scholarly journals Quantum Chemical Calculations and Molecular Docking Studies of Some NSAID Drugs (Aceclofenac, Salicylic Acid, and Piroxicam) as 1PGE Inhibitors

2016 ◽  
Vol 2016 ◽  
pp. 1-7
Author(s):  
S. Suresh ◽  
Sethu Gunasekaran ◽  
Shanmugam Srinivasan
Keyword(s):  
Salicylic Acid ◽  
Molecular Docking ◽  
Docking Studies ◽  
Molecular Structures ◽  
Basis Set ◽  
Compound I ◽  
Atomic Numbering Scheme ◽  
B3lyp Method ◽  
Compound Ii ◽  
Cox 1

The molecular structure of the three compounds Aceclofenac (I), Salicylic Acid (II), and Piroxicam (III) has been determined using Gaussian 03W program with B3LYP method using 6-311++G (d,p) basis set calculations. The molecular structures were fully optimized with atomic numbering scheme adopted in the study. To understand the mode of binding and molecular interaction, the docking studies of compounds Aceclofenac (I), Salicylic Acid (II), and Piroxicam (III) have been carried out with prostaglandin H2 synthase-1 (1PGE) as target using induced fit docking. The molecular docking results show that the interactions and energy for Aceclofenac, Salicylic Acid, and Piroxicam show the best results when docked with prostaglandin H2 synthase-1 (1PGE). The hydrogen bonding interactions of compound I (Aceclofenac) are prominent with Arginine moiety, those of compound II (Salicylic Acid) are prominent with Tyrosine and Serine moieties, and compound III (Piroxicam) shows such interaction with Tyrosine and Arginine moieties. These interactions of prostaglandin H2 synthase-1 (1PGE) with substrates are responsible for governing COX-1 inhibitor potency which in turn is a direct measure of the potency of the drug.

Synthesis, anti-inflammatory, analgesic, COX-1/2 inhibitory activities and molecular docking studies of substituted 2-mercapto-4(3H)-quinazolinones

2016 ◽  
Vol 121 ◽  
pp. 410-421 ◽  
Author(s):  
Alaa A.-M. Abdel-Aziz ◽  
Laila A. Abou-Zeid ◽  
Kamal Eldin H. ElTahir ◽  
Rezk R. Ayyad ◽  
Magda A.-A. El-Sayed ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Studies ◽  
Molecular Docking Studies ◽  
Inhibitory Activities ◽  
Anti Inflammatory ◽  
Cox 1

scholarly journals AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Mario S. Valdés-Tresanco ◽  
Mario E. Valdés-Tresanco ◽  
Pedro A. Valiente ◽  
Ernesto Moreno
Keyword(s):  
Molecular Docking ◽  
Search Space ◽  
Docking Studies ◽  
Molecular Structures ◽  
Autodock Vina ◽  
Ligand Selectivity ◽  
Input Structure ◽  
Graphical Tool ◽  
Selectivity Studies ◽  
User Friendly

Abstract AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock Vina and AutoDock4, including the option of using the Autodock4Zn force field for metalloproteins. AMDock integrates several external programs (Open Babel, PDB2PQR, AutoLigand, ADT scripts) to accurately prepare the input structure files and to optimally define the search space, offering several alternatives and different degrees of user supervision. For visualization of molecular structures, AMDock uses PyMOL, starting it automatically with several predefined visualization schemes to aid in setting up the box defining the search space and to visualize and analyze the docking results. One particularly useful feature implemented in AMDock is the off-target docking procedure that allows to conduct ligand selectivity studies easily. In summary, AMDock’s functional versatility makes it a very useful tool to conduct different docking studies, especially for beginners. The program is available, either for Windows or Linux, at https://github.com/Valdes-Tresanco-MS. Reviewers This article was reviewed by Alexander Krah and Thomas Gaillard.

