• Journal of Space Technology and Applications
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• v.2 no.1
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• pp.30-40
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• 2022

This paper illustrates the trajectory design of drift distance recovery after initial launch and proximity operation when verifying rendezvous/docking technology using nanosatellites. The rendezvous/docking is a technology that is the basis of on-orbit servicing technology and is a preemptive process essential for approaching a target object. In particular, since it is difficult to verify in space, nanosatellites have recently been used to reduce the risk and cost of the development stage. Therefore, this paper not only introduces the configuration and specifications of thrusters for nanosatellites but also designs relative trajectories that can take into account the thrust limitations which come from the small size and low power of nanosatellites. In addition, we intend to be helpful in later designing scenarios according to the improvement of available thruster performance through comparison of trajectories and thrust usage with cases without thrust limitations.

• Genomics & Informatics
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• v.19 no.4
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• pp.46.1-46.11
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• 2021

Moringa oleifera is nowadays raising as the most preferred medicinal plant, as every part of the moringa plant has potential bioactive compounds which can be used as herbal medicines. Some bioactive compounds of M. oleifera possess potential anti-cancer properties which interact with the apoptosis protein p53 in cancer cell lines of oral squamous cell carcinoma. This research work focuses on the interaction among the selected bioactive compounds derived from M. oleifera with targeted apoptosis protein p53 from the apoptosis pathway to check whether the bioactive compound will induce apoptosis after the mutation in p53. To check the toxicity and drug-likeness of the selected bioactive compound derived from M. oleifera based on Lipinski's Rule of Five. Detailed analysis of the 3D structure of apoptosis protein p53. To analyze protein's active site by CASTp 3.0 server. Molecular docking and binding affinity were analyzed between protein p53 with selected bioactive compounds in order to find the most potential inhibitor against the target. This study shows the docking between the potential bioactive compounds with targeted apoptosis protein p53. Quercetin was the most potential bioactive compound whereas kaempferol shows poor affinity towards the targeted p53 protein in the apoptosis pathway. Thus, the objective of this research can provide an insight prediction towards M. oleifera derived bioactive compounds and target apoptosis protein p53 in the structural analysis for compound isolation and in-vivo experiments on the cancer cell line.

• Journal of Ginseng Research
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• v.47 no.2
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• pp.228-236
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• 2023

Background: QiShen YiQi pills (QSYQ) is a Traditional Chinese Medicine (TCM) formula, which has a significant effect on the treatment of patients with myocardial infarction (MI) in clinical practice. However, the molecular mechanism of QSYQ regulation pyroptosis after MI is still not fully known. Hence, this study was designed to reveal the mechanism of the active ingredient in QSYQ. Methods: Integrated approach of network pharmacology and molecular docking, were conducted to screen active components and corresponding common target genes of QSYQ in intervening pyroptosis after MI. Subsequently, STRING and Cytoscape were applied to construct a PPI network, and obtain candidate active compounds. Molecular docking was performed to verify the binding ability of candidate components to pyroptosis proteins and oxygen-glucose deprivation (OGD) induced cardiomyocytes injuries were applied to explore the protective effect and mechanism of the candidate drug. Results: Two drug-likeness compounds were preliminarily selected, and the binding capacity between Ginsenoside Rh2 (Rh2) and key target High Mobility Group Box 1 (HMGB1)was validated in the form of hydrogen bonding. 2 μM Rh2 prevented OGD-induced H9c2 death and reduced IL-18 and IL-1β levels, possibly by decreasing the activation of the NLRP3 inflammasome, inhibiting the expression of p12-caspase1, and attenuating the level of pyroptosis executive protein GSDMD-N. Conclusions: We propose that Rh2 of QSYQ can protect myocardial cells partially by ameliorating pyroptosis, which seems to have a new insight regarding the therapeutic potential for MI.

• Genomics & Informatics
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• v.21 no.1
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• pp.4.1-4.18
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• 2023

Coronavirus disease 2019 (COVID-19) is an inflammatory and infectious disease caused by severe acute respiratory syndrome coronavirus 2 virus with a complex pathophysiology. While COVID-19 vaccines and boosters are available, treatment of the disease is primarily supportive and symptomatic. Several research have suggested the potential of herbal medicines as an adjunctive treatment for the disease. A popular herbal medicine approved in the Philippines for the treatment of acute respiratory disease is Vitex negundo L. In fact, the Department of Science and Technology of the Philippines has funded a clinical trial to establish its potential as an adjunctive treatment for COVID-19. Here, we utilized network pharmacology and molecular docking in determining pivotal targets of Vitex negundo compounds against COVID-19. The results showed that significant targets of Vitex negundo compounds in COVID-19 are CSB, SERPINE1, and PLG which code for cathepsin B, plasminogen activator inhibitor-1, and plasminogen, respectively. Molecular docking revealed that α-terpinyl acetate and geranyl acetate have good binding affinity in cathepsin B; 6,7,4-trimethoxyflavanone, 5,6,7,8,3',4',5'-heptamethoxyflavone, artemetin, demethylnobiletin, gardenin A, geranyl acetate in plasminogen; and 7,8,4-trimethoxyflavanone in plasminogen activator inhibitor-1. While the results are promising, these are bound to the limitations of computational methods and further experimentation are needed to completely establish the molecular mechanisms of Vitex negundo against COVID-19.

