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.     

Molecular structure of ErCl<Subscript>3</Subscript> and YbCl<Subscript>3</Subscript> according to the data of the simultaneous electron diffraction and mass spectrometric experiment

The saturated vapors of ErCl₃ and YbCl₃ were studied in a simultaneous electron diffraction and mass spectrometric experiment at 1165 K and 1170 K, respectively. In the vapors of these compounds, we found up to 3 mol.% dimers along with the monomers. The parameters of the r _g effective configuration of the monomer molecules were determined. For ErCl₃ and YbCl₃, the internuclear distances r _g(Ln-Cl) were 2.436(5) Å and 2.416(5) Å, and the bond angles ∠_g(Cl-Ln-Cl) were 117.0(10)° and 117.2(10)°, respectively. The equilibrium configurations and vibration frequencies of the monomer and dimer molecules were calculated by the HF, B3LYP, and MP2 methods using the combination of the ECP_D energy-consistent quasirelativistic core potential, including 4f electrons [Kr4d ¹⁰4f ⁿ ], and the contracted [5s4p3d] valence basis set for Er and Yb atoms and the MIDIX [4s3p1d] basis set for Cl atoms. The parameters of the effective r _g configuration of the monomer molecules corresponding to the temperature of the experiment were calculated. The difference between the calculated equilibrium r _e(Ln-Cl) and temperature-averaged r _g(Ln-Cl) distances was found to be 0.001–0.002 Å and did not exceed the error of the r _g(Ln-Cl) parameter determined in the electron diffraction experiment. The experimental parameters of the r _g structure were shown to be consistent with the idea about the planar equilibrium geometrical configuration of ErCl₃ and YbCl₃ molecules.     

Structural characterization and prediction of Kovats retention indices (RI) for alkylbenzene compounds

A new molecular structural characterization (MSC) method called the molecular vertex eigenvalue correlative index (MVECI) is constructed and used to describe the structures of 122 alkylbenzene compounds. Through multiple linear regression (MLR) and stepwise multiple regression (SMR), a quantitative structure-retention relationship (QSRR) model with correlation coefficient (R) of 0.995 is obtained. Through partial least-square regression (PLS), another QSRR model with correlation coefficient (R) of 0.991 is obtained. The estimation stability and prediction ability of the two models are strictly analyzed by both internal and external validations. For the internal validation, the cross-validation (CV) correlation coefficients (R _CV) of the two models are 0.993 and 0.988. For the external validation, the correlation coefficients (R _test) of the two models are 0.996 and 0.995, respectively. The results show that the stability and predictability of the models are good, and the molecular vertex eigenvalue correlative index can successfully describe the structures of alkylbenzene compounds.     

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.     

Radial distribution function of a hard-sphere fluid for the nearest neighbor surroundings

An expression for RDF as a function of two variables, the distance r and the packing factor η, was obtained by approximating the results of Monte Carlo simulation of a hard-sphere fluid. The mean square accuracy of the expressions presented is about ±0.0002 (1 ≤ r ≤ 1.5, 0 ≤ η ≤ 0.5). A continuous extension of RDF to the region of r < 1 is proposed, which provides the continuity of the first and second derivatives of RDF at the point r = 1. Analysis of the problem of determining the hard sphere diameter in WCA theory of simple liquids shows that the proposed expression makes it possible to directly calculate the hard sphere diameter without any simplifying approximations.     

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.     

Identification of molecular fingerprints of phenylindole derivatives as cytotoxic agents: a multi-QSAR approach

Phenylindole is reported to be an interesting scaffold having promising cytotoxic activities and can overcome the cancer drug resistance possibly via binding to the colchicine binding site of tubulin. In order to find out the molecular fingerprints for the better cytotoxic activity of phenylindole derivatives, multiple validated chemometric modeling approaches namely hologram QSAR (HQSAR), Bayesian classification model, and pharmacophore mapping analyses were applied into a dataset of 102 phenylindole derivatives. The final HQSAR model shows good statistical significance (Q²?=?0.760; R²_Train?=?0.868; R²_Test?=?0.660), and the best pharmacophore hypothesis has the highest regression coefficient value (r?=?0.975) and the lowest RMS value of 0.679. Moreover, the Bayesian model is also statistically validated and robust to discriminate the cytotoxic and non-cytotoxic phenylindoles. These studies suggest that the amine group should be unsubstituted for retaining higher cytotoxicity. The pharmacophore mapping and Bayesian classification study suggest the importance of 2-phenyl group as a ring aromatic feature conducive to cytotoxicity. The steric and hydrophobic effect of long chain linear alkyl group has a positive influence on cytotoxicity as evidenced by the multi-QSAR study. Therefore, this multi-QSAR modeling reported here is beneficial in designing potential phenylindole cytotoxic agents in future.     

