lee, Jung Min,Ju, Hyung Woo,Lee, Ok Joo,Lee, Dong Jin,Kaplan, David L.,Park, Chan Hum Elsevier Science B.V. Amsterdam 2018 ACTA BIOMATERIALIA Vol. No.
<P><B>Abstract</B></P> <P>Silk fibroin (SF) is a well-studied biomaterial for tissue engineering applications including wound healing. However, the signaling mechanisms underlying the impact of SF on this phenomenon have not been determined. In this study, through microarray analysis, regulatory genes of NF-ĸB signaling were activated in SF-treated NIH3T3 cells along with other genes. Immunoblot analysis confirmed the activation of the NF-ĸB signaling pathway as SF induced protein expression levels of IKKα, IKKβ, p65, and the degradation of IκBα. The treatment of NIH3T3 cells with SF also increased the expression of cyclin D1, vimentin, fibronectin, and vascular endothelial growth factor (VEGF). The expression of these factors by SF treatment was abrogated when NF-ĸB was inhibited by a pharmacological inhibitor Bay 11-7082. Knockdown of NF-ĸB using siRNA of IKKα and IKKβ also inhibited the SF-induced wound healing response of the NIH3T3 cells in a wound scratch assay. Collectively, these results indicated that SF-induced wound healing through the canonical NF-κB signaling pathway via regulation of the expression of cyclin D1, vimentin, fibronectin, and VEGF by NIH3T3 cells. Using an <I>in vivo</I> study with a partial-thickness excision wound in rats we demonstrated that SF-induced wound healing via NF-κB regulated proteins including cyclin D1, fibronectin, and VEGF. The <I>in vitro</I> and <I>in vivo</I> data suggested that SF induced wound healing via modulation of NF-ĸB signaling regulated proteins.</P> <P><B>Statement of Significance</B></P> <P>Silk fibroin has been effectively used as a dressing for wound treatment for more than a century. However, mechanistic insight into the basis for wound healing via silk fibroin has not been elucidated. Here we report a key mechanism involved in silk fibroin induced wound healing both <I>in vitro</I> and <I>in vivo.</I> Using genetic- and protein-level analyses, NF-κB signaling was found to regulate silk fibroin-induced wound healing by modulating target proteins. Thus, the NF-κB signaling pathway may be utilized as a therapeutic target during the formulation of silk fibroin-based biomaterials for wound healing and tissue engineering.</P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>
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Lee, Jung Min,Chae, Taesik,Sheikh, Faheem A.,Ju, Hyung Woo,Moon, Bo Mi,Park, Hyun Jung,Park, Ye Ri,Park, Chan Hum Elsevier 2016 Materials science & engineering. C, Materials for Vol.68 No.-
<P>Ideal dermal substitutes should have comparable physicochemical and biological properties to the natural skin tissue. In this study, we report a novel strategy to 'engineer' controlled 3D nanocomposite fibrous matrix of poly(epsilon-caprolactone) (PCL) and silk fibroin (SF) for an artificial dermis application. Using a custom-designed cold-plate electrospinning and automatic magnet agitation system, up to 6 mm of the thickness was achieved resulting from the accumulation of ice crystal layers on the PCL nanofibers surface-modified with the SF particles. The sacrificed ice crystals induced interconnected macro-pores ranging from tens to hundreds pm. The agitation system introduced uniform distribution of the SF protein within/on the nanofibers, preventing the particles from precipitation and agglomeration. NIH 3T3 fibroblasts proliferated in vitro on the PCL and PCL/SF scaffolds for 7 days, but there was no statistical difference between the groups. Conversely, In vivo rat model studies revealed that the wound healing rate and collagen deposition increased with the SF content within the nanocomposites. The unique 3D construct with the PCL/SF nanocomposite fibers provided desirable spatial cues, surface topography, and surface chemistry for the native cells to infiltrate into the scaffolds. The wound healing potential of the nanocomposites was comparable to the commercial Matriderm (R) artificial dermis. (C) 2016 Elsevier B.V. All rights reserved.</P>
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박정흠(Jung Hum Park),장호선(Ho Sun Jang),오창근(Chang Keun Oh),권경술(Kyung Sool Kwon) 대한피부과학회 1999 대한피부과학회지 Vol.37 No.10
Kaposi`s sarcoma(KS) occurs in four distinct subsets : classic, African-endemic, iatrogenic immunosuppressive drug-associated, and AIDS-associated KS. Only two cases of AIDS-associated KS have been reported in Korea. The pathogensis remains unclear but, suggested the relevance to the AIDS-related KS that human herpesvirus-8 DNA is present in the KS tissue. The patient was diagnosed with AIDS in 1993 and had complained of disseminated erythematous to purplish colored papulonodules on the face, neck, chest and back for 5months. He was treated with systemic cytotoxic chemotherapy, but died due to septic condition. (Korean J Dermatol 1999;37(10) : 1473∼1478)
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