Molecular docking and molecular dynamics simulation studies on the adsorption/desorption behavior of bone morphogenetic protein-7 on the β-tricalcium phosphate surface

2020 ◽  
Vol 22 (29) ◽  
pp. 16747-16759
Author(s):  
Xiaoyu Zhao ◽  
Zhiyu Xue ◽  
Kefeng Wang ◽  
Xin Wang ◽  
Dingguo Xu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Dynamic Behavior ◽  
Tricalcium Phosphate ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Bone Morphogenetic Protein 7 ◽  
Morphogenetic Protein ◽  
Adsorption Desorption

Combining Rosetta Docking, MD, and SMD, we investigated the adsorption/desorption dynamic behavior of BMP-7 on β-TCP (001) Ca-rich and P-rich surfaces.

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.

scholarly journals Simulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Suchitra Maheswari Ajjarapu ◽  
Apoorv Tiwari ◽  
Gohar Taj ◽  
Dev Bukhsh Singh ◽  
Sakshi Singh ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Protein Kinase ◽  
Point Mutation ◽  
Protein Kinase B ◽  
3D Qsar ◽  
Dynamics Simulation ◽  
Simulation Studies

Abstract Background Ovarian cancer is the world’s dreaded disease and its prevalence is expanding globally. The study of integrated molecular networks is crucial for the basic mechanism of cancer cells and their progression. During the present investigation, we have examined different flavonoids that target protein kinases B (AKT1) protein which exerts their anticancer efficiency intriguing the role in cross-talk cell signalling, by metabolic processes through in-silico approaches. Method Molecular dynamics simulation (MDS) was performed to analyze and evaluate the stability of the complexes under physiological conditions and the results were congruent with molecular docking. This investigation revealed the effect of a point mutation (W80R), considered based on their frequency of occurrence, with AKT1 protein. Results The ligand with high docking scores and favourable behaviour on dynamic simulations are proposed as potential W80R inhibitors. A virtual screening analysis was performed with 12,000 flavonoids satisfying Lipinski’s rule of five according to which drug-likeness is predicted based on its pharmacological and biological properties to be active and taken orally. The pharmacokinetic ADME (adsorption, digestion, metabolism, and excretion) studies featured drug-likeness. Subsequently, a statistically significant 3D-QSAR model of high correlation coefficient (R2) with 0.822 and cross-validation coefficient (Q2) with 0.6132 at 4 component PLS (partial least square) were used to verify the accuracy of the models. Taxifolin holds good interactions with the binding domain of W80R, highest Glide score of − 9.63 kcal/mol with OH of GLU234 and H bond ASP274 and LEU156 amino acid residues and one pi-cation interaction and one hydrophobic bond with LYS276. Conclusion Natural compounds have always been a richest source of active compounds with a wide variety of structures, therefore, these compounds showed a special inspiration for medical chemists. The present study has aimed molecular docking and molecular dynamics simulation studies on taxifolin targeting W80R mutant protein of protein kinase B/serine- threonine kinase/AKT1 (EC:2.7.11.1) protein of ovarian cancer for designing therapeutic intervention. The expected result supported the molecular cause in a mutant form which resulted in a gain of ovarian cancer. Here we discussed validations computationally and yet experimental evaluation or in vivo studies are endorsed for further study. Several of these compounds should become the next marvels for early detection of ovarian cancer.

scholarly journals Novel huperzine A based NMDA antagonists: insights from molecular docking, ADME/T and molecular dynamics simulation studies

RSC Advances ◽  
2020 ◽  
Vol 10 (43) ◽  
pp. 25446-25455
Author(s):  
Dilep Kumar Sigalapalli ◽  
Raghu Rangaswamy ◽  
Neelima D. Tangellamudi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Huperzine A ◽  
Dynamics Simulation ◽  
Structural Behavior ◽  
Nmda Receptor Antagonists ◽  
Binding Affinities ◽  
Nmda Antagonists ◽  
Simulation Studies

The in silico study explores the structural behavior and binding affinities of 40 novel analogues of huperzine A. Novel NMDA receptor antagonists have been virtually identified by molecular docking, ADME/T and molecular dynamics simulation studies.

Molecular docking and molecular dynamics simulation studies of GPR40 receptor–agonist interactions

2010 ◽  
Vol 28 (8) ◽  
pp. 766-774 ◽  
Author(s):  
Shao-Yong Lu ◽  
Yong-Jun Jiang ◽  
Jing Lv ◽  
Tian-Xing Wu ◽  
Qing-Sen Yu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Receptor Agonist ◽  
Dynamics Simulation ◽  
Simulation Studies

scholarly journals Identification of Potent Inhibitors against Aurora Kinase A Using Molecular Docking and Molecular Dynamics Simulation Studies

2019 ◽  
Author(s):  
Sathishkumar Chinnasamy ◽  
Gurudeeban Selvaraj ◽  
Aman Chandra Kaushik ◽  
Satyavani Kaliamurthi ◽  
Asma Sindhoo Nangraj ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Aurora Kinase ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Aurora Kinase A ◽  
High Binding Affinity ◽  
Kinase A

Aurora kinase A (AURKA) is a normal cell proliferation-inducing enzyme encoded by AURKA gene, with over-expression observed in different types of malignancies. Hence, the goal is to find potential inhibitors against AURKA. In this study, molecular docking, Standard Precision and Extra Precision methods were employed. After the docking study, the ligands showed an extremely low binding score which suggested very high binding affinity of the ligands. Furthermore, Quantum polarized ligand docking (QPLD) was performed to predict the binding status of the molecules. Based on the binding affinity, the top four compounds were chosen for further analysis. The docked complexes were further analyzed in explicit water conditions using 100 ns molecular dynamics simulations and binding free energy calculation. Then, density functional theory (DFT) calculation was used to calculate the molecular properties of the molecules. Finally, systems biology experiments validated the molecular docking and molecular dynamics simulation studies and indicated that quercetin, kaempferol, luteolin and rutin could inhibit the AURKA. The results show that, these four molecules have high binding affinity to the AURKA and significant interactions (LEU139, GLU211and ALA213) were also identified with the hinge region of Aurora kinase A. Thus, LEU139, GLU211, and ALA213 were identified as the crucial protein mechanisms.

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