Synthesis, anti-inflammatory, analgesic and COX-1/2 inhibition activities of anilides based on 5,5-diphenylimidazolidine-2,4-dione scaffold: Molecular docking studies

2016 ◽  
Vol 115 ◽  
pp. 121-131 ◽  
Author(s):  
Alaa A.-M. Abdel-Aziz ◽  
Adel S. El-Azab ◽  
Laila A. Abou-Zeid ◽  
Kamal Eldin H. ElTahir ◽  
Naglaa I. Abdel-Aziz ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Studies ◽  
Molecular Docking Studies ◽  
Anti Inflammatory ◽  
Cox 1

scholarly journals Density Functional Theory Study on Conformers of Benzoylcholine Chloride

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Mustafa Karakaya ◽  
Fatih Ucun ◽  
Ahmet Tokatlı
Keyword(s):  
Density Functional Theory ◽  
Ground State ◽  
Density Functional ◽  
Atomic Orbital ◽  
Nbo Analysis ◽  
Vibrational Frequencies ◽  
Molecular Structures ◽  
Basis Set ◽  
Functional Theory ◽  
B3lyp Method

The optimized molecular structures and vibrational frequencies and also gauge including atomic orbital (GIAO)1H and13C NMR shift values of benzoylcholine chloride [(2-benzoyloxyethyl) trimethyl ammonium chloride] have been calculated using density functional theory (B3LYP) method with 6-31++G(d) basis set. The comparison of the experimental and calculated infrared (IR), Raman, and nuclear magnetic resonance (NMR) spectra has indicated that the experimental spectra are formed from the superposition of the spectra of two lowest energy conformers of the compound. So, it was concluded that the compound simultaneously exists in two optimized conformers in the ground state. Also the natural bond orbital (NBO) analysis has supported the simultaneous exiting of two conformers in the ground state. The calculated optimized geometric parameters (bond lengths and bond angles) and vibrational frequencies for both the lowest energy conformers were seen to be in a well agreement with the corresponding experimental data.

scholarly journals Molecular Modeling of Antimalarial Agents by 3D-QSAR Study and Molecular Docking of Two Hybrids 4-Aminoquinoline-1,3,5-triazine and 4-Aminoquinoline-oxalamide Derivatives with the Receptor Protein in Its Both Wild and Mutant Types

2018 ◽  
Vol 2018 ◽  
pp. 1-15 ◽  
Author(s):  
Hanine Hadni ◽  
Mohamed Mazigh ◽  
El’mbarki Charif ◽  
Asmae Bouayad ◽  
Menana Elhallaoui
Keyword(s):  
Molecular Docking ◽  
3D Qsar ◽  
Qsar Model ◽  
Molecular Structures ◽  
Basis Set ◽  
Receptor Protein ◽  
Quantum Chemical Descriptors ◽  
Qsar Study ◽  
Antimalarial Agents ◽  
Quadruple Mutant

Modeling studies using 3D-QSAR and molecular docking methods were performed on a set of 34 hybrids of 4-aminoquinoline derivatives previously studied as effective antimalarial agents of wild type and quadruple mutant Plasmodium falciparum dihydrofolate reductase (DHFR). So, the famous mathematical method multiple linear regression (MLR) was explored to build the QSAR model. The DFT-B3LYP method with the basis set 6-31G was used to calculate the quantum chemical descriptors, chosen to represent the electronic descriptors of molecular structures. On the contrary, the MM2 method was used to calculate lipophilic, geometrical, physicochemical, and steric descriptors. The QSAR model tested with artificial neural network (ANN) method shows high performance towards its predictability. The predicted model was confirmed by three validation methods: leave-one-out (LOO) cross validation, Y-randomization, and validation external. The molecular docking study of three compounds 9, 11, and 26 on both wild and quadruple mutant types of pf-DHFR-TS as the protein target helps to understand more and then predict the binding modes with the binding sites.

scholarly journals Molecular Docking Studies of Some Novel Fluoroquinolone Derivatives

2019 ◽  
Author(s):  
Lucia Pintilie ◽  
Amalia Stefaniu
Keyword(s):  
Molecular Docking ◽  
Dft Calculation ◽  
Docking Studies ◽  
Target Protein ◽  
Basis Set ◽  
Receptor Interaction ◽  
Stable Conformer ◽  
Interaction Mode ◽  
Fluoroquinolone Derivatives ◽  
Protein Enzyme

