scholarly journals Enhanced Plant–microbe Remediation of PCBs in Soil using Enzyme Modification Technique Combined with Molecular Docking and Molecular Dynamics

2021 ◽  
Author(s):  
Minghao Li ◽  
Wei He ◽  
Yu Li
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Environmental Conditions ◽  
Contaminated Soils ◽  
Simulation Method ◽  
Site Directed Mutagenesis ◽  
Dynamics Simulation ◽  
Plant Degradation ◽  
Modification Technique ◽  
Microbial Mineralization

The study on the enhanced mechanisms of the enzymes involved in plant absorption, plant degradation, and microbial mineralization in the remediation of soils contaminated with polychlorinated biphenyls (PCBs) is of great significance for the application of plant-microbe combined remediation technique in PCB-contaminated soils. The present study first used a combination of molecular docking and molecular dynamics methods to calculate the effects of the plant absorption enzyme, plant degradation enzyme, and microbial mineralization enzyme on the PCBs in the soil environment. A multifunctional plant degradation enzyme was constructed with three functional roles of absorption, degradation, and mineralization using amino acid sequence recombination and site-directed mutagenesis to modify the template of plant degradation enzyme. Finally, using the Taguchi experimental design-assisted molecular dynamics simulation method, the suitable external environmental conditions of plant-microbe combined remediation of the PCB­-contaminated soil were determined. In total, six multifunctional plant degradation enzymes were designed, which exhibited a significantly improved efficiency of PCB degradation. In comparison to the complex of plant absorption enzyme, plant degradation enzyme, and microorganism mineralization enzyme (6QIM-3GZX-1B85), the six multifunctional plant degradation enzymes exhibited significantly higher efficiency (2.10–2.38 times) in degrading the PCBs, with a maximum of 2.69 times under suitable external environmental conditions.

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

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.

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