A theoretical study on cyclometalated iridium (III) complexes by using a density functional theory

2020 ◽  
Vol 19 (02) ◽  
pp. 2050006
Author(s):  
Sultan Erkan ◽  
Duran Karakaş

Cyclometalated iridium (III) complexes (Ir1–Ir4) are calculated in detail with computational chemistry methods. The calculated structural parameters of Ir3 are compared with experimental values and a good fit is obtained. IR spectra are calculated at B3LYP/LANL2DZ/6-31G(d) level in the gases phase. Calculated 1H-NMR chemical shift values of the mentioned complexes are compared with the experimental data and all chemical shifts are assigned to the respective atoms. The quantum chemical parameters such as absolute hardness ([Formula: see text]), absolute softness ([Formula: see text]) electronegativity ([Formula: see text]), chemical potential ([Formula: see text]) and electronic charges ([Formula: see text]) are calculated and are associated with the experimental anti-cancer properties of the related complexes. Nonlinear optic properties of the Ir1–Ir4 were investigated with the average linear polarizability ([Formula: see text]), the anisotropy of the polarizability ([Formula: see text]), first hyperpolarizability ([Formula: see text]) values. Hole transfer ([Formula: see text]), electron transfer integrals ([Formula: see text]), hole reorganization energies ([Formula: see text]) and electron reorganization energies ([Formula: see text]) are examined. In addition, molecular docking study was performed. It was found that the molecular docking results are similar to the experimental anti-cancer trend.

2021 ◽  
Author(s):  
Heerak Chugh ◽  
Pramod Kumar ◽  
Neeraj Kumar ◽  
Rajesh K. Gaur ◽  
Gagan Dhawan ◽  
...  

Noscapine binds human hemoglobin spontaneously forming a stable complex that affects noscapine's ADMET profile, bioavailability and toxicity.


Author(s):  
Muhammad Torequl Islam ◽  
Pranta Ray ◽  
Abul Bashar Ripon Khalipha ◽  
SM Hafiz Hassan ◽  
Md. Roich Khan ◽  
...  

This study aimed to determine the activity of PYT and its derivatives against COX-2, including 5IKR protein induced inflammation by using the computational tools. PYT and its derivatives have been designed by utilizing density functional theory (DFT) and the performance of the drugs was also evaluated by molecular docking study. Results suggest that the NH2 derivative of PYT (D-NH2) showed binding energy -6.4 (Kcal/mol) with protein 5IKR of COX-2 compared to the main drug (D) that showed binding energy -5.1 (Kcal/mol) with the same protein. HOMO and LUMO energy values were also calculated to determine the chemical reactivity of all the modified drugs. Non-covalent interactions of PYT and its derivatives were essential in improving the performance. In conclusion, D-NH2 showed better preference in inhibiting to the protein 5IKR of COX-2 compared to other modified drugs and it can be claimed that D-NH2 will be the best conformer for COX-2 induced inflammation.


2021 ◽  
pp. 152-160
Author(s):  
Thangavelu Ranjanamala ◽  
Vanmathiselvi Krishanan ◽  
Ramanatha Shreemaya ◽  
Sundarajan Nagarajan Rajeswari ◽  
Casimeer C Sangeetha ◽  
...  

Recent advances demonstrate phytochemicals to be a potent anticancer therapeutic agent as various anti-cancer targets. This study depicts the anti-cancer potential against certain crucial common cancer targets leading to cancer cell proliferation and survival. The main objective of this study is to study the anti-cancer potential of phloretin against certain cancer targets. Ligand analysis was performed and Phloretin was chosen as the experimental ligand and Bcl-2, NF Kappa B, Carbonic anhydrase I (CA-1), Inducible Nitric Oxide Synthase (iNOS), Endothelial Nitric oxide synthase (eNOS), Caspase 3, and Caspase 9 proteins were chosen as targets. Induced fit molecular docking was performed by the use of Glide 6.5 software (Schrodinger - 2015). The docked poses were further evaluated based on binding energy, Conformational changes, and the amino acid residues involved in the protein-ligand interaction. The docking results depicted that phloretin showed notable binding affinity especially with carbonic anhydrase I, ENOS, and INOS. It also showcased significant potential against Caspase 3 and NF Kappa, thereby showing its potential as an effective anti-cancer therapeutics. During this study, the Inhibitory potential of Phloretin was studied as a result of this molecular docking study. This Insilico study revealed the binding efficiency of phloretin against the aforementioned targets. In vitro analysis is required for further validation of this data.


