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.     

QSAR models of cytochrome P450 enzyme 1A2 inhibitors using CoMFA,CoMSIA and HQSAR

Quantitative structure–activity relationship (QSAR) studies were conducted on an in-house database of cytochrome P450 enzyme 1A2 inhibitors using the comparative molecular field analysis (CoMFA), comparative molecular similarity analysis (CoMSIA) and hologram QSAR (HQSAR) approaches. The database consisted of 36 active molecules featuring varied core structures. The model based on the naphthalene substructure alignment incorporating 19 molecules yielded the best model with a CoMFA cross validation value q² of 0.667 and a Pearson correlation coefficient r² of 0.976; a CoMSIA q² value of 0.616 and r² value of 0.985; and a HQSAR q² value of 0.652 and r² value of 0.917. A second model incorporating 34 molecules aligned using the benzene substructure yielded an acceptable CoMFA model with q² value of 0.5 and r² value of 0.991. Depending on the core structure of the molecule under consideration, new CYP1A2 inhibitors will be designed based on the results from these models.     

QSAR studies on hepatitis C virus NS5A protein tetracyclic inhibitors in wild type and mutants by CoMFA and CoMSIA

ABSTRACT

Several 3D-QSAR models were built based on 196 hepatitis C virus (HCV) NS5A protein inhibitors. The bioactivity values EC₉₀ for three types of inhibitors, the wild type (GT1a) and two mutants (GT1a Y93H and GT1a L31V), were collected to build three datasets. The programs OMEGA and ROCS were used for generating conformations and aligning molecules of the dataset, respectively. Each dataset was randomly divided into a training set and a test set three times to reduce the contingency of only one random selection. QSAR models were computed by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). For the datasets GT1a, GT1a Y93H, and GT1a L31V, the best models CoMFA-INDX, CoMSIA-SEHA, and CoMSIA-SEHA showed an r² value of 0.682 ± 0.033, 0.779 ± 0.036, and 0.782 ± 0.022 on the test sets, respectively. From the contour maps of the three best models, we summarized the favourable and unfavourable substituents on the tetracyclic core, the Z group, the proline group, and the valine group of inhibitors. We guessed the mutants could change the electrostatic surfaces of the wild type active pocket. In addition, we used ECFP analyses to find important substructures and could intuitively understand the results from QSAR models.     

Three-dimensional Quantitative Structure-Activity Relationship Analyses of a Series of Butenolide ETA Antagonists

Two kinds of Three-dimensional Quantitative Structure-activity Relationship(3D-QSAR) methods,comparative molecular filed analysis(CoMFA) and comparative molecular similarity indices analysis (CoMSIA) ,were applied to analyze the structure-activity relationship of a series of 63 butenolide ETA selective antagonists with respect to their inhibition against human ETA receptor,The CoMFA and CoMSIA models were developed for the conceivable alignment of the molecules based on a template structure from the crystallized data.The statistical results from the initial orientation of the aligned molecules show that the 3D-QSAR model from CoMFA(q^2=0.543) is obviously superior to that from the conventional CoMSIA(q^2=0.407).In order to refine the model,all-space search (ASS) was applied to minimize the field sampling process.By rotating and translating the molecular aggregate within the grid systematically,all the possible samplings of the molecular fields were tested and subsequently the one with the highest q^2 was picked out .The comparison of the sensitivity of CoMFA and CoMSIA to different space orientation shows that the CoMFA q^2 values are more sensitive to the translations and rotations of the aligned molecules with respect to the lattice than those of CoMSIA.The best CoMFA model from ASS was further refined by the region focused technique.The high quality of the best model is indicated by the high corss-validated correlation and the prediction on the external test set.The CoMFA coefficient contour plots identify several key features that explain the wide range of activities,which may help us to design new effective ETA selective antagonists.     