Thermodynamic characteristics of complexation between Ho<Superscript>3+</Superscript> and ethylenediamine-<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>'-disuccinic acid in aqueous solutions at 298.15 K

The thermodynamic characteristics of complexation between ethylenediamine-N,N'-disuccinic acid (H₄Y; EDDA) and Ho³⁺ ion were determined calorimetrically and potentiometrically at 298.15 K and ionic strengths of 0.1, 0.5, 1.0, and 1.5 (KNO₃). The logK, Δ_rG, Δ_rH, and Δ_rS values for the formation of HoY^– and HOHY complexes were calculated at the studied and zero ionic strength values. The changes in thermodynamic parameters of the reactions are discussed.     

Discovery of novel inhibitors for <Emphasis Type="Italic">Leishmania</Emphasis> nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization

Nucleoside diphosphate kinases (NDKs) are ubiquitous enzymes that catalyze the transfer of the γ-phosphate moiety from an NTP donor to an NDP acceptor, crucial for maintaining the cellular level of nucleoside triphosphates (NTPs). The inability of trypanosomatids to synthesize purines de novo and their dependence on the salvage pathway makes NDK an attractive target to develop drugs for the diseases they cause. Here we report the discovery of novel inhibitors for Leishmania NDK based on the structural and functional characterization of purified recombinant NDK from Leishmania amazonensis. Recombinant LaNDK possesses auto-phosphorylation, phosphotransferase and kinase activities with Histidine 117 playing an essential role. LaNDK crystals were grown by hanging drop vapour diffusion method in a solution containing 18% PEG-MME 500, 100 mM Bis-Tris propane pH 6.0 and 50 mM MgCl₂. It belongs to the hexagonal space group P6₃22 with unit cell parameters a?=?b?=?115.18, c?=?62.18 Å and α?=?β?=?90°, γ?=?120°. The structure solved by molecular replacement methods was refined to crystallographic R-factor and R_free values of 22.54 and 26.52%, respectively. Molecular docking and dynamics simulation-based virtual screening identified putative binding compounds. Protein inhibition studies of selected hits identified five inhibitors effective at micromolar concentrations. One of the compounds showed ~45% inhibition of Leishmania promastigotes proliferation. Analysis of inhibitor-NDK complexes reveals the mode of their binding, facilitating design of new compounds for optimization of activities as drugs against leishmaniasis.     

Thermodynamic Parameters of the Complex Formation of Copper(II) Ions with L-Serine and L-Homoserine

Complex formation of copper(II) ions with L-serine and L-homoserine at 298.15 K and ionic strength I 0.5, 1.0, and 1.5 (KNO₃) has been studied by means of potentiometry and calorimetry. Standard thermodynamic parameters (log K⁰, Δ_rG⁰, Δ_rH⁰, Δ_rS⁰) of the studied coordination equilibriums have been calculated.     

The thermodynamic parameters of the step dissociation of L-phenylalanyl in aqueous solution

The heats of interaction of L-phenylalanine with solutions of nitric acid and potassium and lithium hydroxides were determined calorimetrically at 288.15, 298.15, and 308.15 K and solution ionic strengths of 0.5, 0.75, and 1.0 in the presence of LiNO₃ and KNO₃. The standard thermodynamic characteristics (Δ_r H°, Δ_r G°, Δ_r S°, and ΔC _p ^° of acid-base interactions in aqueous solutions of L-phenylalanine were calculated. The influence of the concentration of background electrolytes and temperature on the heats of dissociation of L-phenylalanine was considered. A comparative analysis of the standard thermodynamic characteristics of step dissociation of L-phenylalanine and alanine was performed in terms of the modern concepts of the structure and physicochemical properties of these compounds and their solutions.     

