DFT-based QSAR Models to Predict the Antimycobacterial Activity of Chalcones

QSAR model and mechanism research on color removal efficiency of dying wastewater by FeCl3 coagulation

Coagulation is the most widely used method in the treatment of printing and dying wastewater. To better understand the relationship between the coagulation effect and dye molecular structures, quantitative structure activity relationship (QSAR) analyses were performed to elucidate the factors affecting the coagulation in ferric chloride (FeCl₃) coagulation process. First, the coagulation experiments on 38 dye molecules were conducted to determine their color removal rates (R_exp) by FeCl₃ under different pH conditions (i.e., pH = 4 and 10). The results showed that the average R_exp of dyes were 41.36% ± 2.40% at pH value of 4 and 55.70% ± 2.83% at pH value of 10. Subsequently, a multiple linear regression (MLR) method was used to construct QSAR models based on R_exp and 42 molecular parameters calculated by Gaussian 09, Materials Studio 7.0 and Multiwfn. The developed QSAR models exhibited excellent stability, reliability, and robustness with values of R² = 0.7950, 0.8170, Q²_INT = 0.6401, 0.7382, Q²_EXT = 0.5168, 0.5441, at pH values of 4 and 10, respectively. Through analysis of quantum parameter values, electrostatic adsorption and hydrogen bonding adsorption were primarily responsible for the coagulation process. Therefore, this study could be useful in providing critical information for evaluating the removal efficiency and a feasible way to predict the removal rate of dyes by FeCl₃ when no coagulation experiments were conducted.

DFT-based reactivity and QSPR studies of platinum (IV) anticancer drugs

In the present work the influence of different axial ligands on reactivity of some selected Pt(IV) complexes with anticancer activities are investigated in both gas and solvent phases using Density Functional Theory (DFT) calculations. Calculated geometries of the complexes are in good agreement with their available X-ray data. The reactivity descriptors such as hardness, chemical potential and electrophilicity are calculated to measure stability and reactive nature of the complexes. It has been interesting to observe that the increase in the number of carbon chain of carboxylato axial ligand has no influence on reactivity of Pt(IV) complexes. Multiple linear regression analyses are performed to build Quantitative Structure Property Relationship (QSPR) models using DFT and molecular mechanics (MM+) based descriptors in gas and solvent phases. Chemical potential is found to be the most significant single descriptor to measure reduction potential of Pt(IV) complexes giving 87% correlation with experimental data. While gas phase derived descriptors are not statistically significant, inclusion of solvent medium increases the correlation of each descriptor with reduction potential and hydrophobicity of the complexes.

Molecular docking, spectroscopic studies on 4-[2-(Dipropylamino) ethyl]-1,3-dihydro-2H-indol-2-one and QSAR study of a group of dopamine agonists by density functional method

Density functional theory is one of the most popular accepted computational quantum mechanical techniques used in the analysis of molecular structure and vibrational spectra. Experimental and theoretical investigations of the molecular structure, electronic and vibrational characteristics of 4-[2-(Dipropylamino) ethyl]-1,3-dihydro-2H-indol-2-one are presented in this work. The title compound was characterized using FT-IR, FT-Raman and UV-Vis spectroscopic techniques. The results were compared with the theoretical calculations obtained using DFT/B3LYP with 6-311++G(d,p) as basis sets and was found to be in good agreement. The complete optimization of the molecular geometry of the title compound was carried out. Further, the vibrational assignments and calculation of potential energy distribution (PED) were reported. NLO has emerged as a key factor in recent researches. Materials showing nonlinear optical properties form the basis of nonlinear optics and development of such materials plays an important role in the present scenario. The current work provides sufficient justification for the title compound to be selected as a good non-linear optical (NLO) candidate. The electronic properties were reported using TD-DFT approach. The HOMO (EHOMO = -5.96 eV), LUMO (ELUMO = -0.80 eV) energies, energy gap and electrophilicity (2.22) was calculated in order to understand the stability, reactivity and bioactivity of the compound under investigation. To comprehend the bonding interactions we have performed the total (TDOS), partial (PDOS) and overlap population or COOP (Crystal Orbital Overlap Population) density of states. The drug likeness values were analyzed to evaluate the potential of the title compound to be an active pharmaceutical component. As a positive proof the paper further explains the molecular docking studies of the said compound. In addition, the stereochemistry of the protein structure was checked using Ramachandran plot. The title compound is a directly acting dopamine D2 agonist. In order to establish relationship between molecular descriptors of compound and its biological activity, QSAR studies have been done within the framework of DFT for 10 dopamine agonist including the title compound. Hence, the research exploration provides requisite information pertaining to the geometry, stability, reactivity and bioactivity of the compound through spectroscopic and quantum chemical methods.

