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Research paper thumbnail of In Silico Drug Design and Molecular Docking Study of Some Related Structural Isomers of Nocodazole Analogues as Tubulin-Polymerization Inhibitors

NU. International Journal of Science, 2020

The molecular docking simulation and ADMET prediction have been performed to calculate and predic... more The molecular docking simulation and ADMET prediction have been performed to calculate and predict the new available drugs as tubulin-polymerization inhibitors, focusing on the specific groups of 2-substituted benzimidazole based which are some related structural isomers of nocodazole analogues. The ADMET prediction shows that the toxicity for the structural isomers substituted at (2,7) or (2,4) positions (for A i or D i ) are significantly lower than at (2,6) or (2,5) positions (for B i or C i ) for all substituents. The receptor-ligand interaction energies suggest that the representative compounds of A10 & D10 , A8 & D8 , and A4 & D4 , respectively, are the most reactive with significantly low toxicity compared to a true drug. These available drugs provide the lowest-energy conformations within colchicine-binding site that belongs to PDB code: 3E22, rather than PDB code: 5CA1, 1SA0, or 1SA1.

Research paper thumbnail of In silico Study of the Interaction between the Modified B-ring Analogues of Colchicine with Tubulin Heterodimer

Theoretical investigation of the interaction between the modifications at the C-5, C-6, and C-7 p... more Theoretical investigation of the interaction between the modifications at the C-5, C-6, and C-7 positions of the B-ring of colchicine and tubulin heterodimer has been investigated by using the molecular docking simulation. The docking results provide the energetic and structural information in terms of the binding energy, binding affinity, hydrogen bonding, and conformations of docked ligand poses with residues within colchicine binding site. Overall results show that the modified C-5 (in Model A ) and C-7 (in Model C ) of B-ring analogues give the highest binding affinities to tubulin, whereas all lowest-affinity isomers belong to the C-6 substituents (in Model B ). As expected, the docked ligands of the C-5, C-6, and C-7 of B-ring analogues which are located at the a/b intradimer interface of tubulin were shifting toward the a-subunit binding space to form drug-tubulin complexes. Keywords : colchicine, B-ring analogues, tubulin, binding affinity, molecular docking

Research paper thumbnail of Combination of the Metropolis Monte Carlo and Lattice Statics Method for Geometry Optimization of H-(Al)-ZSM-5

Journal of Computational Chemistry

In this article, the combination of the Metropolis Monte Carlo and Lattice Statics (MMC-LS) metho... more In this article, the combination of the Metropolis Monte Carlo and Lattice Statics (MMC-LS) method is applied to perform the geometry optimization of crystalline aluminosilicate zeolite system in the presence of cationic species (H(+)), i.e., H-(Al)-ZSM-5. It has been proved that the MMC-LS method is very useful to allow H(+) ions in (Al)-ZSM-5 extra-framework to approach the global minimum energy sites. The crucial advantage of the combination MMC-LS method is that, in stead of simulating over thousands random configurations via the only LS method, the only one configuration is needed for the MMC-LS simulation to achieve the lowest energy configuration. Therefore, the calculation time can be substantially reduced via the performance of the MMC-LS method with respect to the only LS method. The calculated results obtained from the MMC-LS and the only LS methods have been comparatively represented in terms of the thermodynamic and structural properties.

Research paper thumbnail of In Silico Drug Design and Molecular Docking Study of Some Related Structural Isomers of Nocodazole Analogues as Tubulin-Polymerization Inhibitors

NU. International Journal of Science, 2020

The molecular docking simulation and ADMET prediction have been performed to calculate and predic... more The molecular docking simulation and ADMET prediction have been performed to calculate and predict the new available drugs as tubulin-polymerization inhibitors, focusing on the specific groups of 2-substituted benzimidazole based which are some related structural isomers of nocodazole analogues. The ADMET prediction shows that the toxicity for the structural isomers substituted at (2,7) or (2,4) positions (for A i or D i ) are significantly lower than at (2,6) or (2,5) positions (for B i or C i ) for all substituents. The receptor-ligand interaction energies suggest that the representative compounds of A10 & D10 , A8 & D8 , and A4 & D4 , respectively, are the most reactive with significantly low toxicity compared to a true drug. These available drugs provide the lowest-energy conformations within colchicine-binding site that belongs to PDB code: 3E22, rather than PDB code: 5CA1, 1SA0, or 1SA1.

Research paper thumbnail of In silico Study of the Interaction between the Modified B-ring Analogues of Colchicine with Tubulin Heterodimer

Theoretical investigation of the interaction between the modifications at the C-5, C-6, and C-7 p... more Theoretical investigation of the interaction between the modifications at the C-5, C-6, and C-7 positions of the B-ring of colchicine and tubulin heterodimer has been investigated by using the molecular docking simulation. The docking results provide the energetic and structural information in terms of the binding energy, binding affinity, hydrogen bonding, and conformations of docked ligand poses with residues within colchicine binding site. Overall results show that the modified C-5 (in Model A ) and C-7 (in Model C ) of B-ring analogues give the highest binding affinities to tubulin, whereas all lowest-affinity isomers belong to the C-6 substituents (in Model B ). As expected, the docked ligands of the C-5, C-6, and C-7 of B-ring analogues which are located at the a/b intradimer interface of tubulin were shifting toward the a-subunit binding space to form drug-tubulin complexes. Keywords : colchicine, B-ring analogues, tubulin, binding affinity, molecular docking

Research paper thumbnail of Combination of the Metropolis Monte Carlo and Lattice Statics Method for Geometry Optimization of H-(Al)-ZSM-5

Journal of Computational Chemistry

In this article, the combination of the Metropolis Monte Carlo and Lattice Statics (MMC-LS) metho... more In this article, the combination of the Metropolis Monte Carlo and Lattice Statics (MMC-LS) method is applied to perform the geometry optimization of crystalline aluminosilicate zeolite system in the presence of cationic species (H(+)), i.e., H-(Al)-ZSM-5. It has been proved that the MMC-LS method is very useful to allow H(+) ions in (Al)-ZSM-5 extra-framework to approach the global minimum energy sites. The crucial advantage of the combination MMC-LS method is that, in stead of simulating over thousands random configurations via the only LS method, the only one configuration is needed for the MMC-LS simulation to achieve the lowest energy configuration. Therefore, the calculation time can be substantially reduced via the performance of the MMC-LS method with respect to the only LS method. The calculated results obtained from the MMC-LS and the only LS methods have been comparatively represented in terms of the thermodynamic and structural properties.