An important parameter in the development of a new drug is the drug's affinity to the identified target (protein/enzyme). Predicting the ligand binding to the target (protein/enzyme) by molecular simulation would allow the synthesis to be restricted to the most promising compounds.A restricted hybrid HF-DFT calculation was performed in order to obtain the most stable conformer of each ligand and a series of DFT calculations using the B3LYP levels with 6-31G* basis set has been conducted. The docking studies of the quinolone compounds will be performed with the CLC Drug Discovery Workbench to identify and visualize the ligand-receptor interaction mode.

scholarly journals Steric repulsion and supramolecular assemblies via a two-dimensional plate by C—H...O hydrogen bonds in two closely related 2-(benzofuran-2-yl)-2-oxoethyl benzoates

2017 ◽  
Vol 73 (8) ◽  
pp. 1227-1231
Author(s):  
Li Yee Then ◽  
C. S. Chidan Kumar ◽  
Huey Chong Kwong ◽  
Yip-Foo Win ◽  
Siau Hui Mah ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Molecular Structures ◽  
Steric Repulsion ◽  
Two Dimensional ◽  
Compound I ◽  
Intermolecular Hydrogen Bonds ◽  
Π Interactions ◽  
Phenyl Rings ◽  
Compound Ii

2-(Benzofuran-2-yl)-2-oxoethyl 2-chlorobenzoate, C17H11ClO4 (I), and 2-(benzofuran-2-yl)-2-oxoethyl 2-methoxybenzoate, C18H14O5 (II), were synthesized under mild conditions. Their chemical and molecular structures were analyzed by spectroscopic and single-crystal X-ray diffraction studies, respectively. These compounds possess different ortho-substituted functional groups on their phenyl rings, thus experiencing extra steric repulsion force within their molecules as the substituent changes from 2-chloro (I) to 2-methoxy (II). The crystal packing of compound (I) depends on weak intermolecular hydrogen bonds and π–π interactions. Molecules are related by inversion into centrosymmetric dimers via C—H...O hydrogen bonds, and further strengthened by π–π interactions between furan rings. Conversely, molecules in compound (II) are linked into alternating dimeric chains propagating along the [101] direction, which develop into a two-dimensional plate through extensive intermolecular hydrogen bonds. These plates are further stabilized by π–π and C—H...π interactions.

Quantum Computational, Spectroscopic and Molecular Docking Studies on N-(4-Hydroxyphenyl)picolinamide

2021 ◽  
Vol 6 (3) ◽  
pp. 186-203
Author(s):  
Meenakshi Singh ◽  
Mukesh Kumar ◽  
Neha Singh ◽  
Shikha Sharma ◽  
Neha Agarwal ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Geometry ◽  
Energy Difference ◽  
Docking Studies ◽  
Basis Set ◽  
Fukui Functions ◽  
Homo And Lumo ◽  
Gibb’S Free Energy

In this work, the quantum computations of newly synthesized N-(4-hydroxyphenyl)picolinamide (4-HPP) is focused. Density functional theory (DFT) was used to perform the quantum calculations. The optimized molecular geometry was obtained using the B3LYP and MP2 methods employing 6-311++G(d,p) basis set, which served as the foundation for all subsequent calculations. The experimental data was compared with the calculated vibrational frequencies and NMR spectra. With the use of the molecular electrostatic potential surface (MEP) and the Fukui functions, the charge distribution, reactive regions and electrostatic potential were displayed. The chemical activity of the 4-HPP was evaluated by the energy difference between HOMO and LUMO. For better understanding of the intermolecular charge transfer (ICT), natural bond order analysis (NBO) was used. At various temperatures, thermodynamic parameters such as Gibb’s free energy, enthalpy and entropy were determined. The electrophilicity index was used to portray the molecule’s bioactivity and molecular docking was used to show the interaction between the ligand and the protein. The nature of the molecule was determined by drug similarity when expecting its application for medical purposes.

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