• Bulletin of the Korean Chemical Society
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• v.28 no.2
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• pp.200-206
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• 2007

Pharmacophore models for lymphocyte-specific protein tyrosine kinase (P56 LCK) were developed using CATALYST HypoGen with a training set comprising of 25 different P56 LCK inhibitors. The best quantitative pharmacophore hypothesis comprises of one hydrogen bond acceptor, one hydrogen bond donor, one hydrophobic aliphatic and one ring aromatic features with correlation coefficient of 0.941, root mean square deviation (RMSD) of 0.933 and cost difference (null cost-total cost) of 66.23. The pharmacophore model was validated by two methods and the validated model was further used to search databases for new compounds with good estimated LCK inhibitory activity. These compounds were evaluated for their binding properties at the active site by molecular docking studies using GOLD software. The compounds with good estimated activity and docking scores were evaluated for physiological properties based on Lipinski's rules. Finally 68 compounds satisfied all the properties required to be a successful inhibitor candidate.

• Bulletin of the Korean Chemical Society
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• v.34 no.2
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• pp.545-548
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• 2013

It has been shown that calculating atomic charges using quantum mechanical level theory greatly improves the accuracy of docking. A protocol was developed and shown to be effective. That this protocol works is just a manifestation of the fact that electrostatic interactions are important in protein-ligand binding. In order to investigate how the same protocol helps in prediction of binding affinities, we took a series of known cocrystal structures of influenza neuraminidase inhibitors with the receptor and performed docking with Glide SP, Glide XP, and QPLD, the last being a workflow that incorporates QM/MM calculations to replace the fixed atomic charges of force fields with quantum mechanically recalculated ones at a given docking pose, and predicted the binding affinities of each cocrystal. The correlation with experimental binding affinities considerably improved with QPLD compared to Glide SP/XP yielding $r^2$ = 0.83. The results suggest that for binding sites, such as that of neuraminidase, which are laden with hydrophilic residues, protocols such as QPLD which utilizes QM-based atomic charges can better predict the binding affinities.

• Genomics & Informatics
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• v.13 no.2
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• pp.60-67
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• 2015

The leading cause of cancer mortality globally amongst the women is due to human papillomavirus (HPV) infection. There is need to explore anti-cancerous drugs against this life-threatening infection. Traditionally, different natural compounds such as withaferin A, artemisinin, ursolic acid, ferulic acid, (-)-epigallocatechin-3-gallate, berberin, resveratrol, jaceosidin, curcumin, gingerol, indol-3-carbinol, and silymarin have been used as hopeful source of cancer treatment. These natural inhibitors have been shown to block HPV infection by different researchers. In the present study, we explored these natural compounds against E6 oncoprotein of high risk HPV18, which is known to inactivate tumor suppressor p53 protein. E6, a high throughput protein model of HPV18, was predicted to anticipate the interaction mechanism of E6 oncoprotein with these natural inhibitors using structure-based drug designing approach. Docking analysis showed the interaction of these natural inhibitors with p53 binding site of E6 protein residues 108-117 (CQKPLNPAEK) and help reinstatement of normal p53 functioning. Further, docking analysis besides helping in silico validations of natural compounds also helped elucidating the molecular mechanism of inhibition of HPV oncoproteins.

• Journal of the Korean Society for Precision Engineering
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• v.18 no.12
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• pp.137-144
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• 2001

The major movement blocks of the container are the range between the apron and the designation points on yard in container terminals. The yard tractor drived by operator takes charge of it's movement in conventional container terminals. In automated container terminal, AGV(automatic guided vehicle) takes charge of a yard tractor's role and information of navigation path are ordered from upper control system. The automated container terminal facilities must have the docking system that guides landing zinc to execute high speed travelling and precision positioning. This paper describes the new docking method with the rotating LSB(laser slit beam) generator and two pair of photo receiver. The LSB generator is installed on the fixed ground and the photo receiver is implemented on the moving vehicle such as AGV. The proposed docking system is implemented to confirm it's function and accuracy. The accuracy of measured moving position is represented in ±5mm at 1 data sampling.

• Journal of the Korean Chemical Society
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• v.65 no.2
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• pp.106-112
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• 2021

12 kinds of (-)-catechin derivatives were designed and synthesized. The catechin derivatives were evaluated their antioxidant activities using DPPH method. Most of them showed good antioxidant activity, particularly compounds 1d, 1e and 1j exhibited more activity than butylated hydroxytoluene (BHT). Molecular docking studies for compounds 1d, 1e and 1j with STAT1 showed not only sufficent characteristics binding cavity but also agreement with the observed biological activity. Acording to docking results, the compounds showed greater than hydrogen bonding, hydrophobic interactions, electrostatic interactions, and Van der Waals interactions as compared to the reference compound. They formed hydrogen bonds with important residues such as Lys566, His568, Leu570, and Phe644. The compounds showed a novel hydrogen bonding interaction with Arg649, which was not reported previously. Our results might suggest the compounds could serve as a novel anti-oxidant agent.

