Furanone derivatives as new inhibitors of CDC7 kinase: development of structure activity relationship model using 3D QSAR,molecular docking,and in silico ADMET

Cell division cycle 7 (CDC7) is a serine/threonine kinase, which plays a vital role in the replication initiation of DNA synthesis. Overexpression of the CDC7 in various tumor growths and in cell proliferation makes it a promising target for treatment of cancers. To investigate the binding between the CDC7 and furanone inhibitors, and in order to design highly potent inhibitors, a three-dimensional quantitative structure activity relationship (3D-QSAR) with molecular docking was performed. The optimum CoMSIA model showed significant statistical quality on all validation methods with a determination coefficient (R²?=?0.945), bootstrapping R² mean (BS-R²?=?0.960), and leave-one-out cross-validation (Q²) coefficient of 0.545. The predictability of this model was evaluated by external validation using a test set of nine compounds with a predicted determination coefficient R²_test of 0.96, besides the mean absolute error (MAE) of the test set was 0.258 log units. The extracted contour maps were used to identify the important regions, where the modification was necessary to design a new molecule with improved activity. Furthermore, a good consistency between the molecular docking and contour maps strongly demonstrates that the molecular modeling is reliable. Based on those obtained results, we designed several new potent CDC7 inhibitors, and their inhibitory activities were validated by the molecular models. Additionally, those newly designed inhibitors showed promising results in the preliminary in silico ADMET evaluations.     

Molecular Docking and 3D QSAR Research of Indolocarbazole Series as Cyclin-Dependent Kinase Inhibitors

Fifty indolocarbazole series as cyclin-dependent kinase inhibitors (CDKs) are used to establish a threedimensional quantitative structure-activity relationship (3D QSAR) model based on docking conformations resulting from the Topomer comparative molecular field analysis (Topomer CoMFA). The statistic parameters show that the cross-validation (q²), the multiple correlation coefficient of fitting (r²), and external validation statistic (Q_ext²) are 0.953, 0.968, and 0.954, respectively. It is demonstrated that this Topomer CoMFA model has good stability and prediction ability. The methodology of the fragment-based drug design (FBDD) was also used to virtually screen new CDKs by the Topomer Search technology. Four similar substitutional groups selected from the ZINC database were added to the basic scaffold. As a result, 18 new CDKs with high activities were obtained. The template molecule and new designed compounds are used to study the binding relationship between the ligands and the receptor protein with Surflex-Dock. The docking results suggest good binding interactions of the designed compounds with protein. There are several hydrogen bondings between CDKs with amino acid residues of LYS33, LYS89, ASP86, LEU83, GLU81.     

Investigation of indirubin derivatives: a combination of 3D-QSAR,molecular docking,and ADMET towards the design of new DRAK2 inhibitors

Kinase-related apoptosis-inducing kinase 2 (DRAK2) is a serine/threonine kinase and belongs to the death-associated protein kinase DPAK family, which is responsible for induction of apoptosis in many cell types. Thus, DRAK2 is regarded as a promising target for treatment of autoimmune diseases. To investigate the binding between DRAK2 and indirubin inhibitors and design potent inhibitors, a three-dimensional quantitative structure-activity relationship (3D-QSAR) and molecular docking were performed. Comparative Molecular Similarity Indices Analysis (CoMSIA) was developed using 33 molecules having pIC₅₀ ranging from 8.523 to 5.000 (IC₅₀ in nM). The best CoMSIA model gave a significant coefficient of determination (R²?=?0.93), as well as a (leave-one-out cross-validation coefficient Q² of 0.81. The predictive ability of this model was evaluated by external validation using a test set of eight compounds and yielded a predicted coefficient of determination R²_test of 0.94. The contour maps could provide structural features to improve inhibitory activity. Good consistency between contour maps and molecular docking strongly suggests that the molecular modeling is reliable. Based on these satisfactory results, we designed several new DRAK2 inhibitors and their inhibitory activities were predicted using different models, which are developed on different training and test sets. Additionally, these newly designed inhibitors showed promising results in the preliminary in silico ADMET evaluations compared to the best inhibitor from the studied dataset. This study could be useful in lead identification and optimization for early drug discovery of DRAK2 inhibitors.     

