QSAR, action mechanism and molecular design of flavone and isoflavone derivatives with cytotoxicity against HeLa

Revisiting the Use of Quantum Chemical Calculations in LogPoctanol-water Prediction

The partition coefficients of drug and drug-like molecules between an aqueous and organic phase are an important property for developing new therapeutics. The predictive power of computational methods is used extensively to predict partition coefficients of molecules. The application of quantum chemical calculations is used to develop methods to develop structure-activity relationship models for such prediction, either based on molecular fragment methods, or via direct calculation of solvation free energy in solvent continuum. The applicability, merits, and shortcomings of these developments are revisited here.

Synthesis, anticancer activity, and molecular modeling of 1,4-naphthoquinones that inhibit MKK7 and Cdc25

Cell division cycle 25 (Cdc25) and mitogen-activated protein kinase kinase 7 (MKK7) are enzymes involved in intracellular signaling but can also contribute to tumorigenesis. We synthesized and characterized the biological activity of 1,4-naphthoquinones structurally similar to reported Cdc25 and(or) MKK7 inhibitors with anticancer activity. Compound 7 (3-[(1,4-dioxonaphthalen-2-yl)sulfanyl]propanoic acid) exhibited high binding affinity for MKK7 (K_d = 230 nM), which was greater than the affinity of NSC 95397 (K_d = 1.1 μM). Although plumbagin had a lower binding affinity for MKK7, this compound and sulfur-containing derivatives 4 and 6-8 were potent inhibitors of Cdc25A and Cdc25B. Derivative 22e containing a phenylamino side chain was selective for MKK7 versus MKK4 and Cdc25 A/B, and its isomer 22f was a selective inhibitor of Cdc25 A/B. Docking studies performed on several naphthoquinones highlighted interesting aspects concerning the molecule orientation and hydrogen bonding interactions, which could help to explain the activity of the compounds toward MKK7 and Cdc25B. The most potent naphthoquinone-based inhibitors of MKK7 and/or Cdc25 A/B were also screened for their cytotoxicity against nine cancer cell lines and primary human mononuclear cells, and a correlation was found between Cdc25 A/B inhibitory activity and cytotoxicity of the compounds. Quantum chemical calculations using BP86 and ωB97X-D3 functionals were performed on 20 naphthoquinone derivatives to obtain a set of molecular electronic properties and to correlate these properties with cytotoxic activities. Systematic theoretical DFT calculations with subsequent correlation analysis indicated that energy of the lowest unoccupied molecular orbital E(LUMO), vertical electron affinity (VEA), and reactivity index ω of these molecules were important characteristics related to their cytotoxicity. The reactivity index ω was also a key characteristic related to Cdc25 A/B phosphatase inhibitory activity. Thus, 1,4-naphthoquinones displaying sulfur-containing and phenylamino side chains with additional polar groups could be successfully utilized for further development of efficacious Cdc25 A/B and MKK7 inhibitors with anticancer activity.

The value of pyrans as anticancer scaffolds in medicinal chemistry

Pyran-based heterocycles are promising for anticancer drug discovery.

Synthesis and crystal structure of new temephos analogues as cholinesterase inhibitor: molecular docking, QSAR study, and hydrogen bonding analysis of solid state

A series of temephos (Tem) derivatives were synthesized and characterized by 31P, 13C, and 1H NMR and FT-IR spectral techniques. Also, the crystal structure of compound 9 was investigated. The hydrogen bonding energies (E2) were calculated by NBO analysis of the crystal cluster. The activities and the mixed-type mechanism of Tem derivatives were evaluated using the modified Ellman's and Lineweaver-Burk's methods on cholinesterase (ChE) enzymes. The inhibitory activities of Tem derivatives with a P═S moiety were higher than those with a P═O moiety. Docking analysis disclosed that the hydrogen bonds occurred between the OR (R=CH3 and C2H5) oxygen and N-H nitrogen atoms of the selected compounds and the receptor site (GLN and GLU) of ChEs. PCA-QSAR indicated that the correlation coefficients of the electronic variables were dominant compared to the structural descriptors. MLR-QSAR models clarified that the net charges of nitrogen and phosphorus atoms contribute important electronic function in the inhibition of ChEs. The validity of the QSAR model was confirmed by a LOO cross-validation method with q2=0.965 between the training and testing sets.