H/D isotope effect on charge‐inverted hydrogen‐bonded systems: Systematic classification of three different types in H3XH…YH3 (X = C,Si, or Ge,and Y = B,Al, or Ga) with multicomponent calculation

Three different H/D isotope effect in nine H₃XH(D)^…YH₃ (X = C, Si, or Ge, and Y = B, Al, or Ga) hydrogen‐bonded (HB) systems are classified using MP2 level of multicomponent molecular orbital method, which can take account of the nuclear quantum nature of proton and deuteron. First, in the case of H₃CH(D)^…YH₃ (Y = B, Al, or Ge) HB systems, the deuterium (D) substitution induces the usual H/D geometrical isotope effect such as the contraction of covalent R(C? H(D)) bonds and the elongation of intermolecular R(H(D)^…Y) and R(C^…Y) distances. Second, in the case of H₃XH(D)^…YH₃ (X = Si or Ge, and Y = Al or Ge) HB systems, where H atom is negatively charged called as charge‐inverted hydrogen‐bonded (CIHB) systems, the D substitution leads to the contraction of intermolecular R(H(D)^…Y) and R(X^…Y) distances. Finally, in the case of H₃XH(D)^…BH₃ (X = Si or Ge) HB systems, these intermolecular R(H(D)^…Y) and R(X^…Y) distances also contract with the D substitution, in which the origin of the contraction is not the same as that in CIHB systems. The H/D isotope effect on interaction energies and spatial distribution of nuclear wavefunctions are also analyzed. © 2015 Wiley Periodicals, Inc.     

具有除草活性的大环内酯类衍生物的定量构效关系

研究了一系列结构新颖的具有除草活性的大环内酯衍生物的定量构效关系(QSAR). 构建的比较分子力场分析(CoMFA)、比较分子近似指数分析(CoMSIA)和全息定量构效关系(HQSAR)分子模型的交叉验证系数r2cv均大于0.5, 非交叉验证系数r2都超过0.8, 表明获取的QSAR模型具有可信的预测能力. 对CoMFA、CoMSIA模型的三维(3D)等势图分析, 发现除了立体场和静电场外, 疏水场和氢键受体场也是影响大环内酯类化合物除草活性的重要因素. 构建的HQSAR模型的原子贡献图提示的结构改造信息与三维QSAR的结果基本一致. 利用CoMFA、CoMSIA模型提供的信息,对目前已合成的活性最高化合物B1-3进行分子结构改造, 预测结果发现部分化合物可能具有更好的除草活性.     

Die Photoelektron-Spektren der Dihalogen-acetylene

The photoelectron-spectra of the six dihaloacetylenes XC?CY with X, Y ? Cl, Br, I have been recorded. The first five bands of these spectra can be assigned (in order of increasing ionization potentials) to the states ²∏_(u)(1), ²∏_(g)(2), ²∏_(u)(3), ²∑_(g)⁺(4), ²∑_(u)⁺(5) where the lower indices g, u are valid only for the centro-symmetric molecules I(X, X). The first three states correspond to π-ionization, the last two to σ-ionization of the axially symmetrical lone pairs. The ²∏-states split under the influence of spin-orbit-coupling into components ²∏_3/2 and ²∏_1/2, the former having the lower energy. The assignment of states and components to the individual bands is confirmed by the size of the split due to spin-orbit-coupling, the vibrational fine structure of the bands and by a simple parametrization of the ZDO. molecular orbital model assumed as a basis for the qualitative discussion.     

The molecular and electronic structure features of silatranes, germatranes, and their carbon analogs

Molecular geometries of fifty-six metallatranes N(CH₂CH₂Y)₃M-X and fifty-six carbon analogs HC(CH₂CH₂Y)₃M-X (M = Si, Ge; X = H, Me, OH, F; Y = CH₂, O, NH, NMe, NSiMe₃, PH, S) were optimized by the DFT method. Correlations between changes in the bond orbital populations, electron density ρ(r), electron density laplacian ∇²ρ(r), |λ₁|/λ₃ ratio, electronic energy density E(r), bond lengths, and displacement of the central atom from the plane of three equatorial substituents and the nature of substituents X and Y were studied. As the number of electronegative substituents at the central atom increases, the M←N, M-X, and M-Y bond lengths decrease, while the M←N bond strength and the electron density at critical points of the M←N, M-X, and M-Y bonds increase. An increase in electronegativity of a substituent (X or Y) is accompanied by a decrease in the ionicities of the other bonds (M-X, M-Y, and M←N) formed by the central atom (Si, Ge). A new molecular orbital diagram for bond formation is proposed, which takes into account the interaction of all five substituents at the central atom (M = Si, Ge) in atrane molecules. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 448–460, March, 2006.     