Computational explorations to gain insight into the structural features of TNF-α receptor I inhibitors

TNF-α is a crucial cytokine in the process of inflammatory diseases. The adverse effect of TNF-α is mostly mediated by interaction of TNF-α with TNF-α receptor type I (TNFR1); therefore, discovery of molecules which can bind to TNFR1 preventing TNF-α-receptor complex formation would be of great interest. In the current study, using GRID/GOLPE program, a 3D-QSAR study was conducted on a series of synthetic TNFR1 binders, which resulted in a 3D-QSAR model with appropriate power of predictivity in internal (r²?=?0.94 and q²_LOO?=?0.74) and external (r²?=?0.66 and SDEP?=?0.42) validations. The structural features of TNFR1 inhibitors essential for exerting activity were explored by analyzing the contour maps of the 3D-QSAR model showing that steric interactions and hydrogen bonds are responsible for exerting TNFR1 inhibitory activity. To propose potential chemical entities for TNFR1 inhibition, PubChem database was searched and the selected compounds were virtually tested for anti-TNFR1 activity using the generated model, resulting in two potential anti-TNFR1 compounds. Finally, the possible interactions of the compounds with TNFR1 were investigated using docking studies. The findings in the current work can pave the way for designing more potent anti-TNFR1 inhibitors.     

3D QSAR Studies on Benzyl Phenyl Ether Diamidine Derivatives with Antiprotozoal Activities

Human African trypanosomiasis (HAT) is a neglected tropical disease, and some drugs treating HAT have been used for even more than 60 years. Currently, a series of benzyl phenyl ether diamidine derivatives are discovered, which exhibit high antiprotozoal activities and low cytotoxicity, leading to good development prospects. The comparative molecular field analysis (CoMFA) and the comparative molecular similarity indices analysis (CoMSIA) are used to study the relationship between the structure and antiprotozoal activities. The established 3D QSAR model shows not only significant statistical quality, but also satisfies predictive ability: the best CoMFA model had r² = 0.958 and q² = 0.766, the best CoMSIA model had r² = 0.957 and q² = 0.812, the predictive ability of CoMFA and CoMSIA model were further confirmed by a test set which had 11 compounds, giving the correlation coefficient Q_ext² of 0.792, 0.873, respectively. The contour maps and contribution maps show important features that can improve the antiprotozoal activity: position 3 from substituent R4 should be a low electronegativity group, position 4 from substituent R₄ should have higher electronegativity, substituent R₂ should be selected to a low electronegativity and small bulk group. Together these results may offer some useful theoretical information in designing potential inhibitors.     

Combining ligand-based and structure-based drug design approaches to study the structure-activity relationships of a β-carboline derivative series

In this study, we investigated the structure-activity relationships of a series of β-carboline alkaloid derivatives using the 2D-QSAR and molecular docking, in order to identify the mode of interaction between β-carboline derivatives and the PLK1 kinase, and determine their key substituents responsible for the cytotoxic activity. The obtained QSAR models using multiple linear regression (MLR) and partial least squares (PLS) methods showed a high correlation between the experimental activity and the predicted one by PLS (R²_PLS?=?0.82, q²?=?0.72) and MLR (R²_MLR?=?0.82, q²?=?0.72). An external dataset was used to test the extrapolation power of the models which resulted in an R²_PLS (EV)?=?0.76; RMSE?=?0.39. The 2D-QSAR analysis reveals that lipophilicity plays an important role in the cytotoxic activity of this group of β-carboline derivatives. Indeed, the molecular docking study into the active site of the polo-like kinase (PLK1) revealed that the most active ligand 57 shows higher binding energy and interacts, especially by H-bonds and hydrophobic interactions, with the active site of the PLK1 kinase. Consequently, the results obtained from the 2D-QSAR and docking studies provided a useful tool to design new and potent β-carboline derivatives as cytotoxic agents.     

