Molecular profiling of melanocortin 4 receptor variants and agouti-related peptide interactions in morbid obese phenotype: a novel paradigm from molecular docking and dynamics simulations

Bima, Abdulhadi; Elsamanoudy, Ayman Z.; Alghamdi, Kawthar Saad; Shinawi, Thoraia; Mujalli, Abdulrahman; Kaipa, Prabhakar Rao; Aljeaid, Deema; Awan, Zuhier; Shaik, Noor Ahmad; Banaganapalli, Babajan

doi:10.1007/s11756-022-01037-3

Cited by 2 publications

(2 citation statements)

References 65 publications

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“…Atoms and molecules can interact for 100 ns in the GROMACS (GROningenMAchine for Chemical Simulations) ( Van Der Spoel et al, 2005 ). Macromolecular structure-to-function interactions may now be efficiently understood using an advanced technology known as molecular dynamics simulations ( Awan et al, 2021 ; Bima et al, 2022 ). MD simulations were performed by using the GROMOS96 43a1 force field.…”

Section: Methodsmentioning

confidence: 99%

Targeting potential receptor molecules in non-small cell lung cancer (NSCLC) using in silico approaches

Kirubhanand

Leonora²,

Anitha³

et al. 2023

Front. Mol. Biosci.

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Introduction: Non-Small Cell Lung Cancer is the most prevalent type of cancer in lung cancer. Chemotherapy, radiation therapy, and other conventional cancer treatments have a low success rate. Thus, creating new medications is essential to halt the spread of lung cancer.Methods: In this study bioactive nature of lochnericine against Non-Small Cell Lung Cancer (NSCLC) was analyzed using various computational approaches such as quantum chemical calculations, molecular docking, and molecular dynamic simulation. Furthermore, the MTT assay shows the anti-proliferation activity of lochnericine.Results and Discussion: Using Frontier Molecular Orbital (FMO), the calculated band gap energy value associated with bioactive compounds and the molecule’s potential bioactivity is confirmed. The H38 hydrogen atom and O1 oxygen atom in the molecule are effectively electrophilic, and potential nucleophilic attack sites were confirmed through analysis of the Molecular electrostatic potential surface. Furthermore, the electrons within the molecule were delocalized, which confers bioactivity on the title molecule and was authorized through Mulliken atomic charge distribution analysis. A molecular docking study revealed that lochnericine inhibits non-small cell lung cancer-associated targeted protein. The lead molecule and targeted protein complex were stable during molecular dynamics simulation studies till the simulation period. Further, lochnericine demonstrated remarkable anti-proliferative and apoptotic features against A549 lung cancer cells. The current investigation powerfully suggests that lochnericine is a potential candidate for lung cancer.

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Section: Methodsmentioning

confidence: 99%

Targeting potential receptor molecules in non-small cell lung cancer (NSCLC) using in silico approaches

Kirubhanand

Leonora²,

Anitha³

et al. 2023

Front. Mol. Biosci.

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“…The inferred sequence alignment is then visualized in the plugin window and the 3D structures are superimposed in PyMOL ( Figure 2 d). Many analyses [ 68 , 69 ] are now relying on iPBAVizu for efficient protein structure-based superimposition. For instance, iPBAVizu guided the structural comparison of the primary contributors to SARS-CoV-2 antigenicity for the in-silico design of a multi-epitope vaccine candidate [ 70 ].…”

Section: Protein Sequences and Structures Analyses (Pssas)mentioning

confidence: 99%

Boosting the Full Potential of PyMOL with Structural Biology Plugins

Rosignoli

Paiardini

2022

Biomolecules

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Over the past few decades, the number of available structural bioinformatics pipelines, libraries, plugins, web resources and software has increased exponentially and become accessible to the broad realm of life scientists. This expansion has shaped the field as a tangled network of methods, algorithms and user interfaces. In recent years PyMOL, widely used software for biomolecules visualization and analysis, has started to play a key role in providing an open platform for the successful implementation of expert knowledge into an easy-to-use molecular graphics tool. This review outlines the plugins and features that make PyMOL an eligible environment for supporting structural bioinformatics analyses.

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Molecular profiling of melanocortin 4 receptor variants and agouti-related peptide interactions in morbid obese phenotype: a novel paradigm from molecular docking and dynamics simulations

Cited by 2 publications

References 65 publications

Targeting potential receptor molecules in non-small cell lung cancer (NSCLC) using in silico approaches

Targeting potential receptor molecules in non-small cell lung cancer (NSCLC) using in silico approaches

Boosting the Full Potential of PyMOL with Structural Biology Plugins

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