• Biomolecules & Therapeutics
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• v.29 no.5
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• pp.519-526
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• 2021

In a search for effective PPAR-γ agonists, 110 clinical drugs were screened via molecular docking, and 9 drugs, including parecoxib, were selected for subsequent biological evaluation. Molecular docking of parecoxib to the ligand-binding domain of PPAR-γ showed high binding affinity and relevant binding conformation compared with the PPAR-γ ligand/antidiabetic drug rosiglitazone. Per the docking result, parecoxib showed the best PPAR-γ transactivation in Ac2F rat liver cells. Further docking simulation and a luciferase assay suggested parecoxib would be a selective (and partial) PPAR-γ agonist. PPAR-γ activation by parecoxib induced adipocyte differentiation in 3T3-L1 murine preadipocytes. Parecoxib promoted adipogenesis in a dose-dependent manner and enhanced the expression of adipogenesis transcription factors PPAR-γ, C/EBPα, and C/EBPβ. These data indicated that parecoxib might be utilized as a partial PPAR-γ agonist for drug repositioning study.

• Journal of Microbiology and Biotechnology
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• v.33 no.2
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• pp.268-276
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• 2023

Alkyl butyrate with fruity flavor is known as an important additive in the food industry. We synthesized various alkyl butyrates from various fatty alcohol and butyric acid using immobilized Rhodococcus cutinase (Rcut). Esterification reaction was performed in a non-aqueous system including heptane, isooctane, hexane, and cyclohexane. As a result of performing the alkyl butyrate synthesis reaction using alcohols of various chain lengths, it was found that the preference for the alcohol substrate had the following order: C6 > C4 > C8 > C10 > C2. Through molecular docking analysis, it was found that the greater the hydrophobicity of alcohol, the higher the accessibility to the active site of the enzyme. However, since the number of torsions increased as the chain length increased, it became difficult for the hydroxyl oxygen of the alcohol to access the ^γO of serine at the enzyme active site. These molecular docking results were consistent with substrate preference results of the Rcut enzyme. The Rcut maintained the synthesis efficiency at least for 5 days in isooctane solvent. We synthesized as much as 452 mM butyl butyrate by adding 100 mM substrate daily for 5 days and performing the reaction. These results show that Rcut is an efficient enzyme for producing alkyl butyrate used in the food industry.

• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.103-108
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• 2006

Computational prediction of protein-ligand binding has been widely used as a tool to discover lead compounds fur new drugs. Prediction accuracy is determined in part by the scoring function used in docking calculations. Diverse scoring functions are available, and these can be classified into force-field based, empirical, and knowledge-based functions depending upon the basic assumptions made in development. Among these, force-field based functions consider physical interactions the most in detail. However, the force-field based functions have the drawback of not including the entropic effect while considering only the energy contribution such as dispersion or electrostatic forces. In this article, a method to take into account of the entropic effect using the colony energy is suggested when force-field based scoring functions is used by extracting conformational information obtained from the pre-existing docking program. An improved result for decoy discrimination is illustrated when the method is applied to the DOCK scoring function, and this implies that more accurate docking calculation is possible.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.6
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• pp.796-802
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• 2009

The effects of docking on growth traits, fattening performance, carcass characteristics and blood biochemical parameters were investigated using 24 fat-tailed Sanjabi single-born male lambs raised from a large commercial sheep herd. The lambs were randomly divided into two groups. One group (n = 12) were docked at two days of age with rubber-rings using an elastrator. The second group (n = 12) were left intact. After weaning (90 days), all lambs were moved to rustic rangelands for 40 days. Then all the lambs were fed concentrates ad libitum for 60 days during the fattening period. Growth traits, body weight and average daily gain (kg) were recorded at the end of the weaning and fattening periods. Blood biochemical parameters including urea, total protein, glucose, triglycerides, cholesterol, low-density lipoproteins (LDL) and high-density lipoproteins (HDL) were measured during the fattening period. Finally, at the end of the fattening period, eight lambs (4 intact and 4 docked lambs) were slaughtered in order to determine carcass characteristics. Fat-tail docking had no effect (p>0.05) on lamb growth from birth to weaning. Body weight and average daily gain of docked lambs were significantly higher (p<0.05) than for intact lambs at the end of the fattening period. There was no difference in carcass measurements between the two groups, except for chest depth and leg weight which were higher (p<0.05) in docked lambs. During the fattening period, cholesterol and LDL of docked lambs were less than in intact lambs (p<0.05). The current results indicated that docking with rubber rings causes an improvement in growth traits during the fattening period and leads to desirable carcass characteristics compared to intact lambs; interestingly, this procedure had a significant effect on the lowering of blood cholesterol and LDL of docked lambs.

• Journal of Korea Society of Industrial Information Systems
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• v.17 no.7
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• pp.25-33
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• 2012

This paper deals with the development of automatic docking system for the detachable mobile seat(DMS) of a vehicle for the handicapped people who are unable to ride in a car by oneself. Although such vehicles for the handicapped already exist, there is a need for a vehicle with improved docking method for convenience. This paper presents an automatic docking system using two ultrasonic sensors. In order to identify the precise location of the mobile seat in front of the vehicle door, the capability of ultrasonic sensor for detecting the part edge is analyzed and mathematical modeling is performed to measure the exact location of the side edge. And also, this paper presents an automatic docking method using this sensor system and the car lift which is provided in the inside of the car.