3D‐QSAR studies and molecular design on a novel series of pyrimidine benzimidazoles as Lck inhibitors

The development of selective lymphocyte‐specific kinase (Lck) inhibitors has attracted much attention for the research of the treatment of T‐cell mediated autoimmune and inflammatory diseases. In the present work, three‐dimensional quantitative structure–activity relationship (3D‐QSAR) analyses are performed on a novel series of 4‐amino‐6‐benzimidazole‐pyrimidines acting as Lck inhibitors. The established 3D‐QSAR models show significant statistical quality and satisfactory predictive ability, with high q² and R² values: the comparative molecular field analysis (CoMFA) model (q² = 0.802, R² = 0.991), and the comparative molecular similarity indexes analysis (CoMSIA) model (q² = 0.731, R² = 0.982). The systemic external validation indicates that both CoMFA and CoMSIA models are quite robust and possess high predictive abilities with values of 0.881 and 0.877, values of 0.897 and 0.847, values of 0.897 and 0.850, and values of 0.897 and 0.854, respectively. Several key structural features accounting for the inhibitory activities of these compounds are discussed. Based on established models and design considerations, six new compounds with significantly improved activities are theoretically designed, which still await experimental confirmation and evaluation. These theoretical results may provide a useful reference for understanding the action mechanism and designing novel potential Lck inhibitors. © 2014 Wiley Periodicals, Inc.     

Three-dimensional quantitative structure-activity relationship (3D QSAR) and pharmacophore elucidation of tetrahydropyran derivatives as serotonin and norepinephrine transporter inhibitors

Three-dimensional quantitative structure-activity relationship (3D QSAR) using comparative molecular field analysis (CoMFA) was performed on a series of substituted tetrahydropyran (THP) derivatives possessing serotonin (SERT) and norepinephrine (NET) transporter inhibitory activities. The study aimed to rationalize the potency of these inhibitors for SERT and NET as well as the observed selectivity differences for NET over SERT. The dataset consisted of 29 molecules, of which 23 molecules were used as the training set for deriving CoMFA models for SERT and NET uptake inhibitory activities. Superimpositions were performed using atom-based fitting and 3-point pharmacophore-based alignment. Two charge calculation methods, Gasteiger-Hückel and semiempirical PM3, were tried. Both alignment methods were analyzed in terms of their predictive abilities and produced comparable results with high internal and external predictivities. The models obtained using the 3-point pharmacophore-based alignment outperformed the models with atom-based fitting in terms of relevant statistics and interpretability of the generated contour maps. Steric fields dominated electrostatic fields in terms of contribution. The selectivity analysis (NET over SERT), though yielded models with good internal predictivity, showed very poor external test set predictions. The analysis was repeated with 24 molecules after systematically excluding so-called outliers (5 out of 29) from the model derivation process. The resulting CoMFA model using the atom-based fitting exhibited good statistics and was able to explain most of the selectivity (NET over SERT)-discriminating factors. The presence of −OH substituent on the THP ring was found to be one of the most important factors governing the NET selectivity over SERT. Thus, a 4-point NET-selective pharmacophore, after introducing this newly found H-bond donor/acceptor feature in addition to the initial 3-point pharmacophore, was proposed.     

Conceptual DFT properties‐based 3D QSAR: Analysis of inhibitors of the nicotine metabolizing CYP2A6 enzyme

Structure‐activity relationships of 46 P450 2A6 inhibitors were analyzed using the 3D‐QSAR methodology. The analysis was carried out to confront the use of traditional steric and electrostatic fields with that of a number of fields reflecting conceptual DFT properties: electron density, HOMO, LUMO, and Fukui f⁻ function as 3D fields. The most predictive models were obtained by combining the information of the electron density with the Fukui f⁻ function (r² = 0.82, q² = 0.72), yielding a statistically significant and predictive model. The generated model was able to predict the inhibition potencies of an external test set of five chemicals. The result of the analysis indicates that conceptual DFT‐based molecular fields can be useful as 3D QSAR molecular interaction fields. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

Development of docking-based 3D QSAR models for the design of substituted quinoline derivatives as human dihydroorotate dehydrogenase (hDHODH) inhibitors

Abstract

This study has investigated docking-based 3D quantitative structure–activity relationships (QSARs) for a range of quinoline carboxylic acid derivatives by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). A docking study has shown that most of the compounds formed H-bonds with Arg136 and Gln47, which have already been shown to be essential for the binding of ligands at the active site of the hydroorotate dehydrogenase adenovirus (hDHODH). Bioactive conformations of all the molecules obtained from the docking study were used for the 3D QSAR study. The best CoMFA and CoMSIA models were obtained for the training set and were found to be statistically significant, with cross-validated coefficients (q² ) of 0.672 and 0.613, r² _cv of 0.635 and 0.598 and coefficients of determination (r² ) of 0.963 and 0.896, respectively. Both models were validated by a test set of 15 compounds, giving satisfactory predicted correlation coefficients (r² _pred) of 0.824 and 0.793 for the CoMFA and CoMSIA models, respectively. From the docking-based 3D QSAR study we designed 34 novel quinoline-based compounds and performed structure-based virtual screening. Finally, in silico pharmacokinetics and toxicities were predicted for 24 of the best docked molecules. The study provides valuable information for the understanding of interactions between hDHODH and the novel compounds.     