• Journal of Pharmacopuncture
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• v.27 no.2
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• pp.91-100
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• 2024

Objectives: Candida albicans is an opportunistic pathogen that occurs as harmless commensals in the intestine, urogenital tract, and skin. It has been influenced by a variety of host conditions and has now evolved as a resistant strain. The aim of this study was thus detect the fluconazole resistant C. albicans from the root caries specimens and to computationally evaluate the interactions of an opaque-phase ABC transporter protein with the Psidium guajava bio-active compounds. Methods: 20 carious scrapings were collected from patients with root caries and processed for the isolation of C. albicans and was screened for fluconazole resistance. Genomic DNA was extracted and molecular characterization of Cdrp1 and Cdrp2 was done by PCR amplification. P. guajava methanolic extract was checked for the antifungal efficacy against the resistant strain of C. albicans. Further in-silico docking involves retrieval of ABC transporter protein and ligand optimization, molinspiration assessment on drug likeness, docking simulations and visualizations. Results: 65% of the samples showed the presence of C.albicans and 2 strains were fluconazole resistant. Crude methanolic extract of P. guajava was found to be promising against the fluconazole resistant strains of C. albicans. In-silico docking analysis showed that Myricetin was a promising candidate with a high docking score and other drug ligand interaction scores. Conclusion: The current study emphasizes that bioactive compounds from Psidium guajava to be a promising candidate for treating candidiasis in fluconazole resistant strains of C. albicans However, further in-vivo studies have to be implemented for the experimental validation of the same in improving the oral health and hygiene.

• The Journal of Korean Medicine
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• v.45 no.1
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• pp.114-125
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• 2024

Objectives: Network pharmacology is an analysis method that explores drug-centered efficacy and mechanism by constructing a compound-target-disease network based on system biology, and is attracting attention as a methodology for studying herbal medicine that has the characteristics for multi-compound therapeutics. Thus, we investigated the potential functions and pathways of Myrrha on Allergic Rhinitis (AR) via network pharmacology analysis and molecular docking. Methods: Using public databases and PubChem database, compounds of Myrrha and their target genes were collected. The putative target genes of Myrrha and known target genes of AR were compared and found the correlation. Then, the network was constructed using STRING database, and functional enrichment analysis was conducted based on the Gene Ontology (GO) Biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways. Binding-Docking stimulation was performed using CB-Dock. Results: The result showed that total 3 compounds and 55 related genes were gathered from Myrrha. 33 genes were interacted with AR gene set, suggesting that the effects of Myrrha are closely related to AR. Target genes of Myrrha are considerably associated with various pathways including 'Fc epsilon RI signaling pathway' and 'JAK-STAT signaling pathway'. As a result of blinding docking, AKT1, which is involved in both mechanisms, had high binding energies for abietic acid and dehydroabietic acid, which are components of Myrrha. Conclusion: Through a network pharmacological method, Myrrha was predicted to have high relevance with AR by regulating AKT1. This study could be used as a basis for studying therapeutic effects of Myrrha on AR.

• Biomolecules & Therapeutics
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• v.32 no.3
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• pp.390-398
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• 2024

FoxO1, a member of the Forkhead transcription factor family subgroup O (FoxO), is expressed in a range of cell types and is crucial for various pathophysiological processes, such as apoptosis and inflammation. While FoxO1's roles in multiple diseases have been recognized, the target has remained largely unexplored due to the absence of cost-effective and efficient inhibitors. Therefore, there is a need for natural FoxO1 inhibitors with minimal adverse effects. In this study, docking, MMGBSA, and ADMET analyses were performed to identify natural compounds that exhibit strong binding affinity to FoxO1. The top candidates were then subjected to molecular dynamics (MD) simulations. A natural product library was screened for interaction with FoxO1 (PDB ID-3CO6) using the Glide module of the Schrödinger suite. In silico ADMET profiling was conducted using SwissADME and pkCSM web servers. Binding free energies of the selected compounds were assessed with the Prime-MMGBSA module, while the dynamics of the top hits were analyzed using the Desmond module of the Schrödinger suite. Several natural products demonstrated high docking scores with FoxO1, indicating their potential as FoxO1 inhibitors. Specifically, the docking scores of neochlorogenic acid and fraxin were both below -6.0. These compounds also exhibit favorable drug-like properties, and a 25 ns MD study revealed a stable interaction between fraxin and FoxO1. Our findings highlight the potential of various natural products, particularly fraxin, as effective FoxO1 inhibitors with strong binding affinity, dynamic stability, and suitable ADMET profiles.

