Structure Prediction and in Silico Designing of Drugs Against Kallikrein Protein 12

Devgan, Manish

doi:10.22159/ijcpr.2017v9i2.17387

Cited by 2 publications

(2 citation statements)

References 24 publications

(25 reference statements)

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“…DNA Sequencing was performed on PCR products in Macrogen, Korea. Sequencing results were analyzed by BLAST (NCBI) to determine the similarity of isolates with the International database of NCBI (National Center for Biotechnology Information) [19].…”

Section: Analysis Of 16s Rrna Genementioning

confidence: 99%

Antibacterial Substance Produced by a Soil Bacteria Isolated From Rhizosphere of Zingiber Officinale

et al. 2021

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Objective: In our previous study, we have found many isolates of bacteria from Zingiber officinale rhizosphere in Magelang, Central Java, Indonesia. J4, one of the isolates, has been found to contain metabolites which have antibacterial activity. The active chemical compound was unidentified. This study aims to identify the molecular formula of the active compound which has potential antibacterial activity. Methods: Identification of selected bacteria (J4 isolate) was based on the 16S rRNA gene sequence. Extraction of J4 isolate culture broth was carried out using ethyl acetate and followed by fractionation with hexane, chloroform-methanol (7:3), and methanol. The fraction which has antibacterial activity analyzed using IR Spectroscopy and LC-TOF-MS. Results: BLAST analysis result of the 16S rRNA sequence showed that J4 isolate is Burkholderia sp with 99% similarity. According to the IR spectroscopy examination of the active fraction, there were OH, CH, and carbonyl stretching. LC-TOF-MS analysis showed 5 molecular formulas with m/z of 253, 274, 387 (two formulas), and 404 in the active fraction, but there was one formula with no OH groups. Conclusion: J4 isolate is a Burkholderia sp. The molecular formula for the antibacterial substance that might be produced by J4 isolate is C6H12N12, C21H29N3O5, C21H26N2O5, C17H22N8O3, and/or C15H35N3O.

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Section: Analysis Of 16s Rrna Genementioning

confidence: 99%

Antibacterial Substance Produced by a Soil Bacteria Isolated From Rhizosphere of Zingiber Officinale

et al. 2021

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“…The 3D model structures of the proteins have been utilized to identify their probable interactions with other proteins and small ligand molecules, thereby identifying the potential inhibitors by exploiting the technique of in silico docking. [16][17][18][19][20][21][22][23][24] In this study, the vast amount of raw gene expression data for HMGA1 was analyzed, and differentially co-expressed genes were identified. The phylogenetic analysis was performed to establish closely related genes.…”

Section: Abstract a R T I C L E I N F Omentioning

confidence: 99%

Microarray data analysis, structure prediction and in silico docking of drugs for inhibiting the over expression of High Mobility Group A1 in human malignant neoplasias

Devgun

Lal

2020

Int. J. Pharm. Sci. Drug Res.

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The High Mobility Group A1 (HMGA1) gene over expression has been widely observed in various types of cancers. The raw data for microarray data analysis was obtained from the dataset record GDS3525. The SOM and K-means of the Genesis led to the identification of two clusters (each consisting of 30 genes) bearing HMGA1 gene. This on further analysis resulted into identification of 14 similar genes by Easy M-A. The evolutionary similarity of HMGA1 and GORASP2 is clearly observed in the Phylogenetic Tree. Due to the absence of precise structures, the homology modeling was done by using EasyModeller and the resulting models of proteins HMGA1 and GORASP2 were validated by Ramachandran plot. These models were further put to loop optimization by Modloop and the output models were assessed by Ramachandran plot (Rampage) and through SAVS (Procheck). The molecular docking was done by using Autodock, this resulted in two ligands, DB11641 (Vinflunine) and DB12674 (Lurbinectedin), showing potential for the effective treatment of various types of cancers characterized by the over expression of HMGA1 and GORASP2.

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Structure Prediction and in Silico Designing of Drugs Against Kallikrein Protein 12

Cited by 2 publications

References 24 publications

Antibacterial Substance Produced by a Soil Bacteria Isolated From Rhizosphere of Zingiber Officinale

Antibacterial Substance Produced by a Soil Bacteria Isolated From Rhizosphere of Zingiber Officinale

Microarray data analysis, structure prediction and in silico docking of drugs for inhibiting the over expression of High Mobility Group A1 in human malignant neoplasias

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