scholarly journals Docking Studies and Molecular Dynamics Simulation of Compounds Contained in Kaempferia Galanga L. to Lipoxygenase (LOX) for Anti-Inflammatory Drugs

2021 ◽  
Vol 53 (2) ◽  
pp. 218-230
Author(s):  
Supandi Supandi ◽  
Yeni Yeni ◽  
Lusi Putri Dwita
Keyword(s):  
Molecular Dynamics ◽  
Healing Process ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Active Components ◽  
Ligand Complex ◽  
Lipoxygenase Inhibitors ◽  
Bond Stability ◽  
Anti Inflammatory ◽  
Lox Inhibitors

Inflammation is a self-protective response to start the healing process. An anti-inflammatory target worth developing are lipoxygenase inhibitors, which have been studied for several diseases, including severe respiratory disease. This research had the goals of estimating the activity of 21 compounds from K. galanga to inhibit the lipoxygenase (LOX) and estimating the bond stability of the ligand-LOX complex. Based on the compound’s affinity for LOX, the compounds in K. galanga were selected by utilizing the PLANTS docking software, with zileuton as the reference ligand. The GROMACS application was used to simulate the molecular dynamics of the LOX-ligand complex at 310 K. Based on the chemPLP score, most of the 21 K. galanga compounds showed a higher affinity towards 5-LOX compared to zileuton. δ-3-carene had the best affinity for 5-LOX. In the simulation of molecular dynamics until 20 ns, the RMSD of δ-3-carene and 5-LOX was not more than 0.03 nm or 0.3 Å, indicating that the whole system showed decent stability and had ‑1.67392 x 106 kcal/mol as the average potential energy. The results showed that K. galanga contains active components of 5-LOX inhibitors that could be developed.

scholarly journals Molecular dynamics simulation and docking studies reveal NF-κB as a promising therapeutic drug target for COVID-19

2021 ◽  
Author(s):  
Shaban Ahmad ◽  
Piyush Bhanu ◽  
Jitendra Kumar ◽  
Ravi Kant Pathak ◽  
Dharmendra Mallick ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Protein Structures ◽  
Drug Repurposing ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Spike Protein ◽  
Drug Candidate ◽  
Therapeutic Drug ◽  
Ligand Complex

Abstract Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is rampant worldwide and is a deadly disease for humans. Our current work emphasizes on molecular dynamics simulation (MDS) targeting nuclear factor-kappa B (NF-κB), the well-known human transcription factor controlling innate and adaptive immunity, to understand its mechanism of action during COVID-19 in humans. NF-κB was interacted with the SARS-CoV-2 spike protein in an in silico MDS experiment, revealing the NF-κB site at which the SARS-CoV-2 spike protein interacts. We screened some known drugs via docking studies on NF-κB used as a receptor. The MDS software Schrodinger generated more than 2000 complexes from these compounds and using the SMILES format of these complexes, 243 structures were extracted and 411 conformers were generated. The drug used as a ligand that docked with NF-κB with the best docking score and binding affinity was Sulindac sodium as its trade name. Furthermore, RMSF data of sulindac sodium and NF-κB displayed minimal fluctuations in the protein structures, and the protein-ligand complex had reduced flexibility. Sulindac sodium is hence suggested as a suitable drug candidate for repurposing in clinical trials for SARS-CoV-2 infections. This drug potently blocked the spike protein’s interaction with NF-κB by inducing a conformational change in the latter. Arguably, NF-κB inaction is desired to have normal immunity and can possibly be retained using proposed drug. This work provides a significant lead for drug repurposing to combat SARS-CoV-2 and its various mutant forms and reveals new approach for controlling SARS-CoV-2-induced disease.

scholarly journals Molecular Modeling of Some Benzodiazole Derivatives with EGFR Protein 1M17

2020 ◽  
pp. 84-95
Author(s):  
A. S. Sony ◽  
Xavier Suresh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modeling ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Simulation Study ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Ligand Complex ◽  
Drug Candidates ◽  
The Stability