Computational studies on N-phenyl pyrrole derivatives as MmpL3 inhibitors in Mycobacterium tuberculosis

The fight against tuberculosis (TB) is a time immemorial one and the emergence of new drug resistant strains of Mycobacterium tuberculosis keeps throwing new challenges to the scientific community immersed in finding mechanisms to control this dreaded disease. Computer aided drug designing (CADD) is one of the several approaches that can assist in identifying the potent actives against Mycobacterium. In this work, a series of 109 known Mycobacterial membrane proteins large 3 (MmpL3) inhibitors were pooled and atom based 3D QSAR analysis was performed to understand the structural features essential for inhibitory activity against the MmpL3, known to be a key player in transporting substances critical for cell wall integrity of Mycobacterium. The data set employed was randomly split into training set and test set molecules. The training set of 74 molecules was used to derive CoMFA and CoMSIA models that were statistically reliable (CoMFA: q²_loo = 0.53; r²_ncv = 0.93 and CoMSIA: q²_loo = 0.60; r²_ncv = 0.93). The derived models also exhibited good external predictive ability (CoMFA: r²_pred = 0.78 and CoMSIA: r²_pred = 0.79). The results are quite encouraging and information derived from these analyses was applied to design new molecules. The designed molecule showed appreciable predicted activity values and reasonably good ADMET profile. The strategy used in designing new molecules can be pursued in the hunt for new chemical entities targeting MmpL3, expanding the existing arsenal against TB.     

Human Estrogen Receptor Alpha Antagonists,Part 3: 3-D Pharmacophore and 3-D QSAR Guided Brefeldin A Hit-to-Lead Optimization toward New Breast Cancer Suppressants

The estrogen receptor α (ERα) is an important biological target mediating 17β-estradiol driven breast cancer (BC) development. Aiming to develop innovative drugs against BC, either wild-type or mutated ligand-ERα complexes were used as source data to build structure-based 3-D pharmacophore and 3-D QSAR models, afterward used as tools for the virtual screening of National Cancer Institute datasets and hit-to-lead optimization. The procedure identified Brefeldin A (BFA) as hit, then structurally optimized toward twelve new derivatives whose anticancer activity was confirmed both in vitro and in vivo. Compounds as SERMs showed picomolar to low nanomolar potencies against ERα and were then investigated as antiproliferative agents against BC cell lines, as stimulators of p53 expression, as well as BC cell cycle arrest agents. Most active leads were finally profiled upon administration to female Wistar rats with pre-induced BC, after which 3DPQ-12, 3DPQ-3, 3DPQ-9, 3DPQ-4, 3DPQ-2, and 3DPQ-1 represent potential candidates for BC therapy.     

The Non-Grid Technique for Modeling 3D QSAR Using Self-Organizing Neural Network (SOM) and PLS Analysis: Application to Steroids and Colchicinoids

Abstract

A novel method for modeling 3D QSAR has been developed. The method involves a multiple training of a series of self-organizing networks (SOM). The obtained networks have been used for processing the data of one reference molecule. A scheme for the analysis of such data with the PLS analysis has been proposed and tested using the steroids data with corticosteroid binding globulin (CBG) affinity. The predictivity of the CBG models measured with the SDEP parameter is among the best one reported. Although 3-D QSAR models for colchicinoid series is far less predictive, it allows for a discussion on the relative influence of the structural motifs of these compounds.     

