• Journal of Integrative Natural Science
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• v.7 no.3
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• pp.159-165
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• 2014

Pyrazole, hydroxyimino, aldehyde and isoxazole derivatives exhibit a broad spectrum of biological activities such as antimicrobial, anti-inflammatory and antitumor activities. With growing application on their synthesis and bioactivity, chemists and biologists in recent years have considerable attention on the research of these derivatives. In the view of potential importance of these derivatives, we have crystallized few of the derivatives and its report has been published. The present study focuses on docking studies of these derivatives against Phospholipases $A_2$ enzyme. This enzymes has implicated as potential targets for anti-inflammatory drug design. co-crystal structure (PDB ID: 1POE) of $PLA_2$ deposited in Protein Data Bank has been retrieved for docking analysis. Docking studies using Schrodinger's GLIDE reveals that these derivatives shows better binding energy and score in the defined active site. These results may provide a guiding role to design a lead molecule which may reduce inflamation.

• IE interfaces
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• v.19 no.1
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• pp.26-33
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• 2006

Many Firms consider the application of a cross-docking system to reduce inventory and lead-time. However, most studies mainly concentrate on the design of a cross-docking system. This study presents the method that selects the cross-docking center under the existing logistics network. Describing the operation environment to apply the cross-docking system, the selection criteria of the cross-docking center, and the main constraints of transportation planning under the environment of multi-level logistics network, we define the selection problem of the cross-docking center applied to a logistics field. We also define the simulation model that can analyze variously the cross-docking volume and develop the selection methodology of the cross-docking center. The simulation model presents the algorithm and influence factors of the cross-docking system, the decision criteria of the system, policy parameter, and input data. In addition, this study analyzes the effect of increasing the number of simultaneous receiving and shipping docks, and the efficiency of the overnight transportation and cross-docking by evaluating each scenario after simulating the scenarios with the practical data of the logistics field.

• Natural Product Sciences
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• v.28 no.2
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• pp.45-52
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• 2022

The identification of Plasmodium falciparum enoyl acyl-carrier protein reductase (pfENR) is considered as a potential biological target against malaria. Trema orientalis is considered a rich source of phytochemicals useful in malaria treatment. This study evaluated the in-vitro inhibitory activity of the extract and isolated compounds of T. orientalis leaf; the isolated compounds and the analogues of the most active compound were subjected to in-silico molecular docking studies on pfENR. The methanolic extract of T. orientalis was subjected to repeated chromatographic separation which led to the isolation of some compounds. The isolated compounds from the plant were examined for their antimalarial activity using β-hematin inhibition assay. Virtual screening via molecular docking and ADMET studies were conducted to gain insight into the mechanism of binding of ligand and to identify effective pfENR inhibitors. The isolated compounds and the analogues of the most active isolates were gotten from PubChem library for use in docking study. Hexacosanol and β-sitosterol showed inhibition of the β-hematin formation. The docking results showed that hexacosanol, β-sitosterol and the analogues of β-sitosterol displayed binding energy ranging between -6.1 kcal/mol and -11.6 kcal/mol. Sitosterol glucoside has the highest docking score. Some of the ligands showed more binding affinity than known bioactive compounds used as reference. Analogues of β-sitosterol has been shown to be potential inhibitors of pfENR, therefore, the findings from this study suggest that sitosterol glucoside and ergosterol peroxide could act as antimalarial agents after further lead optimisation investigations.

• Journal of Integrative Natural Science
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• v.9 no.3
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• pp.161-165
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• 2016

The p21-activated kinase-1 (PAK1) has emerged as a potential target for anticancer therapy. It is overexpressed in ovarian, breast and bladder cancers. This suggests that PAK1 may contribute to tumorigenesis. 4-azaindole derivatives are reported as potent PAK1 inhibitors. The present work deals with the molecular docking studies of 4-azaindoles with PAK1. Probable binding mode of these inhibitors has been identified by molecular modeling. Docking results indicated that hydrogen bonding interactions with Glu345 and Leu347 are responsible for governing inhibitor potency of the compounds. Additionally, Val284, Val328, Met344 and Leu396 were found to be accountable for hydrophobic interactions inside the active site of PAK1.

• Bulletin of the Korean Chemical Society
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• v.29 no.5
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• pp.959-962
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• 2008

We have performed FlexX docking experiments to predict the best docking poses of 5-androst-16-en-3-ol or 5-androst-16-en-3-one to Boar salivary lipocalin (SAL). Since no steroids were found inside of the binding pocket of the X-ray structure of 1GM6, we tried to find docking structures after opening the pocket using the random tweak option implemented in SYBYL. This operation allowed the ligand to enter the pocket. The best poses generated from FlexX were different from the structures reported earlier, which calculated docking poses by manual docking followed by minimization. Analysis of docking poses allowed us to identify pharmacophores. From this information, virtual screening experiments using UNITY were performed. Among six candidates, 3-(3,7-dimethyloct-6-enylamino)propane-1,2-diol (Leadquest code name: 5755) was chosen for further development. Future work will involve synthesis of some derivatives of 5755 and biological experiments if any derivatives can control the biostimulation and improve reproductive efficiency in pigs.