2016 ◽  
Vol 15 (4) ◽  
pp. 1-21 ◽  
Author(s):  
Karthika Mayan ◽  
Sameera Samarakoon ◽  
Kamani Tennekoon ◽  
Asitha Siriwardana ◽  
José Valverde

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5828
Author(s):  
Amalia Stefaniu ◽  
Lucia Pirvu ◽  
Bujor Albu ◽  
Lucia Pintilie

Several derivatives of benzoic acid and semisynthetic alkyl gallates were investigated by an in silico approach to evaluate their potential antiviral activity against SARS-CoV-2 main protease. Molecular docking studies were used to predict their binding affinity and interactions with amino acids residues from the active binding site of SARS-CoV-2 main protease, compared to boceprevir. Deep structural insights and quantum chemical reactivity analysis according to Koopmans’ theorem, as a result of density functional theory (DFT) computations, are reported. Additionally, drug-likeness assessment in terms of Lipinski’s and Weber’s rules for pharmaceutical candidates, is provided. The outcomes of docking and key molecular descriptors and properties were forward analyzed by the statistical approach of principal component analysis (PCA) to identify the degree of their correlation. The obtained results suggest two promising candidates for future drug development to fight against the coronavirus infection.


Molecules ◽  
2021 ◽  
Vol 26 (24) ◽  
pp. 7622
Author(s):  
Youghourta Belhocine ◽  
Seyfeddine Rahali ◽  
Hamza Allal ◽  
Ibtissem Meriem Assaba ◽  
Monira Galal Ghoniem ◽  
...  

The encapsulation mode of dexamethasone (Dex) into the cavity of β-cyclodextrin (β-CD), as well as its potential as an inhibitor of the COVID-19 main protease, were investigated using density functional theory with the recent dispersion corrections D4 and molecular docking calculations. Independent gradient model and natural bond orbital approaches allowed for the characterization of the host–guest interactions in the studied systems. Structural and energetic computation results revealed that hydrogen bonds and van der Waals interactions played significant roles in the stabilization of the formed Dex@β-CD complex. The complexation energy significantly decreased from −179.50 kJ/mol in the gas phase to −74.14 kJ/mol in the aqueous phase. A molecular docking study was performed to investigate the inhibitory activity of dexamethasone against the COVID-19 target protein (PDB ID: 6LU7). The dexamethasone showed potential therapeutic activity as a SARS CoV-2 main protease inhibitor due to its strong binding to the active sites of the protein target, with predicted free energy of binding values of −29.97 and −32.19 kJ/mol as calculated from AutoDock4 and AutoDock Vina, respectively. This study was intended to explore the potential use of the Dex@β-CD complex in drug delivery to enhance dexamethasone dissolution, thus improving its bioavailability and reducing its side effects.


2016 ◽  
Vol 2016 ◽  
pp. 1-12 ◽  
Author(s):  
Md. Abu Saleh ◽  
Md. Solayman ◽  
Mohammad Mazharol Hoque ◽  
Mohammad A. K. Khan ◽  
Mohammed G. Sarwar ◽  
...  

In this study, mitoxantrone and its halogenated derivatives have been designed by density functional theory (DFT) to explore their structural and thermodynamical properties. The performance of these drugs was also evaluated to inhibit DNA topoisomerase type IIα(TOP2A) by molecular docking calculation. Noncovalent interactions play significant role in improving the performance of halogenated drugs. The combined quantum and molecular mechanics calculations revealed that CF3containing drug shows better preference in inhibiting the TOP2A compared to other modified drugs.


2020 ◽  
Vol 17 (3) ◽  
pp. 211-223
Author(s):  
El-sayed M. Abdelrehim ◽  
Doaa S. El-Sayed