QSAR study of peptide drugs by 3D-HoVAIF

By applying a three-dimensional holographic vector of the atomic interaction field (3D-HoVAIF) to express the structure of three classical peptide drugs, quantitative structure activity relationship (QSAR) models are built by the multiple linear regression. The accuracy of the proposed model is illustrated using Q _LOO ² (cross-validation) and r ² (test set validation). Moreover, the r _m ² metrics is used to further refine the predictive ability of the developed QSAR models. The results show that 3D-HoVAIF, due to the high predictive ability, offers a useful alternative to the costly and time-consuming experiments determining the bioactivity of peptide drugs.     

Syntheses,Structures, and Magnetic Properties of Two Mn(II) Coordination Polymers Based on 4-Fluorocinnamic Acid and 1,10-Phenanthroline

Two Mn(II) coordination polymers, {[Mn₃ (Pfca)₆(Phen)₂] · 2DMF} _n (I) and [Mn(Pfca)₂(Phen)(H₂O)] _n (II) (HPfca = 4-fluorocinnamic acid, Phen = 1,10-phenanthroline), were synthesized and characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, and singlecrystal X-ray diffraction (CIF files CCDC nos. 967513 (I), 1542972 (II)). Complex I crystallizes in the triclinic crystal system, space group Pī with a = 11.0821(11), b = 12.2632(12), c = 15.0288(15) Å, α = 87.3760(10)°, β = 88.4610(10)°, γ = 81.2220(10)°, V = 2016.0(3) Å3, ρ_c = 1.369 g/cm³, M _r = 1662.25, Z = 1, F(000) = 853, μ = 0.543 mm^–1, the final R = 0.0592 and wR = 0.1681 for 15498 observed reflections with I > 2σ(I). Complex II is of monoclinic system, space group P2₁/c with a = 18.0539(19), b = 8.5806(9), c = 18.758(2) Å, β = 116.5700(10)°, V = 2599.0(5) ų, ρ_c = 1.491 g/cm³, M _r = 583.44, Z = 4, F(000) = 1196, μ = 0.567 mm^–1, the final R = 0.0337 and wR = 0.0853 for 18139 observed reflections with I > 2σ(I). Complex I features linear Mn(II)-trinuclear units, which form 1D chain structure through F···F weak interactions, and complex II is 1D polymeric Mn(II)-chains. Antiferromagnetic coupling interactions exist within Mn(II)- carboxylate trinuclear in I (J =–0.40 cm^–1) and Mn(II)-carboxylate chain in II (J =–0.45 cm^–1).     

Ion-solvent and ion-ion interactions of phosphomolybdic acid in aqueous solution of catechol at 298.15, 308.15, and 318.15 K

Apparent molar volume (V _Ø) and viscosity B-coefficients were measured for phosphomolybdicacid in aqueous solution of catechol from solution density (ρ) and viscosity (η) at 298.15, 308.15, and 318.15 K at various solute concentrations. The experimental density data were evaluated by Masson equation and the derived data were interpreted in terms of ion-solvent and ion-ion interactions. The viscosity data have been analyzed using Jones-Dole equation and the derived parameters, B and A, have been interpreted in terms of ion-solvent and ion-ion interactions respectively. The structure-making or breaking capacity of the solute under investigation has been discussed in terms of sign of (δ ² V _Ø ^o /δT ²) _P . The activation parameters of viscous flow were determined and discussed by application of transition state theory.     

3D QSAR Modeling and Molecular Docking Studies on a Series of Triazole Analogues as Antibacterial Agents

The 3D QSAR analysis using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques is performed on novel nalidixic acid based 1,2,4-triazole derivatives suggested earlier as antibacterial agents. The CoMFA and CoMSIA models employed for a training set of 28 compounds gives reliable values of Q² (0.53 and 0.52, respectively) and R² (0.79 and 0.85, respectively). The contour maps produced by the CoMFA and CoMSIA models are used to determine a three-dimensional quantitative structure-activity relationship. Based on the 3D QSAR contours new molecules with high predicted activities are designed. In addition, surflex-docking is performed to confirm the stability of predicted molecules in the receptor.     

