scholarly journals Discovery of Potential Anti-Ischemic Stroke Agents Through Inhibiting Sulfonylurea Receptor 1 (SUR1): A Pharmacophore-based Screening, Docking, and Molecular Dynamic Simulation

2021 ◽  
Vol 12 (5) ◽  
pp. 6915-6932
Keyword(s):  
Ischemic Stroke ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Sulfonylurea Receptor ◽  
Brain Membrane ◽  
Simulation Based ◽  
Intact Brain ◽  
Docking Energy

Stroke is the leading cause of disability and death worldwide. Inhibition of sulfonylurea 1 receptor (SUR1) using glibenclamide previously has been studied in CNS ischemic tissues and faster recovery from stroke injury in different animal models of stroke. Unfortunately, glibenclamide cannot enter the brain through an intact brain membrane (BBB) due to its ionization at physiological pH. Therefore, it was hypothesized that compounds with structural properties similar to glibenclamide but with the ability to penetrate through BBB would be superior to glibenclamide in ischemic stroke. Docking energy and interactions of glibenclamide with SUR1 active site were assessed using AutoDock Vina. NCI databases search engines with limitations for penetration to CNS were used to find the best compounds with desired properties. Then two selected compounds were assessed with dynamic molecular studies. Two compounds called CID-415537 and CID-419074 with docking energies of -10.3 kcal/mol and -11 kcal/mol were identified. CID-415537 was selected as the best compound due to its proper interactions with SUR1 amino acids and stability in molecular dynamic simulation. Based on this study, compound CID-415537 would be a good candidate for a SUR1 inhibitor in ischemic stroke. However, further in vivo investigations are required to confirm these findings.

scholarly journals Identification of Deleterious Mutations inMyostatinGene of Rohu Carp (Labeo rohita) Using Modeling and Molecular Dynamic Simulation Approaches

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Kiran Dashrath Rasal ◽  
Vemulawada Chakrapani ◽  
Swagat Kumar Patra ◽  
Shibani D. Mohapatra ◽  
Swapnarani Nayak ◽  
...  
Keyword(s):  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Negative Impact ◽  
Labeo Rohita ◽  
Functional Relationships ◽  
Simulation Techniques ◽  
Significant Negative Impact ◽  
The Impact

The myostatin (MSTN) is a known negative growth regulator of skeletal muscle. The mutated myostatin showed a double-muscular phenotype having a positive significance for the farmed animals. Consequently, adequate information is not available in the teleosts, including farmed rohu carp,Labeo rohita. In the absence of experimental evidence, computational algorithms were utilized in predicting the impact of point mutation of rohu myostatin, especially its structural and functional relationships. The four mutations were generated at different positions (p.D76A, p.Q204P, p.C312Y, and p.D313A) of MSTN protein of rohu. The impacts of each mutant were analyzed using SIFT, I-Mutant 2.0, PANTHER, and PROVEAN, wherein two substitutions (p.D76A and p.Q204P) were predicted as deleterious. The comparative structural analysis of each mutant protein with the native was explored using 3D modeling as well as molecular-dynamic simulation techniques. The simulation showed altered dynamic behaviors concerning RMSD and RMSF, for either p.D76A or p.Q204P substitution, when compared with the native counterpart. Interestingly, incorporated two mutations imposed a significant negative impact on protein structure and stability. The present study provided the first-hand information in identifying possible amino acids, where mutations could be incorporated into MSTN gene of rohu carp including other carps for undertaking furtherin vivostudies.

Molecular Dynamic Simulation of Escape of Hydrogen Atoms from (5, 5) Carbon Nanotubes

2008 ◽  
Vol 24 (2) ◽  
pp. 173-177 ◽  
Author(s):  
C. S. Wang ◽  
J. S. Chen ◽  
Y. C. Wang ◽  
J. Lee ◽  
Y. P. Chyou
Keyword(s):  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Energy Gap ◽  
Hydrogen Atoms ◽  
Carbon Tube ◽  
Hole Area ◽  
Simulation Based ◽  
Mass And Heat Transfer ◽  
Atom Release

ABSTRACTIn this article the mass and heat transfer between fluid molecule and carbon tube is studied via molecular dynamic simulation based on Lennard-Jones Potentia and Bernner-Tersoff Potential model. Some valve holes are formed by removing different numbers of molecules from flank of (5, 5) armchair carbon tube (the hole area = 17.3 ∼ 116.9Å2). The results indicate that only diffusion behavior is not able to describe the phenomena, otherwise the atom release rate and valve hole size are interdependent. Meanwhile the variation of potential energy barrier, work function, energy gap arose from different valve geometrical size are observed. These variations can influence the dynamic behavior such as flow rate and velocity by molecule penetration.

Discovery of Trypanocidal Bioactive Leads by Docking Study, Molecular Dynamic Simulation and In Vivo Screening

2018 ◽  
Vol 3 (8) ◽  
pp. 2386-2389
Author(s):  
Akachukwu Ibezim ◽  
Chukwunonso B. Obi ◽  
Nneoma M. Oforkansi ◽  
Chika J. Mbah ◽  
Ngozi J. Nwodo
Keyword(s):  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Docking Study ◽  
In Vivo Screening

Molecular Dynamic Simulation of Thermal Conductivity of Carbon Nano-Peapods

2013 ◽  
Author(s):  
Liu Cui ◽  
Yanhui Feng ◽  
Xinxin Zhang ◽  
Wei Li
Keyword(s):  
Thermal Conductivity ◽  
Carbon Nanotubes ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Translational Motion ◽  
Jones Potential ◽  
Simulation Based ◽  
Increasing Temperature ◽  
Equilibrium Molecular Dynamic Simulation

The thermal conductivity of carbon nano-peapods, carbon nanotube (10,10) filled with fullerene molecules, is investigated by Equilibrium Molecular Dynamic Simulation based on Green-Kubo’s equation. Carbon nano-peapods structures are built by HyperChem. C-C bonding interactions are determined by the AIREBO potential, and the Lennard-Jones potential is used for expressing nonbonding interactions. The results show that filled fullerenes lead to the increment of thermal conductivity, relative to the bare carbon nanotubes. The thermal conductivity of carbon nano-peapods always increases with the rising filling ratio only if the filling ration is less than 100%. Once the nanotube is fully filled with fullerene molecules, a sudden drop in the thermal conductivity appears due to the restriction of molecules’ axially translational motion. Thermal conductivity of carbon nano-peapods reduces first and then increases with the increasing temperature. In addition, the thermal conductivity increases sharply with the increasing length. The length of thermal conductivity convergence for carbon nano-peapods seems much shorter than for bare carbon nanotubes.

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