Molecular docking and QSAR studies: noncovalent interaction between acephate analogous and the receptor site of human acetylcholinesterase

Twelve new compounds of acephate (Ace) analogues were synthesized and characterized by (31)P, (13)C, and (1)H NMR and IR spectroscopy. The probable insecticide potential of these compounds as well as 23 previously prepared molecules with a general skeleton of RC(O)-NH-P(O)X1X2 was predicted by PASS software. Docking analysis showed that hydrophobic interaction and hydrogen bonding were created between the functional groups of Ace derivatives and the receptor sites of acetylcholinesterase. PCA-QSAR indicated that the electronic descriptors are dominated in comparison with the structural descriptors. The experimental-QSAR (R(2) = 0.903 and VIF < 2.997) and DFT-QSAR (R(2) = 0.990 and VIF ≤ 10) models clarified that the net charge of functional groups contributes an important function in an inhibition mechanism. Validity and integrity of this model were confirmed by the LOO cross-validation method with q(2) = 0.940 and low residuals between the training and testing sets. The correlation matrix of DFT-QSAR model confirmed the molecular docking results.

Synthesis and biological evaluation of new 5-fluorouracil-substituted ampelopsin derivatives

This study reports two novel 5-fluorouracil-substituted ampelopsin derivatives. The structures of two new derivatives were characterized by elemental analysis, ¹H-NMR, ¹³C-NMR, IR and MS. Their anticancer activities in vitro against two cancer cell lines, K562 and K562/ADR, were investigated using the MTT assay, and the results showed that the two new compounds were more effective than reference drugs such as ampelopsin and verapamil.

The combination of TRAIL and isoflavones enhances apoptosis in cancer cells

Isoflavones are a class of bioactive polyphenols with cancer chemopreventive properties. TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) is a naturally occurring antitumor agent that selectively induces programmed death (apoptosis) in cancer cells. Polyphenols can modulate TRAIL-mediated apoptosis in cancer cells. We examined the cytotoxic and apoptotic activities of isoflavones in combination with TRAIL on HeLa cancer cells. The apoptosis was detected by fluorescence microscopy with annexin V-FITC. The cytotoxicity was evaluated by MTT and LDH assays. The tested isoflavones: genistein, biochanin-A and neobavaisoflavone enhance TRAIL-induced apoptosis in HeLa cells. Our study indicated that isoflavones augmented TRAIL-cytotoxicity against cancer cells and confirmed potential role of those polyphenols in chemoprevention.

In vitro investigations for the QSAR mechanism of lymphocytes apoptosis induced by substituted aromatic toxicants

The objective of this study was to assess the chemicals-induced apoptosis effects on fish lymphocytes and to use the QSAR model to interpret the relationships between apoptotic effects and chemical structures to identify the immune toxicology mechanism. By the use of a simple in vitro toxicological assay, the measured apoptotic parameter (EC50) is used in a QSAR to interpret the apoptotic effects of 25 substituted benzenes at low exposure levels. The apoptotic effects of all tested substituted aromatic chemicals with Carassius auratus lymphocytes were confirmed by DNA ladder and nucleus condensation. For both chlorobenzenes and PCBs, the EC50 values increase with increasing Cl number in the molecule, a result reflecting probably the increased p-pi conjugation of the C-Cl bonds that lowers the molecular reactivity. Furthermore, the apoptotic EC50 data were best correlated with the dipole moment (mu) and the energy of the lowest unoccupied molecular orbital (ELUMO) such that: log(1/EC50)=0.325+0.222 micro-0.163(ELUMO) (with R(2)=0.879). The dependence on the electronic ELUMO factor of the established correlation suggests that during the apoptotic process the ROS (reactive oxygen substance) produced by cells acts as a Lewis base in substituted nucleophilic reactions with toxic chemicals behaving as an electron acceptor. On the basis of the test results, the present toxicological assay offers a rapid tool for assessing the toxic effects of chemicals at low exposure levels.