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Numerical Methods for Modeling of Nanosystems
Published in Alexander V. Vakhrushev, Computational Multiscale Modeling of Multiphase Nanosystems, 2017
It should be pointed out that program complexes for multi-level modeling of nanosystems, as applied to different types of tasks, currently can be quite easily completed from standard software packages, both free for use and commercial ones. There are many program complexes, which contain the sets of rather well selected parameters for single-type molecules and combine them into special libraries—force fields. The force fields most frequently used include: Assisted Model Building with Energy Refinement (AMBER), Chemistry at HARvard Macromolecular mechanics (CHARMM), GROningen MOlecular Simulation (GROMOS), Optimized Potential for Liquid Simulation (OPLS), Consistent Valence Force Field (CVFF), and Merck Molecular Force Field (MMFF).16, 28, 64, 101, 132
Theoretical Models for Investigating The Processes of Nanofilm Deposition onto Porous Templates of Aluminum Oxide
Published in Rishat G. Valeev, Alexander V. Vakhrushev, Aleksey Yu. Fedotov, Dmitrii I. Petukhov, A. N. Beltiukov, A. L. Trigub, A. V. Severyukhin, Nanostructured Semiconductors in Porous Alumina Matrices, 2019
Rishat G. Valeev, Alexander V. Vakhrushev, Aleksey Yu. Fedotov, Dmitrii I. Petukhov
The sets of quite properly chosen parameters for similar molecules are combined into special databases and libraries—force fields. When investigating the processes of obtaining nanofilms on porous templates of aluminum oxide with the help of molecular dynamics, the potentials and force fields applied are: embedded-atom method (EAM); Stillinger–Weber potential; modified embedded-atom method (MEAM); Abell–Tersoff potential; and force fields AMBER, CHARMM, GROMOS, OPLS, CVFF, and Merck Molecular Force Field (MMFF).12–16
Metal-free domino amination-Knoevenagel condensation approach to access new coumarins as potent nanomolar inhibitors of VEGFR-2 and EGFR
Published in Green Chemistry Letters and Reviews, 2021
Essam M. Eliwa, Marcel Frese, Ahmed H. Halawa, Maha M. Soltan, Larissa V. Ponomareva, Jon S. Thorson, Khaled A. Shaaban, Mohamed Shaaban, Ahmed M. El-Agrody, Norbert Sewald
Secondly, the two-dimensional (2D) structure of hit compounds were drawn by ChemBioDraw Ultra 14.0 (PerkinElmer Informatics, Waltham, MA, USA) and converted to 3D structure by ChemBio3D Ultra 14.0 then saved as mol format after energy minimized and Molecular Dynamic (MD) performed using MMFF94 (Merck molecular force field) method [66]. Finally, the docking process has been done by uploading the protein pdb and ligand mol files to the iGEMDOCK program and the result has been analyzed with the Discovery Studio Visualizer Client 2020 (BIOVIA, San Diego, CA, USA). The docking study of compounds 4e, 8e, and 9d toward VEGFR-2 and EGFR have been achieved in comparison with known inhibitors including KIM, gefitinib, sorafenib, and erlotinib (Figure 6). The fitness value (Table 5) is the total energy of a predicted pose in the binding site. The empirical scoring function of iGEMDOCK is estimated as [63]: Fitness = vdW + H-bond + Elec; where, the vdW term is pointed out to van der Waal energy. H-bond and Elec terms are denoted hydrogen bonding energy and electro statistic energy, respectively. As illustrated in Figure 8, the docked ligands (KIM and gefitinib) pretend the same binding mode as the crystal one and the Root Mean Square Distance (RMSD) was within the reliable range (≤2 Å), confirming the robustness of this approach.
MOLECULAR DOCKING INVESTIGATION AND PHARMACOKINETIC PROPERTIES PREDICTION OF SOME ANILINOPYRIMIDINES ANALOGUES AS EGFR T790M TYROSINE KINASE INHIBITORS
Published in Egyptian Journal of Basic and Applied Sciences, 2021
Muhammad Tukur Ibrahim, Adamu Uzairu, Gideon Adamu Shallangwa, Sani Uba
The conversion of 2D to 3D structures of the anilinopyrimidines analogues was carried out by direct importation of the structures on to the Spartan 14 software interface. The search for the stable conformation of all the anilinopyrimidines analogues was performed using Merck molecular force field (MMFF) with density functional theory (DFT) at Becke’s three-parameter hybrid function utilizing LYP correlation functional using 6–311 G* basis set [20]. Then, the stable conformations of the anilinopyrimidines analogues were saved in protein data bank file format [21,22]. Figure 1 presents the 3D structure of stable conformation of an anilinopyrimidine analogue.
Theoretical validation of some third-generation epidermal growth factor receptor (EGFR) Inhibitors as non-small cell lung cancer (NSCLC) drugs
Published in Egyptian Journal of Basic and Applied Sciences, 2023
Muhammad Tukur Ibrahim, Adamu Uzairu
The software developed by the University of Cambridge (Chemdraw) was used in drawing the two-dimensional structures of the sourced dataset [15]. In this work, the Merck molecular force field (MMFF) with density functional theory (DFT) at B3LYP/6-311 G* theory level (Becke’s three-parameter hybrid function utilizing LYP correlation functional using 6-311 G* basis set) was used for the optimum conformational search for all the 27 sets of 2,4-diaminopyrimidine derivatives [10,16].