Structural analysis, molecular docking and molecular dynamics simulations of G-protein-coupled receptor (kisspeptin) in fish

Rather, Mohd Ashraf; Dutta, Subhajit; Guttula, Praveen Kumar; Dhandare, Bhushan C; Yusufzai, S I; Zafar, Mehar Imran

doi:10.1080/07391102.2019.1633407

Cited by 32 publications

(8 citation statements)

References 61 publications

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“…In protein-ligand docking, the docked conformers underwent root mean square deviation (RMSD) and root mean square fluctuation (RMSF) plot analysis to evaluate the stability and fluctuations of the protein-ligand complex during the MD simulation. The RMSD analysis quantifies the structural aberration between the docked complex and the MD trajectory, whereas the RMSF analysis gauges the residue-wise fluctuation of the complex throughout the simulation as per the methods of earlier researchers (Rather et al, 2020;Tabti et al, 2023). The MD simulation outcomes were assessed utilizing various visualization tools, including VMD and Chimera, to acquire perspicacity into the protein-ligand interactions and recognize prospective binding sites and vital residues implicated in the interaction.…”

Section: Molecular Dynamic Simulationmentioning

confidence: 99%

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Amomum subulatum: A treasure trove of anti-cancer compounds targeting TP53 protein using in vitro and in silico techniques

Ali¹,

Noreen

Qamar³

et al. 2023

Front. Chem.

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Cancer is a primary global health concern, and researchers seek innovative approaches to combat the disease. Clinical bioinformatics and high-throughput proteomics technologies provide powerful tools to explore cancer biology. Medicinal plants are considered effective therapeutic agents, and computer-aided drug design (CAAD) is used to identify novel drug candidates from plant extracts. The tumour suppressor protein TP53 is an attractive target for drug development, given its crucial role in cancer pathogenesis. This study used a dried extract of Amomum subulatum seeds to identify phytocompounds targeting TP53 in cancer. We apply qualitative tests to determine its phytochemicals (Alkaloid, Tannin, Saponin, Phlobatinin, and Cardic glycoside), and found that alkaloid composed of 9.4% ± 0.04% and Saponin 1.9% ± 0.05% crude chemical constituent. In the results of DPPH Analysis Amomum subulatum Seeds founded antioxidant activity, and then we verified via observing methanol extract (79.82%), BHT (81.73%), and n-hexane extract (51.31%) found to be positive. For Inhibition of oxidation, we observe BHT is 90.25%, and Methanol (83.42%) has the most significant proportion of linoleic acid oxidation suppression. We used diverse bioinformatics approaches to evaluate the effect of A. subulatum seeds and their natural components on TP53. Compound-1 had the best pharmacophore match value (53.92), with others ranging from 50.75 to 53.92. Our docking result shows the top three natural compounds had the highest binding energies (−11.10 to −10.3 kcal/mol). The highest binding energies (−10.9 to −9.2 kcal/mol) compound bonded to significant sections in the target protein’s active domains with TP53. Based on virtual screening, we select top phytocompounds for targets which highly fit based on pharmacophore score and observe these compounds exhibited potent antioxidant activity and inhibited cancer cell inflammation in the TP53 pathway. Molecular Dynamics (MD) simulations indicated that the ligand was bound to the protein with some significant conformational changes in the protein structure. This study provides novel insights into the development of innovative drugs for the treatment of cancer disorders.

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Section: Molecular Dynamic Simulationmentioning

confidence: 99%

“…Molecular dynamics (MD) simulations are an effective tool for investigating the dynamic behavior of proteins at biologically relevant timescales (Rather et al, 2020). In this study, MD simulations were used to examine how the presence of ligands affects the stability and conformational changes of the TP53 protein.…”

Section: Simulationmentioning

confidence: 99%

Amomum subulatum: A treasure trove of anti-cancer compounds targeting TP53 protein using in vitro and in silico techniques

Ali¹,

Noreen

Qamar³

et al. 2023

Front. Chem.

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“…Sex determination in tilapia species is mainly genetic, although environmental factors also play a role [17], [18]. Identifying of advantageous genes like growth-related genes, disease-related gene, sex determination, sex differentiation, reproductive gene and physiological gene is a key step in aquaculture that will optimized for greater yield, cost-efficiency, quality, and disease resistance [19], [20], [21], [22]…”

Section: Introductionsmentioning

confidence: 99%

Genome-Wide identification of doublesex and Mab-3-Related transcription factor (DMRT) genes in nile tilapia (oreochromis niloticus)

Zafar

Rather

Dhandare

2019

Biotechnology Reports

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“…Kauffman et al [46] showed that templates of low sequence similarity with the query sequence could also be used for developing a good model for docking analysis when the sequence alignment was handled correctly. Different studies for GPCRs also used the c-score and Ramachandran plot for analyzing the predicted protein models [47][48][49][50][51].…”

Section: Discussionmentioning

confidence: 99%

Characterization, Docking and Molecular Dynamics Simulation of Gonadotropin-Inhibitory Hormone Receptor (GnIHR2) in Labeo Catla

Kumar

Wisdom

et al. 2020

Cell Physiol Biochem

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Structural analysis, molecular docking and molecular dynamics simulations of G-protein-coupled receptor (kisspeptin) in fish

Cited by 32 publications

References 61 publications

Amomum subulatum: A treasure trove of anti-cancer compounds targeting TP53 protein using in vitro and in silico techniques

Amomum subulatum: A treasure trove of anti-cancer compounds targeting TP53 protein using in vitro and in silico techniques

Genome-Wide identification of doublesex and Mab-3-Related transcription factor (DMRT) genes in nile tilapia (oreochromis niloticus)

Characterization, Docking and Molecular Dynamics Simulation of Gonadotropin-Inhibitory Hormone Receptor (GnIHR2) in Labeo Catla

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