scholarly journals Molecular Docking in Halogen Bonding

2018 ◽  
Author(s):  
Abel Suárez-Castro ◽  
Mario Valle-Sánchez ◽  
Carlos Jesús Cortés-García ◽  
Luis Chacón-García
Keyword(s):  
Molecular Docking ◽  
Halogen Bonding

scholarly journals The Significance of Halogen Bonding in Ligand–Receptor Interactions: The Lesson Learned from Molecular Dynamic Simulations of the D4 Receptor

Molecules ◽  
2019 ◽  
Vol 25 (1) ◽  
pp. 91 ◽  
Author(s):  
Rafał Kurczab ◽  
Katarzyna Kucwaj-Brysz ◽  
Paweł Śliwa
Keyword(s):  
Molecular Docking ◽  
Hot Spots ◽  
Binding Free Energy ◽  
Halogen Bonding ◽  
Free Energy Calculations ◽  
Dynamic Simulations ◽  
Receptor Complexes ◽  
Molecular Core ◽  
D4 Receptor ◽  
Dynamics Simulations

Recently, a computational approach combining a structure–activity relationship library containing pairs of halogenated ligands and their corresponding unsubstituted ligands (called XSAR) with QM-based molecular docking and binding free energy calculations was developed and used to search for amino acids frequently targeted by halogen bonding, also known as XB hot spots. However, the analysis of ligand–receptor complexes with halogen bonds obtained by molecular docking provides a limited ability to study the role and significance of halogen bonding in biological systems. Thus, a set of molecular dynamics simulations for the dopamine D4 receptor, recently crystallized with the antipsychotic drug nemonapride (5WIU), and the five XSAR sets were performed to verify the identified hot spots for halogen bonding, in other words, primary (V5x40), and secondary (S5x43, S5x461 and H6x55). The simulations confirmed the key role of halogen bonding with V5x40 and H6x55 and supported S5x43 and S5x461. The results showed that steric restrictions and the topology of the molecular core have a crucial impact on the stabilization of the ligand–receptor complex by halogen bonding.

Quadrupole correction for halogen bonding description in virtual screening and molecular docking

2016 ◽  
Vol 471 (1) ◽  
pp. 338-342 ◽  
Author(s):  
O. I. Titov ◽  
D. A. Shulga ◽  
V. A. Palyulin ◽  
N. S. Zefirov
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
Halogen Bonding

The evaluation of QM/MM-driven molecular docking combined with MM/GBSA calculations as a halogen-bond scoring strategy

2017 ◽  
Vol 73 (2) ◽  
pp. 188-194 ◽  
Author(s):  
Rafał Kurczab
Keyword(s):  
Molecular Docking ◽  
Halogen Bond ◽  
Binding Free Energy ◽  
Halogen Bonding ◽  
Free Energy Calculations ◽  
Ligand Docking ◽  
Atomic Charges ◽  
Scoring Functions ◽  
X Ray ◽  
Protein Environment

The combination of quantum mechanics/molecular mechanics-driven (QM/MM) molecular docking with binding free-energy calculations was successfully used to reproduce the X-ray geometries of protein–ligand complexes with halogen bonding. The procedure involves quantum-polarized ligand docking (QPLD) to obtain the QM-derived ligand atomic charges in the protein environment at the B3PW91/cc-pVTZ level and the MM/GBSA (generalized-Born/surface area) algorithm to calculate the binding free energies of resultant complexes. The performance was validated using a set of 106 X-ray complexes and compared with the Glide and AutoDock VinaXB scoring functions in terms of RMSD and the reconstruction of halogen-bond geometry (distance and σ-hole angle). The results revealed that docking and scoring using the QPLD–GBSA procedure outperformed the remaining scoring functions in the majority of instances. Additionally, a comparison of the orientation of the top ranked binding poses calculated using the fixed atomic charges of ligands obtained from force-field parameterization and by QM calculations in the protein environment provides strong evidence that the use of QM-derived charges is significant.

EVALUATION OF IN-SILICO ANTICANCER POTENTIAL OF PYRETHROIDS: A COMPARATIVE MOLECULAR DOCKING STUDY

2015 ◽  
Author(s):  
Manik Ghosh ◽  
Kamal Kant ◽  
Anoop Kumar ◽  
Padma Behera ◽  
Naresh Rangra ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Docking Study ◽  
Molecular Docking Study

Homology Modeling of Mus Musculus CDK5 and Molecular Docking Studies with Flavonoids

2017 ◽  
Vol 9 (6) ◽  
Author(s):  
Sowmya Suri ◽  
Rumana Waseem ◽  
Seshagiri Bandi ◽  
Sania Shaik
Keyword(s):  
Molecular Docking ◽  
3D Model ◽  
Structural Features ◽  
Docking Studies ◽  
Amino Acid Residues ◽  
Cyclin Dependent Kinase ◽  
Ligand Complex ◽  
Ligand Interaction ◽  
Molecular Docking Studies ◽  
Cyclin Dependent Kinase 5

A 3D model of Cyclin-dependent kinase 5 (CDK5) (Accession Number: Q543f6) is generated based on crystal structure of P. falciparum PFPK5-indirubin-5-sulphonate ligand complex (PDB ID: 1V0O) at 2.30 Å resolution was used as template. Protein-ligand interaction studies were performed with flavonoids to explore structural features and binding mechanism of flavonoids as CDK5 (Cyclin-dependent kinase 5) inhibitors. The modelled structure was selected on the basis of least modeler objective function. The model was validated by PROCHECK. The predicted 3D model is reliable with 93.0% of amino acid residues in core region of the Ramachandran plot. Molecular docking studies with flavonoids viz., Diosmetin, Eriodictyol, Fortuneletin, Apigenin, Ayanin, Baicalein, Chrysoeriol and Chrysosplenol-D with modelled protein indicate that Diosmetin is the best inhibitor containing docking score of -8.23 kcal/mol. Cys83, Lys89, Asp84. The compound Diosmetin shows interactions with Cys83, Lys89, and Asp84.

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