A Porous 3D Supramolecular Architecture of Cd（II） Complex with Water Clusters as Pillars

A supramolecular complex of Cd（II） with 1D water tapes as pillars[Cd2（dpa）2（phen）2（H2O）2]·6H2O 1 （H2dpa = diphenic acid, phen = phenanthroline）, has been synthesized and characterized by elemental analysis, IR spectroscopy, and single-crystal X-ray diffraction analysis. The crystal is of triclinic, space group P1^- with a = 9.7029（4）, b = 11.9601（5）, c = 12.1788（4） A, α = 71.6990（10）, β = 71.8740（10）, γ = 74.4680（10）°, V = 1252.39（8） A^3, C52H48Cd2N4O16, Mr = 1209.76, Z= 1, Dc = 1.604 g/cm^3,μ = 0.925 mm^-1, F（000） = 612, R = 0.0679 and wR = 0.2514 for 3870 observed reflections （I 〉 2σ（I））. Two intramolecular Cd（II） centers of this complex are encircled by two dpa^2- ligands forming an 18-membered ring, which is further assembled into a pillared three-dimensional （3D） supramolecular architecture through the synergetic effect of intermolecular face-to-face π…π stacking and weak O-H…O hydrogen-bonding interactions. Moreover, this complex exhibits photoluminescence with the main emission bands located at about 456 nm upon excitation at 355 nm in the solid state at room temperature.     

3D-QSAR studies on indole and 7-azoindole derivatives as ROCK-2 inhibitors: An integrative computational approach

Rho Kinases (ROCK) has been found to regulate a wide range of fundamental cell functions such as contraction, motility, proliferation, and apoptosis. Recent experiments have defined new functions of ROCKs in cells, including centrosome positioning and cell-size regulation, which might contribute to various physiological and pathological states. In this study, we have performed pharmacophore modeling and 3D QSAR studies on a series of 36 indoles and 7-azoindoles derivatives as ROCK2 inhibitors to elucidate the structural variations with their inhibitory activities. Ligand based CoMFA and CoMSIA models were generated based on three different alignment methods such as systematic search, simulated annealing and pharmacophore. A total of 15 CoMFA models and 27 CoMSIA were generated using different alignments. One model from each alignment is selected based on the statistical values. Contour maps of the selected models were compared, analysed and reported. The 3D QSAR study revealed that electro positive group linked to the methoxy-benzene ring position of the structure will enhance the biological activity and bulkier substitutions are preferred in the methyl dihydroindole region. Also, it is found that the hydrogen bond donor substituted at the R₁ position enhances the inhibitory activity. In future, this study would give proper guidelines to further enhance the activity of novel inhibitors for ROCK2.     

溶液中某些镉(II)的混合配体配合物的稳定性研究: 关于混合配体配合物相对稳定性定量表征的讨论

本文用pH电位法研究了在70%(v/v)乙醇-水溶液中Cd(II)与维生素D3(VD3)和乙二胺(en)或2,2'-联吡啶(bipy)在37±0.1℃和离子强度为0.10(KNO3)条件下, 三元混配配合物的稳定性。结果表明, 上述混合配位体系均形成稳定的1:1:1型混配配合物, 且△logK值均为较大的正值(分别为+1.06和+1.54), 但相应的logX值却并不很大(分别为2.18和2.83)。从统计效应和配合物分子内的配体间疏水相互作用, 讨论了造成这种反应常结果的可能原因, 并针对如何判断三元混配配合物相对稳定性高低等问题提出了作者的见解。     

A Zipper‐like Supramolecular Double‐Chain based on 1 D π‐π Stacking Interactions: Synthesis and Crystal Structure of [Cu(phen)(C4H4O4)(H2O)]2 · C4H6O4 (phen = 1,10‐phenanthroline)

[Cu(C₁₂H₈N₂)(C₄H₄O₄)(H₂O)]₂ · C₄H₆O₄ was prepared by the reaction of succinic acid, CuCl₂ · 2 H₂O, 1,10‐phenanthroline (phen = C₁₂H₈N₂), and Na₂CO₃ in a CH₃OH–H₂O solution. The crystal structure (triclinic, P 1 (no. 2), a = 7.493(1), b = 9.758(1), c = 13.517(1) Å; α = 68.89(1)°, β = 88.89(1)°, γ = 73.32(1)°, Z = 1, R = 0.0308, wR² = 0.0799 for 3530 observed reflections (F ≥ 2σ(F ) out of 3946 unique reflections) consists of hydrogen bonded succinic acid molecules and succinato bridged 1 D zipperlike supramolecular [Cu(phen)(C₄H₄O₄)_2/2(H₂O)]₂ double chains based on 1 D π‐π stacking interactions between the chelating phen systems at distances of 3.71 Å and 3.79 Å. The Cu atoms are fivefold trigonal bipyramidally coordinated by two N atoms of the bidentate chelating phen ligand and three O atoms of one water molecule and two bidentate bridging succinate ligands. The water O atom and one phen N atom are at the apical positions (equatorial: d(Cu–O) = 1.945, 2.254(2) Å, d(Cu–N) = 2.034(2) Å; axial: d(Cu–O) = 1.971(2) Å, d(Cu–N) = 1.995 Å).