Study of a highly accurate and fast protein-ligand docking method based on molecular dynamics

2005 ◽  
Vol 17 (14) ◽  
pp. 1627-1641 ◽  
Author(s):  
M. Taufer ◽  
M. Crowley ◽  
D. J. Price ◽  
A. A. Chien ◽  
C. L. Brooks
Keyword(s):  
Molecular Dynamics ◽  
Ligand Docking ◽  
Docking Method

scholarly journals Interaction Studies Between Cyclic Peptide ADT-C3 (Ac-CADTPC-NH2) with E-Cadherin Protein using the Molecular Docking Method Simulated on 120ns

2018 ◽  
Vol 21 (2) ◽  
pp. 85-91
Author(s):  
Parsaoran Siahaan ◽  
Vivitri Dewi Prasasty ◽  
Atiatul Manna ◽  
Dwi Hudiyanti
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Cyclic Peptide ◽  
Intercellular Junctions ◽  
Peptide Conformation ◽  
Binding Energies ◽  
Drug Molecules ◽  
Docking Method ◽  
The Brain ◽  
Molecular Docking Method

The treatment of diseases that attack the brain is very difficult, because the delivery of drug molecules to the brain is often hindered by the blood-brain barrier (BBB). So that the drug delivery is not right on the target cell. Thus, was developed a method in modulation of intercellular junctions using ADTC3 cadherin peptide, Where the cadherin peptide is derived from the cadherin sequence itself. The method used in this research is molecular dynamics (DM) and molecular docking. In this study have been evaluated some peptide conformation in modulating intercellular junction. The results show that cyclic peptide ADT-C3 (Ac-CADTPC-NH2) was conducted DM for 120 ns (120000 ps), which has considerable activity in modulating intercellular junctions with binding energies of -33.10 kJ.mol-1 and Ki of 1.58 μM at the 79187 ps conformation. The binding site on residues Asp1, Trp2, Ile4, Lys25, Ser26, Asn27, Met92 in the adhesion arm-acceptor pocket region.

Structural insights into the binding mode of d-sorbitol with sorbitol dehydrogenase using QM-polarized ligand docking and molecular dynamics simulations

2016 ◽  
Vol 114 ◽  
pp. 244-256 ◽  
Author(s):  
Chandrabose Selvaraj ◽  
Gopinath Krishnasamy ◽  
Sujit Sadashiv Jagtap ◽  
Sanjay K.S. Patel ◽  
Saurabh Sudha Dhiman ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Mode ◽  
Sorbitol Dehydrogenase ◽  
Ligand Docking ◽  
Dynamics Simulations ◽  
Structural Insights

scholarly journals Molecular Dynamics Simulations for Biological Systems

2017 ◽  
pp. 1044-1071 ◽  
Author(s):  
Prerna Priya ◽  
Minu Kesheri ◽  
Rajeshwar P. Sinha ◽  
Swarna Kanchan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Biological Molecules ◽  
Dynamics Simulation ◽  
Ligand Docking ◽  
Protein Protein Interaction ◽  
Dynamics Simulations

Molecular dynamics simulation is an important tool to capture the dynamicity of biological molecule and the atomistic insights. These insights are helpful to explore biological functions. Molecular dynamics simulation from femto seconds to milli seconds scale give a large ensemble of conformations that can reveal many biological mysteries. The main focus of the chapter is to throw light on theories, requirement of molecular dynamics for biological studies and application of molecular dynamics simulations. Molecular dynamics simulations are widely used to study protein-protein interaction, protein-ligand docking, effects of mutation on interactions, protein folding and flexibility of the biological molecules. This chapter also deals with various methods/algorithms of protein tertiary structure prediction, their strengths and weaknesses.

scholarly journals In Silico Exploration of Efficacious Inhibitors for SARS-CoV-2’s Papain-like Protease

2020 ◽  
Author(s):  
Tien Huynh ◽  
Wendy Cornell ◽  
Binquan Luan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Mechanism ◽  
In Silico ◽  
Rank Order ◽  
Md Simulations ◽  
Flexible Docking ◽  
Docking Method ◽  
Approved Drugs ◽  
Fda Approved Drugs

We applied the flexible docking method to rank-order all FDA-approved drugs as inhibitors for the papain-like protease (PLpro) of SRAS-CoV-2. We also evaluated these results using molecular dynamics (MD) simulations. From MD simulations, we unveiled the molecular mechanism for a known inhibitor rac5c's binding with PLpro. <br>

