Molecular screening and analysis of novel therapeutic inhibitors against c-Jun N-terminal kinase

Trinath, Daggupati; Chitrala, Kumaraswamy Naidu; Pamanji, Rishika; Suneetha, Y.

doi:10.1007/s00044-017-1919-5

Cited by 3 publications

(5 citation statements)

References 16 publications

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“…The greater the negative binding affinity, the stronger the ligand-receptor interaction and the better the prediction of molecular docking. [34] The results of the simulation showed the binding affinity for Hb with EtBr is À 7.9 kcal/mol, whereas, for GHb is À 8.5 kcal/mol, which shows a clear indication that EtBr is more strongly bound towards GHb, than Hb. This result is also evident by comparing figures 6a and 6c, where H bond donors are only LYS 99 and PRO 95 for Hb and LYS 99, ALA 130, TRP 37, PRO 95 for GHb.…”

Section: Resultsmentioning

confidence: 90%

“…The strength of the ligand‐receptor interaction is decided by binding affinity. The greater the negative binding affinity, the stronger the ligand‐receptor interaction and the better the prediction of molecular docking [34] . The results of the simulation showed the binding affinity for Hb with EtBr is −7.9 kcal/mol, whereas, for GHb is −8.5 kcal/mol, which shows a clear indication that EtBr is more strongly bound towards GHb, than Hb.…”

Section: Resultsmentioning

confidence: 96%

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A Mutagen Acts as a Potent Reducing Agent of Glycated Hemoglobin: a Combined Ultrafast Electron Transfer and Computational Studies

Roy,

Pan,

Ghosh

et al. 2024

ChemBioChem

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Glycated hemoglobin (GHb) found in mammals undergoes irreversible damage when exposed to external redox agents, which is much more vulnerable than its normal counterpart hemoglobin (Hb). Besides the oxygen regulation throughout the body, Hb plays a vital role in balancing immunological health and the redox cycle. Photoinduced ultra‐fast electron transfer phenomena actively participate in regulation of various kind of homeostasis involved in such biomacromolecules. In the present study we have shown that a well‐known mutagen Ethidium Bromide (EtBr) reduces GHb in femtosecond time scale (efficiently) upon photoexcitation after efficient recognition in the biomolecule. We have performed similar experiment by colocalizing EtBr and Iron (Fe(III)) on the micellar surface as Hb mimic in order to study the excited state EtBr dynamics to rationalize the time scale obtained from EtBr in GHb and Hb. While other experimental techniques including Dynamic Light Scattering (DLS), Zeta potential, absorbance and emission spectroscopy have been employed for the confirmation of structural perturbation of GHb compared to Hb, a detailed computational studies involving molecular docking and density functional theory (DFT) have been employed for the explanation of the experimental observations.

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Section: Resultsmentioning

confidence: 90%

Section: Resultsmentioning

confidence: 96%

A Mutagen Acts as a Potent Reducing Agent of Glycated Hemoglobin: a Combined Ultrafast Electron Transfer and Computational Studies

Roy,

Pan,

Ghosh

et al. 2024

ChemBioChem

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“…This study was performed according to previously reported method [7]. Docking was started by IDO1 enzyme preparation and compound 1 and L-1MT optimization.…”

Section: Methodsmentioning

confidence: 99%

“…Binding affinity determines the strength of ligand-receptor interaction. The more negative binding affinity, the stronger ligand-receptor interaction and the better molecular docking prediction [7]. As shown in Table 1, the binding affinity values from the best pose (pose 1) of each ligand 1a, 1b, and 1c were -1.5, 0. binding affinity is also influenced by the energy of desolvation, conformation, interactions, and motions [19,20].…”

Section: Molecular Dockingmentioning

confidence: 97%

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The Effect of Energy Minimization on The Molecular Docking of Acetone-Based Oxindole Derivatives

Fadlan

Nusantoro

2021

JKPK

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<p>In silico study by molecular docking, drug discovery, and virtual screening are useful for obtaining compounds with promising biological activity. The force fields energy minimization in molecular docking is the overall process to produce better geometry estimation and ligand-receptor affinity. In this study, the divide and conquer algorithm based on the Mikowski matrix in MarvinSketch and the conjugate gradient algorithm of Open Babel were used to minimise acetone-based oxindole derivatives in indoleamine 2,3-dioxygenase 1 (IDO1). The results showed that the binding energy produced by MarvinSketch was generally better than the binding energy obtained with Open Babel. The visualization of molecular docking results indicated that the poses and hydrogen bonding, halogen bonding and π-π interactions are different between MarvinSketch, Open Babel, and no energy minimization. The results revealed that energy minimization affects the molecular docking results.</p><p> </p>

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Investigation of Eco-enzyme from Pineapple (Ananas comosus (L.) Merr.) Waste: Chemical Composition, Antibacterial Activity, and Molecular Docking Approach

Ningrum,

Karima,

Renjana

et al. 2024

Waste Biomass Valor

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Molecular screening and analysis of novel therapeutic inhibitors against c-Jun N-terminal kinase

Cited by 3 publications

References 16 publications

A Mutagen Acts as a Potent Reducing Agent of Glycated Hemoglobin: a Combined Ultrafast Electron Transfer and Computational Studies

A Mutagen Acts as a Potent Reducing Agent of Glycated Hemoglobin: a Combined Ultrafast Electron Transfer and Computational Studies

The Effect of Energy Minimization on The Molecular Docking of Acetone-Based Oxindole Derivatives

Investigation of Eco-enzyme from Pineapple (Ananas comosus (L.) Merr.) Waste: Chemical Composition, Antibacterial Activity, and Molecular Docking Approach

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