• Journal of Integrative Natural Science
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• v.2 no.2
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• pp.55-58
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• 2009

A ligand-receptor docking program is an indispensible tool in modern pharmaceutical design. An accurate prediction of small molecular docking pose to a receptor is essential in drug design as well as molecular recognition. An effective docking program requires the ability to locate a correct binding pose in a surprisingly complex conformational space. However, there is an inherent difficulty to predict correct binding pose. The odds are more demanding than finding a needle in a haystack. This mainly comes from the flexibility of both ligand and receptor. Because the searching space to consider is so vast, receptor rigidity has been often applied in docking programs. Even nowadays the receptor may not be considered to be fully flexible although there have been some progress in search algorithm. Improving the efficiency of searching algorithm is still in great demand to explore other applications areas with inherently flexible ligand and/or receptor. In addition to classical search algorithms such as molecular dynamics, Monte Carlo, genetic algorithm and simulated annealing, rather recent algorithms such as tabu search, stochastic tunneling, particle swarm optimizations were also found to be effective. A good search algorithm would require a good balance between exploration and exploitation. It would be a good strategy to combine algorithms already developed. This composite algorithms can be more effective than an individual search algorithms.

• Journal of Integrative Natural Science
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• v.9 no.4
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• pp.268-274
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• 2016

Filariasis causing nematode Brugia malayi is shown to harbor wolbachia bacteria as symbionts. The sequenced genome of the wolbachia endosymbiont from B.malayi (wBm) offers an unprecedented opportunity to identify new wolbachia drug targets. Hence the enzyme carbonic anhydrase from wolbachia endosymbiont of Brugia malayi (wBm) which is responsible for the reversible interconversion of carbon dioxide and water to bicarbonate and protons (or vice versa) is chosen as the drug target for filariasis. This enzyme is thought to play critical functions in bacteria by involving in various steps of their life cycle which are important for survival, The 3D structure of wBm carbonic anhydrase is predicted by selecting a suitable template using the similarity search tool, BLAST. The BLAST results shows a hexapeptide transferase family protein from Anaplasma phagocytophilum (PDB ID: 3IXC) having 77% similarity and 54% identity with wBm carbonic anhydrase. Hence the above enzyme is chosen as the template and the 3D structure of carbonic anhydrase is predicted by the tool Modeller9v7. Since the three dimensional structure of carbonic anhydrase from wolbachia endosymbiont of Brugia malayi has not yet solved, attempts were made to predict this protein. The predicted structure is validated and also molecular docking studies are carried out with the suitable inhibitors that have been solved experimentally.

• Biomolecules & Therapeutics
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• v.31 no.1
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• pp.108-115
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• 2023

Numerous psychotropic and addictive substances possess structural features similar to those of β-phenethylamine (β-PEA). In this study, we selected 29 β-PEA derivatives and determined their structure-activity relationship (SAR) to their ability to inhibit dopamine (DA) reuptake; conducted docking simulation for two selected compounds; and identified their potential functionals. The compounds were subdivided into arylethylamines, 2-(alkyl amino)-1-arylalkan-1-one derivatives and alkyl 2-phenyl-2-(piperidin-2-yl)acetate derivatives. An aromatic group, alkyl group, and alkylamine derivative were attached to the arylethylamine and 2-(alkyl amino)-1-arylalkan-1-one derivatives. The inhibitory effect of the compounds on dopamine reuptake increased in the order of the compounds substituted with phenyl, thiophenyl, and substituted phenyl groups in the aromatic position; compounds with longer alkyl groups and smaller ring-sized compounds at the alkylamine position showed stronger inhibitory activities. Docking simulation conducted for two compounds, 9 and 28, showed that the (S)-form of compound 9 was more stable than the (R)-form, with a good fit into the binding site covered by helices 1, 3, and 6 of human dopamine transporter (hDAT). In contrast, the (R, S)-configuration of compound 28 was more stable than that of other isomers and was firmly placed in the binding pocket of DAT bound to DA. DA-induced endocytosis of dopamine D₂ receptors was inhibited when they were co-expressed with DAT, which lowered extracellular DA levels, and uninhibited when they were pretreated with compound 9 or 28. In summary, this study revealed critical structural features responsible for the inhibition of DA reuptake and the functional role of DA reuptake inhibitors in regulating D₂ receptor function.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.10a
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• pp.92-92
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• 2019

Excessive or chronic inflammation contributes to the pathogenesis of many inflammatory diseases such as sepsis, rheumatoid arthritis, and ulcerative colitis. Hibiscus syriacus L. has been used as a medicinal plant in many Asian countries, even though its anti-inflammatory activity has been unclear. Therefore, we investigated the anti-inflammatory effect of anthocyanin fractions from the H. syriacus L. varieties Pulsae (PS) on the lipopolysaccharide (LPS)-induced expression of proinflammatory mediators and cytokines in RAW264.7 macrophages. PS suppressed LPS-induced nitric oxide (NO) and prostaglandin $E_2$ ($PGE_2$) secretion concomitant with downregulation of inducible NO synthase (iNOS) and cyclooxygenase-2 (COX-2) expression. Furthermore, PS inhibited the production of proinflammatory cytokines such as tumor necrosis factor-alpha ($TNF-{\alpha}$), interleukin-6 (IL-6), and IL-12 in LPS-stimulated RAW264.7 macrophages. Further study showed that PS significantly decreased LPS-induced nuclear translocation of the nuclear $factor-{\kappa}B$ ($NF-{\kappa}B$) subunits, p65 and p50. Molecular docking data showed that many anthocyanins from PS fit into the hydrophobic pocket of MD2 and bound to Toll-like receptor 4 (TLR4), indicating that PS inhibits the TLR4-MD2-mediated inflammatory signaling pathway. Especially, apigenin-7-O-glucoside most powerfully bound to MD2 and TLR4 through LYS122, LYS122, and SER127 at a distance of $2.205{\AA}$, $3.098{\AA}$, and $2.844{\AA}$ and SER441 at a distance of $2.873{\AA}$ (docking score: -8.4) through hydrogen bonding, respectively. Additionally, PS inhibited LPS-induced TLR4 dimerization/expression on the cell surface, which consequently decreased MyD88 recruitment and IRAK4 phosphorylation. PS completely blocked LPS-mediated mortality in zebrafish larvae by diminishing the recruitment of neutrophil and macrophages accompanied by low levels of proinflammatory cytokines. Taken together, our results indicate that PS attenuates LPS-mediated inflammation in both in vitro and in vivo by blocking the TLR4/MD2-MyD88/IRAK4-$NF-{\kappa}B$ axis. Therefore, PS might be used as a novel modulatory candidate for effective treatment of LPS-mediated inflammatory diseases.