Structure and Function of an Inflammatory Cytokine, Interleukin-2, Analyzed Using the Bioinformatic Approach

Roy, Urmi

doi:10.1007/s10930-019-09833-8

Cited by 3 publications

(6 citation statements)

References 52 publications

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“…The experimental simulation setup for IL-18 and IL-18/IL-18R were similar to those reported previously ( Roy, 2016a , 2016b , 2017 , 2019a , 2019b , 2020 ). Based on the native/original protein, the protein structure file (PSF) along with a corresponding PDB structure was generated.…”

Section: Methodsmentioning

confidence: 55%

“…The computational protocol was designed to obtain the basic frameworks for the IL-18 ligand and the ligand bound holo structures. Additional computational details of the present work have been described elsewhere ( Roy, 2016a , 2016b , 2017 , 2019a , 2019b , 2020 ).…”

Section: Methodsmentioning

confidence: 99%

“…The treatments of IL-18 related diseases may involve the use of selective or potent IL-18 ligand/-receptor inhibitors that would interfere with, or effectively block the targeted functions ( Hamasaki et al, 2005 ; Tsutsumi et al, 2019 ). In our earlier papers we have described the structures and structure-related functional changes of several physiologically relevant proteins ( Roy and Luck, 2007 ; Roy, 2016a , 2016b , 2017 , 2019a , 2019b , 2020 ). The present simulation study examines the structural stabilities of the ligand-protein, IL-18 and IL-18 receptor (IL-18R) bound ligand structures as functions of time.…”

Section: Introductionmentioning

confidence: 99%

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Insight into the structures of Interleukin-18 systems

Roy

2020

Computational Biology and Chemistry

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Section: Methodsmentioning

confidence: 55%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Insight into the structures of Interleukin-18 systems

Roy

2020

Computational Biology and Chemistry

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“…MD simulations of such time scale can be carried out with relatively moderate computational resources and, at the same time, can serve as an effective probe of the basic conformational changes in the protein [43,44]. The detailed output frequencies of the trajectory coordinate files have been described previously [33][34][35][36]. The VMD program [42] was used to analyze these trajectory structures, and the corresponding figures were generated with Discovery Studio Visualizer (DSV) [45].…”

Section: Methodsmentioning

confidence: 99%

“…MD simulation is an established technique, useful for identifying structure-function relationships of proteins in general. Previous MD-based studies by the present author have described the structures and time-dependent dynamics of several immunologically relevant proteins [33][34][35][36][37][38]. Other authors have reported MD simulation studies of the dengue ED3 protein in the aqueous medium [39,40].…”

Section: Introductionmentioning

confidence: 92%

Structural and molecular analyses of functional epitopes and escape mutants in Japanese encephalitis virus envelope protein domain III

Roy

2020

Immunol Res

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The Japanese encephalitis virus (JEV) is one of the vector borne causes of encephalitis found in southeastern Asia. This positive single-stranded RNA virus is a member of the Flaviviridae family, which notably includes dengue, tick-borne, West Nile, Zika as well as yellow fever, and transmits to humans by infected mosquitos. The main site of interactions for antibodies against this virus is the envelope protein domain III (ED3). The present report investigates the time-dependent structural and conformational changes of JEV ED3 functional epitopes and escape mutants by computer simulations. The results indicate the presence of significant structural differences between the functional epitopes and the escape mutants. Mutation-induced structural/ conformational instabilities of this type can decrease the antibody neutralization activity. Among the different escape mutants studied here, Ser40Lys/Asp41Arg appear to be most unstable, while Ser40Glu/Asp41Leu exhibit the lowest structural variations. The highest level of escape mutation observed in Ser40Lys is linked to the relatively higher values of root mean square deviation/ fluctuation found in the molecular dynamics simulation of this protein. Secondary-structure deviations and depletion of H bonding are other contributing factors to the protein's increased instability. Overall, the proteins with residue 41 mutations are found to be structurally more ordered than those with residue 40 mutations. The detailed time-based structural assessment of the mutant epitopes described here may contribute to the development of novel vaccines and antiviral drugs necessary to defend against future outbreaks of JEV escape mutants.

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Identifying molecular targets of Aspiletrein-derived steroidal saponins in lung cancer using network pharmacology and molecular docking-based assessments

Iksen

Witayateeraporn

Wirojwongchai

et al. 2023

Sci Rep

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Lung cancer is one of the leading cancers and causes of cancer-related deaths worldwide. Due to its high prevalence and mortality rate, its clinical management remains a significant challenge. Previously, the in vitro anticancer activity of Aspiletrein A, a steroid and a saponin from Aspidistra letreae, against non-small cell lung cancer (NSCLC) cells was reported. However, the anticancer molecular mechanism of other Aspiletreins from A. letreae remains unknown. Using in silico network pharmacology approaches, the targets of Aspiletreins were predicted using the Swiss Target Prediction database. In addition, key mediators in NSCLC were obtained from the Genetic databases. The compound-target interacting networks were constructed using the STRING database and Cytoscape, uncovering potential targets, including STAT3, VEGFA, HSP90AA1, FGF2, and IL2. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated that several pathways were highly relevant to cancer pathogenesis. Additionally, molecular docking and molecular dynamic analyses revealed the interaction between key identified targets and Aspiletreins, including hydrogen bonding and Van der Waals interaction. This study provides potential targets of Aspiletreins in NSCLC, and its approach of integrating network pharmacology, bioinformatics, and molecular docking is a powerful tool for investigating the mechanism of new drug targets on a specific disease.

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Structure and Function of an Inflammatory Cytokine, Interleukin-2, Analyzed Using the Bioinformatic Approach

Cited by 3 publications

References 52 publications

Insight into the structures of Interleukin-18 systems

Insight into the structures of Interleukin-18 systems

Structural and molecular analyses of functional epitopes and escape mutants in Japanese encephalitis virus envelope protein domain III

Identifying molecular targets of Aspiletrein-derived steroidal saponins in lung cancer using network pharmacology and molecular docking-based assessments

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