DFT-based reactivity and combined QSAR, molecular docking of 1,2,4,5-Tetrazine derivatives as inhibitors of Pim-1 kinase

In the present work we have calculated several DFT reactivity descriptors for 1,2,4,5-Tetrazine at the B3LYP/6–311++G(d,p) level of theory in order to analyze its reactivity in vacuum and solvent phases. Whereas, the influence of the solvent was taken into account employing the PCM model. DFT-based descriptors such as (electronic chemical potential, electrophilicity, condensed Fukui function….) have been determined to predict the reactivity of 1,2,4,5-Tetrazine. A series of eighteen 1,2,4,5-Tetrazine derivatives was studied by using two computational techniques, namely, quantitative structure activity relationship (QSAR) and molecular docking. QSAR models of the antitumor activity of some 1,2,4,5-Tetrazine derivatives were established in gas and solvent phases which exhibited good statistical values for both cases. Whereas, multiple linear regression (MLR) procedure was used to obtain the best QSAR models and the leave-one-out (LOO) method to estimate the predictivity of our models. The most and the least active compounds were docked with the protein (3C4E) to confirm those obtained results from QSAR models and elucidate the binding mode between this type of compounds and corresponding protein.

Inhibition effect of natural flavonoids on red tide alga Phaeocystis globosa and its quantitative structure-activity relationship

Red tides that occur off coasts have become a worldwide phenomenon over the past decades. In order to mitigate the damage of the red tides on the aquatic ecosystems, it is crucial to develop a method for predicting algicidal activities that requires less labor and time, and most importantly, this method can quickly screen potential algicides to control red tides. In this study, we have investigated the algicidal activity of 19 natural flavonoids against a typical red tide alga, Phaeocystis globosa. Our results indicate that after 5 days of flavonoid exposure, the half inhibition concentrations (IC₅₀) ranged from 0.068 to 3.065 mg L^-1, which showed the strong algicidal activities of the flavonoids. Furthermore, quantitative structure activity relationship (QSAR) model has been carried out between negative scale logarithm (pIC₅₀) of the flavonoids and the corresponding molecular descriptors. The developed model was validated, both internally and externally, which displayed statistical robustness (R² = 0.867, p = 0.0002, Q²LOO = 0.825, RMSEC = 0.182, Q²_extF3 = 0.896, RMSEP = 0.161, CCC = 0.935). This indicates that the developed model was obtained successfully with satisfactory predictability and robustness for the future rapid screening of natural flavonoids with high inhibition activity on the red tide alga growth. Moreover, the main descriptors in the QSAR model were the molar refractivity, partition coefficient, lowest unoccupied molecular orbital, and highest occupied molecular orbital, illustrating that the molecular electro-chemical characteristics are significant in the algicidal actions of the flavonoids. Graphical abstract Red tides frequently occur worldwide and have become a global environment problem. Flavonoids showed great potential in allelopathic control of the excessive growth of red tide algae. In this study, the algicidal activity of 19 natural flavonoids was investigated on a typical red tide organism Phaeocystis globosa. Futhermore, we applied the quantitative structure-activity relationship (QSAR) model to the experimental data. The model between molecular descriptors of flavonoids and their antialgal activity displays statistical robustness, and 4 of 45 selected molecular descriptors were obtained by regression of training set. The numbers in the figure represent the half inhibition concentration (IC₅₀) of flavonoids. Our results show that the algicidal activity of flavonoids is closely related to molar refraction, partition coefficient, lowest unoccupied molecular orbital, and highest occupied molecular orbital. The QSAR model can efficaciously predict the algicidal activity and provide insights into the inhibitory mechanisms of flavonoids.

Antifeedant effect of polygodial and drimenol derivatives against Spodoptera frugiperda and Epilachna paenulata and quantitative structure-activity analysis

BACKGROUND

The antifeedant activity of 18 sesquiterpenoids of the drimane family (polygodial, drimenol and derivatives) was investigated.

RESULTS

Polygodial, drimanic and nordrimanic derivatives were found to exert antifeedant effects against two insect species, Spodoptera frugiperda and Epilachna paenulata, which are pests of agronomic interest, indicating that they have potential as biopesticide agents. Among the 18 compounds tested, the epoxynordrimane compound (11) and isonordrimenone (4) showed the highest activity [50% effective concentration (EC₅₀ ) = 23.28 and 25.63 nmol cm^-2 , respectively, against S. frugiperda, and 50.50 and 59.00 nmol/cm² , respectively, against E. paenulata].

CONCLUSION

The results suggest that drimanic compounds have potential as new agents against S. frugiperda and E. paenulata. A quantitative structure-activity relationship (QSAR) analysis of the whole series, supported by electronic studies, suggested that drimanic compounds have structural features necessary for increasing antifeedant activity, namely a C-9 carbonyl group and an epoxide at C-8 and C-9. © 2018 Society of Chemical Industry.

