• Journal of Integrative Natural Science
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• v.6 no.3
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• pp.138-142
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• 2013

The HIV-1 envelope glycoprotein gp120 plays a vital role in the entry of the virus into the host cells. The crucial role of the glycoprotein suggests gp120 as potential drug target for the future antiviral therapies. Identification of the binding mode of small drug like compounds has been an important goal in drug design. In the current study we attempt to propose binding mode of indole derivatives in the binding pocket of gp120. These derivatives are reported to inhibit HIV-1 by acting as attachment inhibitors that bind to gp120 and prevent the gp120-CD4 interaction and thus inhibit the infectivity of HIV-1. To elucidate the molecular basis of the small molecules interactions to inhibit the glycoprotein function we employed the molecular docking simulation approach. This study provides insights to elucidate the binding pattern of indole-based gp120 inhibitors and may help in the rational design of novel HIV-1 inhibitors with improved potency.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.10
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• pp.4301-4305
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• 2014

Tanshinone IIA is a pharmacologically active ingredient extracted from Danshen, a Chinese traditional medicine. Its molecular mechanisms are still unclear. The present study utilized computational approaches to uncover the potential targets of this compound. In this research, PharmMapper server was used as the inverse docking tool andnd the results were verified by Autodock vina in PyRx 0.8, and by DRAR-CPI, a server for drug repositioning via the chemical-protein interactome. Results showed that the retinoic acid receptor alpha ($RAR{\alpha}$), a target protein in acute promyelocytic leukemia (APL), was in the top rank, with a pharmacophore model matching well the molecular features of Tanshinone IIA. Moreover, molecular docking and drug repurposing results showed that the complex was also matched in terms of structure and chemical-protein interactions. These results indicated that $RAR{\alpha}$ may be a potential target of Tanshinone IIA for APL. The study can provide useful information for further biological and biochemical research on natural compounds.

• Biomedical Science Letters
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• v.20 no.1
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• pp.1-7
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• 2014

RNA granules such as Stress Granules (SG) and P-Bodies (PB) are aggregates of translationally stalled messenger ribonucleoprotein (mRNP) complexes induced by a wide range of stresses. Over the past decade, extensive studies described key components of RNA granules, their molecular interactions and signaling pathways require for their assembly and disassembly. However, researches defining their exact roles under stress conditions have not been performed so far, although several studies suggested their roles in neurodegenerative diseases recently. In this review, we provide an introduction about their basic properties, key components, and the dynamic nature for their assembly.

• International Journal of Oral Biology
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• v.43 no.2
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• pp.53-59
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• 2018

In order to understand biological phenomena accurately, single molecule techniques using a physical research approach to molecular interactions have been developed, and are now widely being used to study complex biological processes. In this review, we discuss some of the single molecule methods which are composed of two major parts: single molecule spectroscopy and manipulation. In particular, we explain how these techniques work and introduce the current research which uses them. Finally, we present the oral biology research using the single molecule methods.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.08a
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• pp.32-32
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• 2010

Since the characteristics of plasmas depend strongly on the interactions between plasma particles such as electron, ions, and neutrals, a well-established atomic and molecular database is needed to understand and produce various types of plasma. Thus, National Fusion Research Institute (NFRI) started to establish the plasma property DB for fusion and industrial plasma from last 2002. Here we describe our recent data evaluation activities regarding to production of atomic and molecular data that are needed for modeling plasma in fusion tokamaks and also low temperature industrial plasmas.

• Molecules and Cells
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• v.39 no.9
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• pp.645-653
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• 2016

Morphine is the most potent analgesic for chronic pain, but its clinical use has been limited by the opiate's innate tendency to produce tolerance, severe withdrawal symptoms and rewarding properties with a high risk of relapse. To understand the addictive properties of morphine, past studies have focused on relevant molecular and cellular changes in the brain, highlighting the functional roles of reward-related brain regions. Given the accumulated findings, a recent, emerging trend in morphine research is that of examining the dynamics of neuronal interactions in brain reward circuits under the influence of morphine action. In this review, we highlight recent findings on the roles of several reward circuits involved in morphine addiction based on pharmacological, molecular and physiological evidences.

• Molecules and Cells
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• v.24 no.2
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• pp.153-166
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• 2007

The syndecan family of heparan sulfate proteoglycans is expressed on the surface of all adherent cells. Syndecans interact with a wide variety of molecules, including growth factors, cytokines, proteinases, adhesion receptors and extracellular matrix components, through their heparan sulfate chains. Recent studies indicate that these interactions not only regulate key events in development and homeostasis, but also key mechanisms of the host inflammatory response. This review will focus on the molecular and cellular aspects of how syndecans modulate tissue injury and inflammation, and how syndecans affect the outcome of inflammatory diseases in vivo.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.28 no.5
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• pp.547-553
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• 2004

A hemispherical asperity moving over a flat plane is simulated based on classical molecular dynamics. The asperity and the plane consist of silicon atoms whose interactions are governed by the Tersoff three-body potential. The gap between the asperity and the plane is maintained to produce attractive normal force in order to investigate the adhesive friction and wear. The simulation focuses on the influence of crystallographic orientation of the contacting surfaces and the moving direction. It is demonstrated that the adhesive friction and wear are lower when crystallographic orientations of the contacting surfaces are different, and also depend on the moving direction relative to the crystal1ographic orientation.

• Journal of Integrative Natural Science
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• v.10 no.3
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• pp.137-140
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• 2017

Diabetes mellitus has become a major growing public health problem worldwide. More than 90% of all diabetes cases are classified as type 2 diabetes (T2D), which is also known as non-insulin dependent diabetes. Protein tyrosine phosphatase 1B (PTP1B) plays an important role in the negative regulation of insulin signal transduction pathway and has emerged as novel therapeutic strategy for the treatment of type 2 diabetes. PTP1B inhibitors enhance the sensibility of insulin receptor (IR) and have favorable curing effect for insulin resistance-related diseases. Recently twelve anti-diabetic xanthones were isolated from the bark of Garcinia xanthochymus. Hence, in the present study, molecular docking was carried out for these twelve xanthones. The objective of this work is to study the interaction of the newly isolated xanthones with PTP1B. The docking results showed that xanthones have good interactions and has better docking score with PTP1B and suggest LYS120 and ASP181 are the important residues involved in interaction between PTP1B enzyme and the xanthones.

• Bulletin of the Korean Chemical Society
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• v.34 no.2
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• pp.553-557
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• 2013

The stretching vibration of OH of ice Ih is studied by Car-Parrinello molecular dynamics in regarding the effect of mixed H/D contamination while the vibrational spectrum is considered by velocity-velocity autocorrelations of the sampled ensemble. When hydrogen atoms are immersed randomly into the deuterated ice, a typical vibrational frequency of OH stretching mode is observed to be similar to that from the pure $H_2O$ ice. When focusing on the correlation of isolated neighboring OH stretching, a narrower and blue shifted peak is observed at the high frequency range as a result of the screening from the complex many body correlations by $D_2O$ environment. It is also specifically related to the symmetric intermolecular correlations between neighboring OH stretching modes. More enhanced high frequency range can be explained by the expansion of such two body correlations to collective many body correlations among all possible OH stretching modes. This contribution becomes important when it involves in chemical interactions via excitation of such vibrational states.