Calculating constants of the rates of the reactions of excitation,ionization, and atomic exchange: A model of a shock oscillator with a change of the Hamiltonian of the system

A new model for calculating the rates of reactions of excitation, ionization, and atomic exchange is proposed. Diatomic molecule AB is an unstructured particle M upon the exchange of elastic-vibrational (VT) energy, i.e., a model of a shock forceful oscillator with a change in Hamiltonian (SFOH). The SFOH model is based on the quantum theory of strong perturbations. The SFOH model allows generalization in simulating the rates of the reactions of excitation, ionization, and atomic exchange in the vibrational-vibrational (VV) energy exchange of diatomic molecules, and the exchange of VV- and VT-energy of polyatomic molecules. The rate constants of the excitation of metastables A ³Σ _u ⁺, B ³Π _g , W ³Δ _u , B′³Σ _u ^-, a′³Σ _u ^-, and the ionization of a nitrogen molecules from ground state X²Σ _g ⁺ upon a collision with a heavy structureless particle (a nitrogen molecule), are found as examples.     

Crystal and molecular structures and luminescence properties of [Eu(Cin)<Subscript>3</Subscript>]<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> complex

The crystal structure of europium cinnamate of the composition [Eu(Cin)₃] _n (Cin is cinnamic acid anion C₉H₇O ₂ ^? ) was determined by X-ray crystallography (a = 22.626(1) Å, c = 7.7330(7) Å, space group R3/c, Z = 3, ρ_calc = 1.448 g/cm³). The coordination polyhedron of Eu atoms is a distorted trigonal prism with three centered square faces. The structure is built of infinite polymeric chains [Eu(Cin)₃] _n running along the c axis and linked by van der Waals and π stacking interactions. Luminescent characteristics of the compound were determined.     

QSAR and 3D-QSAR studies of the diacyl-hydrazine derivatives containing furan rings based on the density functional theory

QSAR studies of 27 diacyl-hydrazine derivatives containing furan rings were conducted and compared with the DFT method and AM1-MOPAC method. q ² values of 0.61 and 0.40 validated the predictability and reliability of eq. (5) from the DFT method were higher than those of eq. (6) from the AM1-MOPAC method. The DFT-optimized conformations and ESP-fitting charges of the target compounds were also used for 3D-QSAR analysis, including CoMFA and CoMSIA. The leave-one-out cross-validation correlation coefficient and the good correlation between the predicted and experimental activities of excluded test compounds revealed that CoMFA and CoMSIA models were robust. The QSAR results were consistent with the 3D-QSAR results, indicating that the electrostatic and hydrophobic properties of the target compounds were significant to the biological activity. These models are useful tools for predicting the larvicidal activities of new compounds and designing new specific insect growth regulators.     

Solution Thermodynamics of <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis><Superscript>/</Superscript>-Ethylenebis-(salicylideneiminato)-diaquochromium(III) Chloride in Aqueous Dimethylsulphoxide

The densities, viscosities and refractive indices of N,N ^/-ethylene-bis(salicylideneiminato)-diaquochromium(III) chloride, [Cr(salen)(H₂O)₂]Cl, in aqueous dimethylsulfoxide (DMSO) with different mass fractions (w ₂ = 0.20, 0.40, 0.60, 0.80 and 1.00) of DMSO were determined at 298.15, 308.15 and 318.15 K under atmospheric pressure. From measured densities, viscosities and refractive indices the apparent molar volumes (V _φ ), standard partial molar volume (V _φ ⁰ ), the slope (S _V ^* ), standard isobaric partial molar expansibility (φ _E ⁰ ) and its temperature dependence (?φ _E ⁰ /?T) _p , the viscosity B-coefficient, its temperature dependence (?B/?T), solvation number (S _n ) and apparent molar refractivity (R _D ^φ ), etc., were calculated and discussed on the basis of ion–ion and ion–solvent interactions. These results revealed that the solutions are characterized by ion–solvent interactions rather than by ion–ion interactions and the complex behaves as a long range structure maker. Thermodynamics of viscous flow was discussed in terms of transition state theory.     