• Bulletin of the Korean Chemical Society
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• v.34 no.3
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• pp.899-906
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• 2013

Using generated conformations from docking analysis by Gold algorithm, some 3D-QSAR models; CoMFA and CoMSIA have been created on 39 N-benzoylated phenoxazines and phenothiazines, including their S-oxidized analogues. These molecules inhibit the polymerization of tubulin into microtubules and thus they have been studied for the development of antitumor drugs. Training set for the CoMFA and CoMSIA models using 30 docked conformations gives $q^2$ Leave one out (LOO) values of 0.756 and 0.617, and $r^2$ ncv values of 0.988 and 0.956, respectively. The ability of prediction and robustness of the models were evaluated by test set, cross validation (leave-one-out and leave-ten-out), bootstrapping, and progressive scrambling approaches. The all-orientation search (AOS) was used to achieve the best orientation to minimize the effect of initial orientation of the structures. The docking results confirmed CoMFA and CoMSIA contour maps. The docking and 3D-QSAR studies were thoroughly interpreted and discussed and confirmed the experimental $pIC_{50}$ values.

• YAKHAK HOEJI
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• v.53 no.4
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• pp.222-227
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• 2009

Human topoisomerase I (Topo I) plays a pivotal role in cell replication, transcription and repair and, therefore, is an important anti-cancer target. 20S-camptothecin (CPT) is a representative Topo I inhibitor. Compounds belonging to CPT family inhibit the religation step of Topo I-DNA by binding to the DNA cleavage site. Computational docking studies with Surflex-Dock were carried out to investigate the binding modes between Topo I-DNA binary complex structure and the ligand such as 20S-CPT and 9,10-substituted 20S-CPT analogues. The docking results demonstrated that most of the compounds with $IC_{50}$ value under $0.5{\mu}M$ intercalated exactly between the -1 and +1 DNA bases, deeply toward the cleavage site. The complex was stabilized by hydrogen-bonding and hydrophobic interactions with both the enzyme and the DNA. The compounds with $IC_{50}$ value above $0.5{\mu}M$ were poorly docked and did not intercalate. In addition, the docking results confirmed the overall correlation between the $IC_{50}$ values and docking scores, indicating the possible use of the modeling for the prediction of biological activity and design of potential inhibitors.

• Journal of the Korean Chemical Society
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• v.57 no.1
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• pp.99-103
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• 2013

The present communication deals with the Pharmacophore modeling, 3D QSAR and docking analysis on series of Pyrimidine derivatives as potential calcium channel blockers. The computational studies showed hydrogen bond donor, hydrogen bond acceptor, and hydrophobic group are important features for calcium channel blocking activity. These studies showed that Pyrimidine scaffold can be utilized for designing of novel calcium channels blockers for CVS disorders.

• Journal of the Korean Institute of Intelligent Systems
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• v.19 no.4
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• pp.470-477
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• 2009

Modular reconfigurable robots with physical docking capability easily adapt to a new environment and many studies are necessary for the modular robots. In this paper, we propose a vision-based fuzzy autonomous docking controller for the modular docking robots. A modular docking robot platform which performs real-time image processing is designed and color-based object recognition method is implemented on the embedded system. The docking robot can navigate to a subgoal near a target robot while avoiding obstacles. Both a fuzzy obstacle avoidance controller and a fuzzy navigation controller for subgoal tracking are designed. We propose an autonomous docking controller using the fuzzy obstacle avoidance and navigation controllers, absolute distance information and direction informations of robots from PSD sensors and a compass sensor. We verify the proposed docking control method by docking experiments of the developed modular robots in the various environments with different distances and directions between robots.

• Journal of Ocean Engineering and Technology
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• v.36 no.3
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• pp.181-193
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• 2022

This study presents a mission management technique that is a key component of underwater docking system used to expand the operating range of autonomous underwater vehicle (AUV). We analyzed the docking scenario and AUV operating environment, defining the feasible initial area (FIA) level, event level, and global path (GP) command to improve the rate of docking success and AUV safety. Non-holonomic constraints, mounted sensor characteristic, AUV and mission state, and AUV behavior were considered. Using AUV and docking station, we conducted experiments on land and at sea. The first test was conducted on land to prevent loss and damage of the AUV and verify stability and interconnection with other algorithms; it performed well in normal and abnormal situations. Subsequently, we attempted to dock under the sea and verified its performance; it also worked well in a sea environment. In this study, we presented the mission management technique and showed its performance. We demonstrated AUV docking with this algorithm and verified that the rate of docking success was higher compared to those obtained in other studies.