Molecular Dynamics Simulations for Biological Systems

2016 ◽  
pp. 286-313 ◽  
Author(s):  
Prerna Priya ◽  
Minu Kesheri ◽  
Rajeshwar P. Sinha ◽  
Swarna Kanchan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Biological Molecules ◽  
Dynamics Simulation ◽  
Ligand Docking ◽  
Protein Protein Interaction ◽  
Dynamics Simulations

Molecular dynamics simulation is an important tool to capture the dynamicity of biological molecule and the atomistic insights. These insights are helpful to explore biological functions. Molecular dynamics simulation from femto seconds to milli seconds scale give a large ensemble of conformations that can reveal many biological mysteries. The main focus of the chapter is to throw light on theories, requirement of molecular dynamics for biological studies and application of molecular dynamics simulations. Molecular dynamics simulations are widely used to study protein-protein interaction, protein-ligand docking, effects of mutation on interactions, protein folding and flexibility of the biological molecules. This chapter also deals with various methods/algorithms of protein tertiary structure prediction, their strengths and weaknesses.

INTERACTIONS BETWEEN HUMAN SLINGSHOT PHOSPHATASE 2 AND PHOSPHO-COFILIN: A MOLECULAR DYNAMICS STUDY

2009 ◽  
Vol 08 (02) ◽  
pp. 233-250 ◽  
Author(s):  
JIN-HUI ZHAN ◽  
XI ZHAO ◽  
XU-RI HUANG ◽  
CHIA-CHUNG SUN
Keyword(s):  
Molecular Dynamics ◽  
Molecular Mechanics ◽  
Complex Dynamics ◽  
Protein Tyrosine Phosphatases ◽  
Interaction Model ◽  
Solvation Energy ◽  
Dual Specificity ◽  
Docking Method ◽  
Poisson Boltzmann ◽  
Specificity Protein

Human slingshot phosphatase 2 (SSH2) is one of the dual specificity protein tyrosine phosphatases, which can activate cofilin substrate by binding its phosphorylation state. Because the interaction model of SSH2 and phospho-cofilin (P-cofilin) was unknown, we obtained the complex through macromolecular docking method. The molecular dynamics studies were used to investigate the complex dynamics in an aqueous solution. To understand the binding specificity, the free energy was calculated with the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) approach and the interaction mode in active site was analyzed. The results indicated that the interaction of the P-loop of SSH2 with phosphoserine of human P-cofilin was stabilized by molecular mechanics energy and nonpolar solvation energy components, while polar solvation energy and the entropic contributions were unfavorable for the combination of the two proteins. In addition, the electrostatic contributions were negative for the formation of the complex on the whole, but seen from the active local, the Coulomb interaction between the phosphoserine and the P-loop residues could play an important role in determining substrate specificity.

scholarly journals Design of a New α-1-C-Alkyl-DAB Derivative Acting as a Pharmacological Chaperone for β-Glucocerebrosidase Using Ligand Docking and Molecular Dynamics Simulation

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2683 ◽  
Author(s):  
Izumi Nakagome ◽  
Atsushi Kato ◽  
Noriyuki Yamaotsu ◽  
Tomoki Yoshida ◽  
Shin-ichiro Ozawa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Binding Site ◽  
Binding Affinity ◽  
Gaucher Disease ◽  
Point Mutations ◽  
Dynamics Simulation ◽  
Ligand Docking ◽  
Pharmacological Chaperone ◽  
Pharmacological Chaperones ◽  
Dynamics Simulations

Some point mutations in β-glucocerebrosidase cause either improper folding or instability of this protein, resulting in Gaucher disease. Pharmacological chaperones bind to the mutant enzyme and stabilize this enzyme; thus, pharmacological chaperone therapy was proposed as a potential treatment for Gaucher disease. The binding affinities of α-1-C-alkyl 1,4-dideoxy-1,4-imino-d-arabinitol (DAB) derivatives, which act as pharmacological chaperones for β-glucocerebrosidase, abruptly increased upon elongation of their alkyl chain. In this study, the primary causes of such an increase in binding affinity were analyzed using protein–ligand docking and molecular dynamics simulations. We found that the activity cliff between α-1-C-heptyl-DAB and α-1-C-octyl-DAB was due to the shape and size of the hydrophobic binding site accommodating the alkyl chains, and that the interaction with this hydrophobic site controlled the binding affinity of the ligands well. Furthermore, based on the aromatic/hydrophobic properties of the binding site, a 7-(tetralin-2-yl)-heptyl-DAB compound was designed and synthesized. This compound had significantly enhanced activity. The design strategy in consideration of aromatic interactions in the hydrophobic pocket was useful for generating effective pharmacological chaperones for the treatment of Gaucher disease.

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