Molecular structure of 2-methoxy-4-pyrrolidinyl-6-trinitromethyl-1,3,5-triazine

An X-ray diffraction study of 2-methoxy-4-pyrrolidinyl-6-trinitromethyl-1,3,5-triazine was carried out. The crystals are triclinic; C₉H₁₁N₇O₇; M = 329.25; a = 8.536(1) Å, b = 9.378(2) Å, c = 9.7401(8) Å; α = 79.13(1)°, β = 73.974(8)°; γ = 72.76(1)°; V = 710.8(2) ų, d _c = 1.54 g/cm³, Z = 2, space group P1ˉ. The molecule on the whole is planar, except the pyrrolidine ring, which has a twist conformation. No significant π-π interactions and hydrogen bonds of C-H⋯N or C-H⋯O type were found in the crystal, and the molecule packing is stabilized only due to van der Waals interactions. Original Russian Text Copyright ? 2008 by V. V. Bakharev, A. A. Gidaspov, I. A. Litvinov, and E. V. Mironova __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 49, No. 1, pp. 187–189, January–February, 2008.     

Synthesis,crystal structure,and kinetics of thermal decomposition of the Zn(II) complex with vanillin

A complex [Zn(C₈H₇O₃)₂(H₂O)₂] (C₈H₈O₃ is vanillin) has been synthesized and characterized by IR, elemental analysis, and X-ray diffraction single-crystal analysis. The crystals are monoclinic, space group C2/c, a = 22.236(8) Å, b = 10.594(2) Å, c = 7.8190(16) Å, α = 89.90(3)°, β = 106.87(4)°, γ = 89.99(3)°, V = 1762.6(8) ų, Z = 4, F(000) = 832, S = 1.079, ρ _c = 1.521g cm^?3, R = 0.0221, R _w = 0.0604, μ = 1.433 mm^?1. The Zn²⁺ ion is six-coordinated with a distorted octahedron geometry. The complex forms a three-dimensional network through intermolecular hydrogen bonds. The thermal decomposition kinetics of the complex for the second stage was studied under non-isothermal conditions by the TG and DTG methods. The kinetic equation can be expressed as dα/dt = Ae^?E/RT 2(1 ? α)[1 ? ln(1 ? α)]^1/2. The kinetic parameters (E, A), activation entropy ΔS ^≠, and activation free-energy ΔG ^≠ were also gained.     

Copper(II) trinuclear complex with trimesic acid salicylidene hydrazone: Synthesis,structure, and magnetic properties

A trinuclear copper(II) complex of trimesic acid salicylidene hydrazone (H₆L) having the composition [Cu₃L · 4Py] · CH₃OH was synthesized and characterized. By X-ray crystallography, the crystals are triclinic: a = 11.7940(4) Å, b = 13.7241(5) Å, c = 15.8993(6) Å, α = 107.4120(10)°, β = 94.2900(10)°, γ = 105.5650(10)°, space group \(P\bar 1\), Z = 2. The number of symmetrically unique reflections having I > 2σ(I) is 7636, R = 0.0465, and R _w = 0.1198. The newly prepared complex contains, in its unit cell, two [Cu₃L · 4Py] molecules which are linked to form a dimer on account of phenoxo bridges (the Cu-O bond length is 2.555 the Cu…Cu distance is 3.348 Separations between them are 9.414, 9.371, and 9.667 of temperature is satisfactorily fitted in terms of a triangular cluster model (?2J = 2.2 cm^?1) with extra intermolecular interactions (zJ′ = 0.4 cm^?1). EPR spectra of solutions at 360–380 K feature a poorly resolved HFS, whose modeling gives a satisfactory result with allowance for the interaction of unpaired electrons with three equivalent copper nuclei (g = 2.098; a _Cu = 25.8 × 10^?4 cm^?1).     

Molecular statistical model of spin crossover equilibrium in the crystal state taking into account the phenomenon of ordering

Formalism is developed in which contributions of binary and ternary interactions towards free energy of a mixture of low-spin (A) and high-spin (B) isomers of spin crossover compounds as well as effects of ordering are taken into account. Parameters characterising non-ideality in this formalism are the excess free energy (ΔF _ex) and absolute asymmetries (Δ ^A , Δ ^B ) of splittings of free energy levels. The excess free energy characterises the effects of binary interactions whereas asymmetries arise from ternary interactions. According to this model, the plateau in the spin crossover transition curve originates from the phenomenon of ordering taken into account in the Gorsky-Bragg-Williams approximation.