• Natural Product Sciences
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• v.19 no.2
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• pp.150-154
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• 2013

A new oleanane-type triterpenoid saponin together with six known saponins were isolated from the roots of Pulsatilla cernua. Their structures were elucidated on the basis of spectroscopic data, including 2D NMR spectra and chemical evidence. Compounds 1 and 6 are reported from this genus for the first time.

• Journal of Engineering Education Research
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• v.21 no.6
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• pp.54-62
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• 2018

This study is an analysis of the process of the discovery of the DNA double helix structure from an engineering literacy education perspective. The explanation of the DNA double helix structure by James Watson and Francis Crick in 1952 is a well-known scientific episode. The process is also a combination of various incidents that can frequently happen in competitive engineering research and development situations. Therefore, the process of the discovery of the DNA structure is a remarkable event that can cover all subjects, such as engineering and ethics, research ethics, communication between researchers, engineering and leadership, engineering and teamwork, and engineering and women. This paper focuses on analyzing the research ethics issues associated with Rosalind Franklin and comparing and analyzing the three teams that were very close to the discovery of the DNA structure. By looking at why the Watson and Crick team got the final answer instead of the Linus Pauling's team or the Maurice Wilkins and Rosalind Franklin's team, the virtues of the technology development process that should be taught in engineering literacy education will be naturally presented.

• The Plant Pathology Journal
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• v.33 no.6
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• pp.529-542
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• 2017

Control of plant diseases is largely dependent on use of agrochemicals. However, there are widening gaps between our knowledge on plant diseases gained from genetic/mechanistic studies and rapid translation of the knowledge into target-oriented development of effective agrochemicals. Here we propose that the time is ripe for computer-aided drug discovery/design (CADD) in molecular plant pathology. CADD has played a pivotal role in development of medically important molecules over the last three decades. Now, explosive increase in information on genome sequences and three dimensional structures of biological molecules, in combination with advances in computational and informational technologies, opens up exciting possibilities for application of CADD in discovery and development of agrochemicals. In this review, we outline two categories of the drug discovery strategies: structure- and ligand-based CADD, and relevant computational approaches that are being employed in modern drug discovery. In order to help readers to dive into CADD, we explain concepts of homology modelling, molecular docking, virtual screening, and de novo ligand design in structure-based CADD, and pharmacophore modelling, ligand-based virtual screening, quantitative structure activity relationship modelling and de novo ligand design for ligand-based CADD. We also provide the important resources available to carry out CADD. Finally, we present a case study showing how CADD approach can be implemented in reality for identification of potent chemical compounds against the important plant pathogens, Pseudomonas syringae and Colletotrichum gloeosporioides.

• BMB Reports
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• v.37 no.1
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• pp.28-34
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• 2004

The discovery of biochemical and cellular functions of unannotated gene products begins with a database search of proteins with structure/sequence homologues based on known genes. Very recently, a number of frontier groups in structural biology proposed a new paradigm to predict biological functions of an unknown protein on the basis of its three-dimensional structure on a genomic scale. Structural proteomics (genomics), a research area for structure-based functional discovery, aims to complete the protein-folding universe of all gene products in a cell. It would lead us to a complete understanding of a living organism from protein structure. Two major complementary experimental techniques, X-ray crystallography and NMR spectroscopy, combined with recently developed high throughput methods have played a central role in structural proteomics research; however, an integration of these methodologies together with comparative modeling and electron microscopy would speed up the goal for completing a full dictionary of protein folding space in the near future.

• Applied Microscopy
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• v.51
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• pp.13.1-13.7
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• 2021

The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has arisen as a global pandemic affecting the respiratory system showing acute respiratory distress syndrome (ARDS). However, there is no targeted therapeutic agent yet and due to the growing cases of infections and the rising death tolls, discovery of the possible drug is the need of the hour. In general, the study for discovering therapeutic agent for SARS-CoV-2 is largely focused on large-scale screening with fragment-based drug discovery (FBDD). With the recent advancement in cryo-electron microscopy (Cryo-EM), it has become one of the widely used tools in structural biology. It is effective in investigating the structure of numerous proteins in high-resolution and also had an intense influence on drug discovery, determining the binding reaction and regulation of known drugs as well as leading the design and development of new drug candidates. Here, we review the application of cryo-EM in a structure-based drug design (SBDD) and in silico screening of the recently acquired FBDD in SARS-CoV-2. Such insights will help deliver better understanding in the procurement of the effective remedial solution for this pandemic.

• Journal of the Korean Society for Library and Information Science
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• v.48 no.4
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• pp.5-23
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• 2014

This study reports the first step in the Classification-based Search and Knowledge Discovery (CSKD) project, which aims to combine information organization and retrieval approaches for building digital library applications. In this study, we explored the generation and application of a faceted vocabulary as a potential mechanism to enhance knowledge discovery. The faceted vocabulary construction process revealed some heuristics that can be refined in follow-up studies to further automate the creation of faceted classification structure, while our concept search application demonstrated the utility and potential of integrating classification-based approach with retrieval-based approach. Integration of text- and classification-based methods as outlined in this paper combines the strengths of two vastly different approaches to information discovery by constructing and utilizing a flexible information organization scheme from an existing classification structure.

• Journal of Integrative Natural Science
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• v.5 no.4
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• pp.216-219
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• 2012

Structure-based drug design possibly benefit from in silico methods that precisely predict the binding affinity of small molecules to target macromolecules. There are many limitations arise from the difficulty of predicting the binding affinity of a small molecule to a biological target with the current scoring functions. There is thus a strong interest in novel methodologies based on MD simulations that claim predictions of greater accuracy than current scoring functions, helpful for a regular use designed for drug discovery in the pharmaceutical industry. Herein, we report a short review on free energy calculations using MMPBSA method a useful method in structure based drug discovery.

• Proceedings of the PSK Conference
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• 2003.10a
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• pp.92-92
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• 2003

The drug discovery landscape is changing rapidly in the post-genomic era. Mapping of the human genome has led to an abundance of potential drug targets. Drug discovery times and costs can be significantly reduced by developing methods for high throughput target identification/ validation, multiplexed assay development and high efficient combinatorial chemistry. (omitted)

• Genomics & Informatics
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• v.5 no.1
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• pp.24-29
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• 2007

Computational virtual screening has become an essential platform of drug discovery for the efficient identification of active candidates. Moleculardocking, a key technology of receptor-centric virtual screening, is commonly used to predict the binding affinities of chemical compounds on target receptors. Despite the advancement and extensive application of these methods, substantial improvement is still required to increase their accuracy and time-efficiency. Here, we evaluate several advanced structure-based virtual screening approaches for elucidating the rank-order activity of chemical libraries, and the quantitative structureactivity relationship (QSAR). Our results show that the ensemble-average free energy estimation, including implicit solvation energy terms, significantly improves the hit enrichment of the virtual screening. We also demonstrate that the assignment of quantum mechanical-polarized (QM-polarized) partial charges to docked ligands contributes to the reproduction of the crystal pose of ligands in the docking and scoring procedure.

• Bulletin of the Korean Chemical Society
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• v.34 no.10
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• pp.2909-2914
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• 2013

p-Hydroxyphenylpyruvate dioxygenase (HPPD) is a potent herbicide target that is in current use. In this study, we developed a predictive pharmacophore model that uses known HPPD inhibitors based on a theoretically constructed HPPD homology model. The pharmacophore model derived from the three-dimensional (3D) structure of a target protein provides helpful information for analyzing protein-ligand interactions, leading to further improvement of the ligand binding affinity.