Aims: To study the anticancer potential of benzodiazole derivatives using molecular modeling studies. Study Design: Molecular Dynamics simulation study. Place and Duration of Study: Sathyabama Institute of Science and Technology (SIST), Chennai, between June 2020 and August 2020. Methodology: We studied the anticancer potential of benzodiazole derivatives using molecular modeling. Docking studies of the ligands with EGFR protein 1M17 was carried out using AutoDock.Molecular Dynamics simulation study was carried out using Playmolecule was used to verify the stability of the protein-ligand complex. Results: Molecular docking studies showed a good binding affinity of the ligands with the protein 1m17. Benzodiazole derivative 4,6-dichloro-2-(trifluoromethyl)-1H-1,3-benzodiazole exhibited the lowest binding energy of (-6.42 kcal/mol) at the active site of EGFR (PDB code:1M17) consistent with its least inhibition coefficient (Ki =32.54 uM). Molecular dynamics simulation showed better stability of the ligand and protein complex. Conclusion: Molecular modeling study of selected benzodiazole derivatives showed a very good binding affinity to EGFR protein 1m17. MD simulation of the best-docked ligand showed that the complex was stable. Our study demonstrated that benzodiazole derivatives can be potential anticancer drug candidates

scholarly journals In Silico Study of Compounds Contained in Hemigraphis alternata Leaves against 5-LOX for Anti-Inflammatory

2021 ◽  
Vol 8 (1) ◽  
pp. 34
Author(s):  
Yeni Yeni ◽  
Rizky Rachmania ◽  
Mochamad D. Yanuar
Keyword(s):  
In Silico ◽  
Healing Process ◽  
Active Components ◽  
Lipoxygenase Inhibitors ◽  
In Silico Study ◽  
Anti Inflammatory ◽  
Self Protection

Inflammation is a self-protection response to begin the healing process. One of the anti-inflammatory targets worth developing is lipoxygenase inhibitors, which have been studied for several diseases, including severe airways disease. The aim of this study was to predict the affinity of 23 compounds that contained in Hemigraphis alternata leaves against 5-lipoxygenase (5-LOX). The compounds of Hemigraphis alternata leaves were screened for its affinity againts 5-LOX using docking software, DOCK 6.9, with zileuton as the comparator. Based on the grid score, most of the 23 of Hemigraphis alternata leaves compounds showed a higher affinity towards 5-LOX compare to zileuton. The highest affinity was shown by n-hexadecanoid acid. The study showed that Hemigraphis alternata leaves contains potential active components that could be developed as 5-LOX-inhibitor.Keywords: In silico, Hemigraphis alternata, lipoxygenase, anti-inflammatory

Molecular Dynamics Simulation and Docking Studies of Selenocyanate Derivatives as Anti-Leishmanial Agents

2016 ◽  
Vol 19 (10) ◽  
Author(s):  
Maryam Iman ◽  
Hamid Bakhtiari Kaboutaraki ◽  
Rahim Jafari ◽  
Seyed Ayoub Hosseini ◽  
Abolghasem Moghimi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Docking Studies ◽  
Dynamics Simulation

scholarly journals Molecular Docking and Molecular Dynamics Simulation Studies of Triterpenes from Vernonia patula with the Cannabinoid Type 1 Receptor

2021 ◽  
Vol 22 (7) ◽  
pp. 3595
Author(s):  
Md Afjalus Afjalus Siraj ◽  
Md. Sajjadur Rahman ◽  
Ghee T. Tan ◽  
Veronique Seidel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Cannabinoid Type 1 Receptor ◽  
Docking Approach

A molecular docking approach was employed to evaluate the binding affinity of six triterpenes, namely epifriedelanol, friedelin, α-amyrin, α-amyrin acetate, β-amyrin acetate, and bauerenyl acetate, towards the cannabinoid type 1 receptor (CB1). Molecular docking studies showed that friedelin, α-amyrin, and epifriedelanol had the strongest binding affinity towards CB1. Molecular dynamics simulation studies revealed that friedelin and α-amyrin engaged in stable non-bonding interactions by binding to a pocket close to the active site on the surface of the CB1 target protein. The studied triterpenes showed a good capacity to penetrate the blood–brain barrier. These results help to provide some evidence to justify, at least in part, the previously reported antinociceptive and sedative properties of Vernonia patula.

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