Quantitative molecular similarity analysis (QMSA) methods for property estimation: A comparison of property-based,arbitrary, and tailored similarity spaces

Three classes of arbitrary quantitative molecular similarity analysis (QMSA) methods have been computed using atom pairs, topological indices, and physicochemical properties. Tailored QMSA models have been developed using a selected number of TIs chosen by ridge regression. The methods have been applied to the K -nearest neighbor based estimation of log P of two sets of chemicals. Results show that the property-based and tailored QMSA methods are superior to the arbitrary similarity methods in estimating log P of both sets of chemicals     

Substituent Effects on Reduction Potentials of Meta-substituted and Para-substituted Benzylideneanilines

Effects of meta-substituent of 3,4'/4,3'/3,3'-substituted benzylideneanilines (XBAYs) on the electrochemical reduction potentials (E_(Red)) were investigated, in which 49 samples of target compounds were synthesized, and their reduction potentials were measured by cyclic voltammetry. The substituent effects on the E_(Red) of target compounds were analyzed and an optimality equation with four parameters (Hammett constant σ of X, Hammett constant σ of Y, excited-state substituent constant σ_CC^ex of X, and the substituent specific cross-interaction effect Δσ_CC^ex2 between X and Y) was obtained. The results show that the factors affecting the E_(Red) of 3,4'/4,3'/3,3'-substituted XBAYs are different from those of 4,4'-substituted XBAYs. For 3,4'/4,3'/3,3'-substituted XBAYs, σ(X) and σ(Y) must be employed, and the contribution of Δσ_CC^ex2 is important and not negligible. Compared with 4,4'-substituted XBAYs, X group contributes less to 3,4'/4,3'/3,3'-substituted XBAYs, while Y group contributes more to them. Additionally, it was observed that either para-substituted XBAYs or meta-substituted XBAYs, the substituent effects of X are larger than those of Y on the E_(Red) of substituted XBAYs.     

Behavior of Halogen Bonds of the Y−X⋅⋅⋅π Type (X,Y=F,Cl, Br,I) in the Benzene π System,Elucidated by Using a Quantum Theory of Atoms in Molecules Dual‐Functional Analysis

The nature of halogen bonds of the Y?X‐?‐π(C₆H₆) type (X, Y=F, Cl, Br, and I) have been elucidated by using the quantum theory of atoms in molecules (QTAIM) dual‐functional analysis (QTAIM‐DFA), which we proposed recently. Asterisks (?) emphasize the presence of bond‐critical points (BCPs) in the interactions in question. Total electron energy densities, H_b( r _c), are plotted versus H_b( r _c)?V_b( r _c)/2 [=(?²/8m)?²ρ_b( r _c)] for the interactions in QTAIM‐DFA, in which V_b( r _c) are potential energy densities at the BCPs. Data for perturbed structures around fully optimized structures were used for the plots, in addition to those of the fully optimized ones. The plots were analyzed by using the polar (R, θ) coordinate for the data of fully optimized structures with (θ_p, κ_p) for those that contained the perturbed structures; θ_p corresponds to the tangent line of the plot and κ_p is the curvature. Whereas (R, θ) corresponds to the static nature, (θ_p, κ_p) represents the dynamic nature of the interactions. All interactions in Y?X‐?‐π(C₆H₆) are classified by pure closed‐shell interactions and characterized to have vdW nature, except for Y?I‐?‐π(C₆H₆) (Y=F, Cl, Br) and F?Br‐?‐π(C₆H₆), which have typical hydrogen‐bond nature without covalency. I?I‐?‐π(C₆H₆) has a borderline nature between the two. Y?F‐?‐π(C₆H₆) (Y=Br, I) were optimized as bent forms, in which Y‐?‐π interactions were detected. The Y‐?‐π interactions in the bent forms are predicted to be substantially weaker than those in the linear F?Y‐?‐π(C₆H₆) forms.     