Crystal structures of a family of layered coordination polymers containing divalent metal ions (Mn<Superscript>2+</Superscript>, Co<Superscript>2+</Superscript>, Ni<Superscript>2+</Superscript> and Zn<Superscript>2+</Superscript>) and the 3-amino 4-methyl benzoate ion

The syntheses and crystal structures of the layered coordination polymers M(C₈H₈NO₂)₂ [M = Mn (1), Co (2), Ni (3) and Zn (4)] are described. These isostructural compounds contain centrosymmetric trans-MN₂O₄ octahedra as parts of infinite sheets; the ligand bonds to three adjacent metal ions in μ³-N,O,O′ mode from both its carboxylate O atoms and its amine N atom. In each case, weak intra-sheet N–H?O and C–H?O hydrogen bonds may help to consolidate the structure. Crystal data: 1, C₁₆H₁₆MnN₂O₄, M _r = 355.25, monoclinic, P2₁/c (No. 14), a = 10.6534(2) Å, b = 4.3990(1) Å, c = 15.5733(5) Å, β = 95.1827(10)°, V = 726.85(3) ų, Z = 2, R(F) = 0.026, wR(F ²) = 0.067. 2, C₁₆H₁₆CoN₂O₄, M _r = 359.24, monoclinic, P2₁/c (No. 14), a = 10.6131(10) Å, b = 4.3374(4) Å, c = 15.3556(17) Å, β = 95.473(4)°, V = 703.65(12) ų, Z = 2, R(F) = 0.041, wR(F ²) = 0.091. 3, C₁₆H₁₆N₂NiO₄, M _r = 359.02, monoclinic, P2₁/c (No. 14), a = 10.6374(4) Å, b = 4.2964(2) Å, c = 15.2827(8) Å, β = 95.9744(14)°, V = 694.66(6) ų, Z = 2, R(F) = 0.028, wR(F ²) = 0.070. 4, C₁₆H₁₆N₂O₄Zn, M _r = 365.68, monoclinic, P2₁/c (No. 14), a = 10.6385(5) Å, b = 4.2967(3) Å, c = 15.2844(8) Å, β = 95.941(3)°, V = 694.89(7) ų, Z = 2, R(F) = 0.038, wR(F ²) = 0.107.     

Complex formation of magnesium and calcium ions with trimethylenediamine-<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>’,<Emphasis Type="Italic">N</Emphasis>’-tetraacetic acid

Stability constants and heat effects of the formation reactions of magnesium and calcium trimethylenediaminetetraacetates at 298.15 K and ionic strength of 0.1, 0.5, and 1.0 (mol/L KNO₃) have been determined by means of potentiometry and calorimetry. Standard thermodynamic parameters (log K⁰, Δ_rG⁰, Δ_rH⁰, and Δ_rS⁰) of the studied equilibriums have been determined.     

Mixed-Ligand Complexation of Zinc and Cobalt(II) Complexonates with Amino Acids in an Aqueous Solution

The formation of mixed-ligand complexes in the M(II)–Nta and Ida–L systems (M = Co, Zn; L = His, Orn, Lys, Gly, Im, en), where Ida and Nta are the residues of iminodiacetic and nitrilotriacetic acids, was studied by pH-metry, calorimetry, and NMR spectroscopy. The thermodynamic parameters (logK, Δ _r G⁰, Δ _r H, Δ _r S) of formation for these complexes were determined at 298.15 K and an ionic strength I = 0.5 (KNO3). The most probable pattern of coordination between a complexone and an amino acid in mixed-ligand complexes was revealed.     

Dynamics of the photoinduced desorption of nitric oxide molecules from the surface of pure and modified platinum

The distribution of NO molecules desorbed from a Pt(111) surface due to valence electron excitation over rotational energy levels N(J) is analyzed using a simple impulse-induced model. A linear dependence is found between lnN(J) and (E_r)^1/2, where E_r is the rotational energy of the desorbed molecules. The lifetime of the excited state and the critical time of residence in the excited state estimated using this dependence are found to be close to one another (~10^?15 s). The frequency and amplitude of the tilting vibrations of the adsorbed molecules in the excited state are estimated.     

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.     

Relationship between the hydrogen bridge length and proton position in it

By means of the formula \(e^{ - ((r^{XH} - r_0^{XH} )/b^{XHX} )^{5/3} } + e^{ - ((r^{YH} - r_0^{YH} )/b^{YHY} )^{5/3} } = 1\) that characterizes the correlation between the parameters of XH?Y linear fragments (r ₀ ^XH , r ₀ ^YH are the bond lengths in free molecules, b ^XHX, b ^YHY are the dimensional coefficients) r ^XX(r ^XH) and r ^XY(r ^YH) dependences are obtained. Given the length of a hydrogen bridge formed by O, N, and F atoms, they enable us to find the proton position in the bridge. The definition “a quasi-symmetric hydrogen bond,” based on the invariance of the r ^XX distance when the proton shifts by 0.1 Å, is established to be applicable to OHO, FHF, NHN, and ClHCl fragments. It is shown that the hydrogen bridge length remains almost constant (exceeds the minimum length by no more than 0.1 Å) if its bond orders are above 0.1. Here the displacement of the central proton can reach 0.2–0.3 Å.     

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.