Ld/Mm+ Simulation of Some Aristolochic and Humic Acids Species Coupled in Periodic Box with Water

2020 ◽  
Vol 16 ◽  
Author(s):  
Alina-Maria Petrescu ◽  
Mihai Viorel Putz ◽  
Feng Chen Ifrim ◽  
Gheorghe Ilia ◽  
Virgil Paunescu
Keyword(s):  
Molecular Docking ◽  
Humic Acid ◽  
Molecular Model ◽  
Dynamics Simulation ◽  
Major Objective ◽  
Total Energy Density ◽  
Aristolochic Acids ◽  
Pubchem Database ◽  
Langevin Dynamics Simulation ◽  
Acid Structure

Background: This study is one of the dynamics molecular docking that presents the interactions between a molecular model of the mixture of humic acid structure and 18 aristolochic acids structures, from PubChem database in a water box that simulates the environment reactions. Objective: The major objective was to identify what happens in this procedure(LD/MM+) with the coupled species. Method: LD/MM+ SIMULATION ( Langevin dynamics simulation) Results: The R-Squared statistic indicates that the model as fitted by MLR , explains 90.9437% of the variability in Volume. Conclusion: The interactions of these acids, the types of forces, and the way that these molecules can get closer to each other, in terms of total energy density, while identifying the specificities vis-à-vis of wateraromaticity or water-reactivity behaviors.

Synthesis, Molecular Docking and Dynamics Simulation Studies of New 7-oxycoumarin Derivatives as Potential Antioxidant Agents

2018 ◽  
Vol 18 (18) ◽  
pp. 1572-1587
Author(s):  
Nehad A. Abdel Latif ◽  
Rasha Z. Batran ◽  
Salwa F. Mohamed ◽  
Mohammed A. Khedr ◽  
Mohamed I. Kobeasy ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Antioxidant Agents ◽  
Molecular Docking And Dynamics

Exploring the effect of inhibitor AKB‐9778 on VE‐PTP by molecular docking and molecular dynamics simulation

2019 ◽  
Vol 120 (10) ◽  
pp. 17015-17029 ◽  
Author(s):  
Wen‐Shan Liu ◽  
Rui‐Rui Wang ◽  
Ying‐Zhan Sun ◽  
Wei‐Ya Li ◽  
Hong‐Lian Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation

Effects of active crowder size and activity-crowding coupling on polymer translocation

Soft Matter ◽  
2020 ◽  
Author(s):  
Fei Tan ◽  
Ying Chen ◽  
Nanrong Zhao
Keyword(s):  
Langevin Dynamics ◽  
Dynamics Simulation ◽  
Biological Processes ◽  
Two Dimensional ◽  
Complex Environments ◽  
Polymer Translocation ◽  
Langevin Dynamics Simulation

Polymer translocation in complex environments is crucially important to many biological processes in life. In the present work, we adopted two-dimensional Langevin dynamics simulation to study the forced and unbiased...

scholarly journals Computational Study on Selective PDE9 Inhibitors on PDE9-Mg/Mg, PDE9-Zn/Mg, and PDE9-Zn/Zn Systems

Biomolecules ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 709
Author(s):  
Dakshinamurthy Sivakumar ◽  
Sathish-Kumar Mudedla ◽  
Seonghun Jang ◽  
Hyunjun Kim ◽  
Hyunjin Park ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Erectile Dysfunction ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Cardiovascular Diseases ◽  
Neurodegenerative Disorders ◽  
Computational Study ◽  
Dynamics Simulation ◽  
Interaction Patterns

PDE9 inhibitors have been studied to validate their potential to treat diabetes, neurodegenerative disorders, cardiovascular diseases, and erectile dysfunction. In this report, we have selected highly potent previously reported selective PDE9 inhibitors BAY73-6691R, BAY73-6691S, 28r, 28s, 3r, 3s, PF-0447943, PF-4181366, and 4r to elucidate the differences in their interaction patterns in the presence of different metal systems such as Zn/Mg, Mg/Mg, and Zn/Zn. The initial complexes were generated by molecular docking followed by molecular dynamics simulation for 100 ns in triplicate for each system to understand the interactions’ stability. The results were carefully analyzed, focusing on the ligands’ non-bonded interactions with PDE9 in different metal systems.

scholarly journals Identification of Anti-SARS-CoV-2 Compounds from Food Using QSAR-Based Virtual Screening, Molecular Docking, and Molecular Dynamics Simulation Analysis

2021 ◽  
Vol 14 (4) ◽  
pp. 357
Author(s):  
Magdi E. A. Zaki ◽  
Sami A. Al-Hussain ◽  
Vijay H. Masand ◽  
Siddhartha Akasapu ◽  
Sumit O. Bajaj ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Virtual Screening ◽  
Simulation Analysis ◽  
Qsar Model ◽  
Quantitative Structure Activity Relationship ◽  
Dynamics Simulation ◽  
Multilinear Regression ◽  
Qsar Analysis ◽  
Main Protease

Due to the genetic similarity between SARS-CoV-2 and SARS-CoV, the present work endeavored to derive a balanced Quantitative Structure−Activity Relationship (QSAR) model, molecular docking, and molecular dynamics (MD) simulation studies to identify novel molecules having inhibitory potential against the main protease (Mpro) of SARS-CoV-2. The QSAR analysis developed on multivariate GA–MLR (Genetic Algorithm–Multilinear Regression) model with acceptable statistical performance (R2 = 0.898, Q2loo = 0.859, etc.). QSAR analysis attributed the good correlation with different types of atoms like non-ring Carbons and Nitrogens, amide Nitrogen, sp2-hybridized Carbons, etc. Thus, the QSAR model has a good balance of qualitative and quantitative requirements (balanced QSAR model) and satisfies the Organisation for Economic Co-operation and Development (OECD) guidelines. After that, a QSAR-based virtual screening of 26,467 food compounds and 360 heterocyclic variants of molecule 1 (benzotriazole–indole hybrid molecule) helped to identify promising hits. Furthermore, the molecular docking and molecular dynamics (MD) simulations of Mpro with molecule 1 recognized the structural motifs with significant stability. Molecular docking and QSAR provided consensus and complementary results. The validated analyses are capable of optimizing a drug/lead candidate for better inhibitory activity against the main protease of SARS-CoV-2.

Sign in / Sign up

Export Citation Format

Share Document