• Interdisciplinary Bio Central
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• v.1 no.1
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• pp.3.1-3.6
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• 2009

Introduction: GTPases known as translation factor play a vital role as ribosomal subunit assembly chaperone. The bacterial Obg proteins ($Spo{\underline{0B}}$-associated ${\underline{G}}TP$-binding protein) belong to the subfamily of P-loop GTPase proteins and now it is considered as one of the new target for antibacterial drug. The majority of bacterial Obgs have been commonly found to be associated with ribosome, implying that these proteins may play a fundamental role in ribosome assembly or maturation. In addition, one of the experimental evidences suggested that Bacillus subtilis Obg (BsObg) protein binds to the L13 ribosomal protein (BsL13) which is known to be one of the early assembly proteins of the 50S ribosomal subunit in Escherichia coli. In order to investigate binding mode between the BsObg and the BsL13, protein-protein docking simulation was carried out after generating 3D structure of the BsL13 structure using homology modeling method. Materials and Methods: Homology model structure of BsL13 was generated using the EcL13 crystal structure as a template. Protein-protein docking of BsObg protein with ribosomal protein BsL13 was performed by DOT, a macro-molecular docking software, in order to predict a reasonable binding mode. The solvated energy minimization calculation of the docked conformation was carried out to refine the structure. Results and Discussion: The possible binding conformation of BsL13 along with activated Obg fold in BsObg was predicted by computational docking study. The final structure is obtained from the solvated energy minimization. From the analysis, three important H-bond interactions between the Obg fold and the L13 were detected: Obg:Tyr27-L13:Glu32, Obg:Asn76-L13:Glu139, and Obg:Ala136-L13:Glu142. The interaction between the BsObg and BsL13 structures were also analyzed by electrostatic potential calculations to examine the interface surfaces. From the results, the key residues for hydrogen bonding and hydrophobic interaction between the two proteins were predicted. Conclusion and Prospects: In this study, we have focused on the binding mode of the BsObg protein with the ribosomal BsL13 protein. The interaction between the activated Obg and target protein was investigated with protein-protein docking calculations. The binding pattern can be further used as a base for structure-based drug design to find a novel antibacterial drug.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.19
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• pp.8155-8159
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• 2014

Background: Breast cancer is the serious health concern in India causing the highest mortality rate in females, which occurs due to uncontrolled cell division and can be metastasize to other parts of the human body. Interactions with estrogen receptor (ER) alpha are mainly responsible for the malignant tumors with regulation of the transcription of various genes as a transcription factor. Most of the drugs currently used for the breast cancer treatment produce various side effects and hence we focused on natural compounds which do not exhibit any toxic effect against normal human cells. Materials and Methods: Structure of human ER was retrieved from the Protein Data Bank and the structures of flavonoid compounds have been collected from PubChem database. Molecular docking and drug likeness studies were performed for those natural compounds to evaluate and analyze the anti-breast cancer activity. Results: Finally two compounds satisfying the Lipinski's rule of five were reported. The two compounds also exhibited highest binding affinity with human ER greater than 10.5 Kcal/mol. Conclusions: The results of this study can be implemented in the drug designing pipeline.

• Genomics & Informatics
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• v.15 no.4
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• pp.142-146
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• 2017

More effective production of human insulin is important, because insulin is the main medication that is used to treat multiple types of diabetes and because many people are suffering from diabetes. The current system of insulin production is based on recombinant DNA technology, and the expression vector is composed of a preproinsulin sequence that is a fused form of an artificial leader peptide and the native proinsulin. It has been reported that the sequence of the leader peptide affects the production of insulin. To analyze how the leader peptide affects the maturation of insulin structurally, we adapted several in silico simulations using 13 artificial proinsulin sequences. Three-dimensional structures of models were predicted and compared. Although their sequences had few differences, the predicted structures were somewhat different. The structures were refined by molecular dynamics simulation, and the energy of each model was estimated. Then, protein-protein docking between the models and trypsin was carried out to compare how efficiently the protease could access the cleavage sites of the proinsulin models. The results showed some concordance with experimental results that have been reported; so, we expect our analysis will be used to predict the optimized sequence of artificial proinsulin for more effective production.