Mono- and bi-metallic complexes based on redox-active tris(3,5-dimethylpyrazolyl)borato-molybdenum nitrosyls,part III.(1) Complexes containing meta-substituted benzene- and naphthalenediols or -diamines

Summary The complexes [MoL^*(NO)Cl(YC₆H₄YH-m)] (Y = O or NH), [MoL^*(NO)Cl(YC₁₀H₆YH-1,5)], (Y = O or NH), [MoL^*(NO)Cl(OC₁₀H₆OH-2,7)], [{MoL^*(NO)Cl}₂(XC₆H₄Y-m)] (X=Y=O, NH or S; X=O, Y=NH), [{MoL^*(NO)-C1}₂(YC₁₀H₆Y-1,5)] (Y=O or NH) and [{MoL^*(NO)Cl₂-(OC₁₀H₆-2,7)] have been prepared and studied by cyclic voltammetry. The monometallic species undergo a reversible oneelectron reduction, whereas the bimetallics undergo two oneelectron reductions. A comparison of E_1/2 (E_1/2(1)-E_1/2(2)) values for those new species with those obtained frompara- substituted analogues and bimetallics containing extended bridges YC₆H₄ZC₆H₄Y (e.g. Z = S or CH₂CH₂) established that the interaction between the redox centres in these new species is intermediate (YC₆H₄Y-m; NHC₁₀H₆NH-1,5) or weak (OC₁₀H₆O).In earlier papers^1,2 we have described the synthesis and electrochemical properties of a series of mono- and bi-metallic complexes of the type [MoL^*(NO)X(YC₆H₄YH)], [MoL^*(NO)X}₂(YC₆H₄Y)] and [{MoL^*(NO)X}₂(YC₆H₄-ZC₆H₄Y)] [L^*=tris(3,5-dimethylpyrazolyl)borate, HB(Me₂C₃HN₂)₃] where the arene ring ispara-substituted (X=Cl or I while Y=O, S or NH and Z = nothing, CH₂, CH₂CH₂, S, SO₂ or O). We have shown that the E_1/2-values of these species are dependent on X and Y, and that the bimetallic species undergo two one-electron reduction processes.We have established that there is strong interaction between the redox centres in bimetallics bridged byp-YC₆H₄Y, but that weak-to-negligible interaction occurs in those species containing YC₆H₄ZC₆H₄Y bridges. In this paper we describe our investigations ofmete-substituted bridging systems,m-YC₆H₄Y, and comparable systems containing naphthalene bridges,e.g. 1,5- or 2,7-YC₁₀H₂Y. From these studies we hoped to establish the extent of interaction between the two redox centres and how this compared to thepara-substituted arene counterparts.     

3D-QSAR and molecular modeling of HIV-1 integrase inhibitors

Three-dimensional quantitative structure-activity relationship (3D QSAR) methods were applied on a series of inhibitors of HIV-1 integrase with respect to their inhibition of 3-processing and 3-end joining steps in vitro.The training set consisted of 27 compounds belonging to the class of thiazolothiazepines. The predictive ability of each model was evaluated using test set I consisting of four thiazolothiazepines and test set II comprised of seven compounds belonging to an entirely different structural class of coumarins. Maximum Common Substructure (MCS) based method was used to align the molecules and this was compared with other known methods of alignment. Two methods of 3D QSAR: comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were analyzed in terms of their predictive abilities. CoMSIA produced significantly better results for all correlations. The results indicate a strong correlation between the inhibitory activity of these compounds and the steric and electrostatic fields around them. CoMSIA models with considerable internal as well as external predictive ability were obtained. A poor correlation obtained with hydrophobic field indicates that the binding of thiazolothiazepines to HIV-1 integrase is mainly enthalpic in nature. Further the most active compound of the series was docked into the active site using the crystal structure of integrase. The binding site was formed by the amino acid residues 64-67, 116, 148, 151-152, 155-156, and 159. The comparison of coefficient contour maps with the steric and electrostatic properties of the receptor shows high level of compatibility.