Background: 2-amino-3-cyanopyridines are good starting reagents that have been used in synthesis of many heterocyclic compounds such as pyridopyrimidines, [1,2,4]triazolo and [1,2,3,4] tetrazolo derivatives which have biological activities as anti-microbial and cytotoxic activities. Meanwhile [1,2,4]triazolo and [1,2,3,4]tetrazolo derivatives are well known to possess many physiological activities, such as anticancer , antifungal, muscle relaxant, hypnotic, anti-inflammatory, diuretic and antihypertensive activities. A broad class of heterocyclic compounds has been studied to demonstrate their biological activity on the structures of DNA and RNA. Several of important functions make Tankyrases acts as targets in potential drug. Objective: The article focuses on synthesis of [1,2,4]triazolo and [1,2,3,4]tetrazolo derivatives and their theoretical calculations that suggest they are anti-cancer substances. Materials and Methods: DFT and computational studies were performed on the structural properties of experimental molecules experimentally, and significant theoretical calculations were performed based on density functional theory (DFT) with Becke’s three-parameter exchange function21-22 of correlation functional Lee Yang Parr (B3LYP) with the basis set 6-31G (d,p) using Gaussian 03 software23. Geometrical parameters of the optimized structures were calculated and also the charge on each atom (Mulliken charge). Chemcraft program24 was used to visualize the optimized structure and ChemBio3D ultra 12.0 was used to visualize the highest occupied and lowest unoccupied molecular orbitals. Results: Preliminary screening in five studied ligands acts as inhibitors for different active sites along the target. The molecular docking study also revealed that the compound 6c was the most effective compounds in inhibiting Tankyrase I enzyme (2rf5), this result can help strongly in inhibition of carcinogenic cells and cancer treatment. Conclusion: We have described a new practical cyclocondensation synthesis for a series of [1,2,4]triazolo[4,3- c]pyrido[3,2-e] pyrimidine and pyrido[2',3':4,5] pyrimido[6,1-c][1,2,4] triazine from 2-amino-3-cyano-4.6- diarylpyridines. Also polyheterocyclic compounds containing [1,2,4]triazolo and [1,2,3,4]tetrazolo moieties were also synthesized through the reactions of 3-hydrazino-8,10-diaryl [1,2,4]triazolo[4,3-c]pyrido[3,2- e]pyrimidine with both formic acid and the formation of diazonuim salt respectively. Newly synthesized heterocycles structures were confirmed using elemental analysis, IR, 1H-NMR, 13C-NMR and mass spectral data. DFT and computational studies were carried out on five of the synthesized poly heterocyclic compounds to show their structural and geometrical parameters involved in the study. Molecular docking using Tankyrase I enzyme as a target showed how the studied heterocyclic compounds act as a ligand interacting most of active sites on Tankyrase I with a type of interactions specified for H-bonding and VDW. We investigated that the five studied ligands act as inhibitors for different active sites along the target. The molecular docking study also revealed that the compound 6c was the most effective compounds in inhibiting Tankyrase I enzyme (2rf5), this result can help strongly in inhibition of carcinogenic cells and cancer treatment.


Author(s):  
Taibi Ben Hadda ◽  
Vesna Rastija ◽  
Faisal AlMalki ◽  
Abderrahim Titi ◽  
Rachid Touzani ◽  
...  

Background: Studies on the interaction between bioactive molecules and HIV-1 virus has been the focus of recent research in the scope of medicinal chemistry and pharmacology. Objective: Investigating the structural parameters and physic-chemical properties of elucidating and identifying of the antiviral pharmacophore sites. Method: A mixed computational Petra/Osiris/Molinspiration/DFT (POM/DFT) based model has been developed for the identification of physico-chemical parameters governing the bioactivity of 22 3-hydroxy-indolin-2-one derivatives of diacetyl-L-tartaric acid and aromatic amines containing combined antiviral/antitumor/antibacterial pharmacophore sites. Molecular docking study was carried out with HIV-1 integrase (pdb ID: 5KGX) in order to provide information about interactions in the binding site of enzyme. Results: The POM analyses of physic-chemical properties and geometrical parameters of compounds 3a-5j, show that they are bearing a two combined (O,O)-pockets leading to a special platform which able to coordinate two transition metals. The increased activity of series 3a-5j, as compared to standard drugs, contains an (Osp2,O sp3,O sp2)-pharmacophore site. The increase of bioactivity from 4b (R1, R2 = H, H) to 3d (R1, R2 = 4-Br, 2-OCH3) could be attributed to the existence of pi-charge transfer from para-bromo-phenyl to its amid group (COδ---NHδ+). Similar to the indole-based reference ligand (pdb: 7SK), compound 3d forms hydrogen bonding interactions between the residues Glu170, Thr174 and His171 of HIV-1 integrase in catalytic core domain of enzyme. Conclusion: Study confirmed the importance of oxygen atoms, especially from the methoxy group of the phenyl ring, and electrophilic amide nitrogen atom for formation of interactions.


2020 ◽  
Vol 5 (3) ◽  
pp. 197-207
Author(s):  
A. Harikrishnan ◽  
R. Madivanane

In this work, the geometry optimization and harmonic vibrational wavenumbers of kaempferide (5,7-dihydroxy-4-methoxyflavone) were computed by density functional theory (DFT) method. Theoretically computed vibrational wavenumbers were compared with experimental values and the interpretation of the vibrational spectra has been studied. Frontier molecular orbitals (FMO) and molecular electrostatic potential (MEP) analysis of the title compound have been carried out. The 1H & 13C NMR, UV visible and electronic properties of the compound were investigated theoretically and compared with the experimental values. Molecular docking study of the compound against cytochrome P450 family enzymes (CYPs 1A1, 1A2, 3A4, 2C8, 2C9 and 2D6) were also studied and the results revealed that the title compound interact with human CYP2C8 enzymes with minimum binding energy of -9.43 kcal/mol. The compound forms hydrogen bond with the residues of Thr302, Thr305, Leu361, Val362, Cys435, Gln356 and Ala297. Thus, these studies assist to understand the inhibitory mechanism of kaempferide with CYP450 enzymes and may facilitate significant clinical implications in the prevention and treatment of various therapeutic diseases.


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