Structure-Activity Relationship of Dialkoxychalcones to Combat Fish Pathogen Saprolegnia australis

To investigate the anti-Saprolegnia activities of chalconic compounds, nine dialkoxychalcones 2–10, along with their key building block 2′,4′-dihydroxychalcone 1, were evaluated for their potential oomycide activities against Saprolegnia australis strains. The synthesis afforded a series of O-alkylated derivatives with typical chalcone skeletons. Compounds 4–10 were reported for the first time. Interestingly, analogue 8 with the new scaffold demonstrated remarkable in vitro growth-inhibitory activities against Saprolegnia strains, displaying greater anti-oomycete potency than the standard drugs used in the assay, namely fluconazole and bronopol. In contrast, a dramatic loss of activity was observed for O-alkylated derivatives 2, 3, 6, and 7. These findings have highlighted the therapeutic potential of the natural compound 1 scaffold to be exploitable as a drug lead with specific activity against various Saprolegnia strains.

Synthesis, Spectra, and Theoretical Investigations of 1,3,5-Triazines Compounds as Ultraviolet Rays Absorber Based on Time-Dependent Density Functional Calculations and three-Dimensional Quantitative Structure-Property Relationship

A series of 1,3,5-triazines were synthesized and their UV absorption properties were tested. The computational chemistry methods were used to construct quantitative structure-property relationship (QSPR), which was used to computer aided design of new 1,3,5-triazines ultraviolet rays absorber compounds. The experimental UV absorption data are in good agreement with those predicted data using the Time-dependent density functional theory (TD-DFT) [B3LYP/6-311 + G(d,p)]. A suitable forecasting model (R > 0.8, P < 0.0001) was revealed. Predictive three-dimensional quantitative structure-property relationship (3D-QSPR) model was established using multifit molecular alignment rule of Sybyl program, which conclusion is consistent with the TD-DFT calculation. The exceptional photostability mechanism of such ultraviolet rays absorber compounds was studied and confirmed as principally banked upon their ability to undergo excited-state deactivation via an ultrafast excited-state proton transfer (ESIPT). The intramolecular hydrogen bond (IMHB) of 1,3,5-triazines compounds is the basis for the excited state proton transfer, which was explored by IR spectroscopy, UV spectra, structural and energetic aspects of different conformers and frontier molecular orbitals analysis.

Oxidation of disinfectants with Cl-substituted structure by a Fenton-like system Cu(2+)/H2O2 and analysis on their structure-reactivity relationship

As widely used chemicals intended to protect human being from infection of microorganisms, disinfectants are ubiquitous in the environment. Among them chlorine-substituted phenol is a basic structure in many disinfectant molecules. Removal of these pollutants from wastewater is of great concern. The oxidative degradation of antimicrobial agents such as triclosan, chlorofene, and dichlorofene by a Fenton-like system Cu(2+)/H2O2 was examined. Reaction conditions such as temperature, initial concentrations of H2O2 and Cu(2+), and pH were optimized using triclosan as a representative. The degradation kinetics of the above disinfectants followed pseudo-first-order kinetics under the investigated conditions. Fourteen chlorophenols (CPs) with different chlorine substitution were also studied to evaluate the influence of molecular structure on the degradation process in the Cu(2+)/H2O2 system. Fourteen structure-related parameters were calculated using Gaussian 09 program. A quantitative structure-activity relationship (QSAR) model was established using SPSS software with measured rate constant (k) as dependent variable and calculated molecular descriptors as independent variables. A three-parameter model including energy of HOMO (E homo), molar heat capacity at constant volume (Cv(θ)), and the most positive net charge of hydrogen atoms (qH(+)) was selected for k prediction, with correlation coefficient R(2) = 0.878. Analyses of the model demonstrated that the Cv(θ) was the most significant factor affecting the k of chlorophenols. Variance analysis and standard t-value test were used to validate the model.

Synthesis and quantitative structure-activity relationships study for phenylpropenamide derivatives as inhibitors of hepatitis B virus replication

A series of new phenylpropenamide derivatives containing different substituents was synthesized, characterized and evaluated for their anti-hepatitis B virus (HBV) activities. The quantitative structure-activity relationships (QSAR) of phenylpropenamide compound have been studied. The 2D-QSAR models, based on DFT and multiple linear regression analysis methods, revealed that higher values of total energy (TE) and lower entropy (S(ө)) enhanced the anti-HBV activities of the phenylpropenamide molecules. Predictive 3D-QSAR models were established using SYBYL multifit molecular alignment rule. The optimum models were all statistically significant with cross-validated and conventional coefficients, indicating that they were reliable enough for activity prediction.