Multiple field three dimensional quantitative structure-activity relationship (MF-3D-QSAR)

A new drug design method, the multiple field three-dimensional quantitative structure-activity relationship (MF-3D-QSAR), is proposed. It is a combination and development of classical 2D-QSAR and traditional 3D-QSAR. In addition to the electrostatic and van der Waals potentials, more potential fields (such as lipophilic potential, hydrogen bonding potential, and nonthermodynamic factors) are integrated in the MF-3D-QSAR. Meanwhile, a principal component analysis (PCA) and iterative double least square (IDLS) technique is developed for predicting the bioactivity of query drug candidates. As an example, the MF-3D-QSAR is applied to the design of neuraminidase inhibitor and to prove its predictive power, and some useful findings are obtained for developing drugs against influenza virus.     

Predicting toxicity of benzene derivatives by molecular hologram derived quantitative structure-activity relationships (QSARS)

Holographic quantitative structure-activity relationship (HQSAR) is an emerging QSAR technique with the combined application of molecular hologram, which encodes the frequency of occurrence of various molecular fragment types, and the subsequent partial least squares (PLS) regression analysis. Based on molecular hologram, alignment-free QSAR models could be rapidly and easily developed with highly statistical significance and predictive ability. In this paper, the toxicity data for a series of 83 benzene derivatives to the autotrophic Chlorella vulgaris (IGC50, negative logarithmic form of 6-h 50% population growth inhibition concentration in mmol/l) were subjected to HQSAR analysis and this resulted in a model with a high predictive ability. The robustness and predictive ability of the model were validated by "leave-one-out" (LOO) cross-validation procedure and an external testing set. The influence of fragment distinction parameters and fragment size on the quality of the HQSAR model have been also discussed.     

Quantitative Series Enrichment Analysis (QSEA): a novel procedure for 3D-QSAR analysis

A novel procedure is proposed for 3D-QSAR analysis. The composition of 16 published QSAR datasets has been examined using Quantitative Series Enrichment Analysis (QSEA). The procedure is based on topomer technologies. A heatmap display in combination with topomer CoMFA and a novel series trajectory analysis revealed critical information for the assembly of structures into meaningful series. Global and local centroid structures can be determined from a similarity distance matrix and build the origins for stepwise model building by increasing the similarity radius around the centroid nucleus. The results indicate that the new procedure allows determination of whether compounds belong to an emerging structure-activity relationship and which compounds can be predicted within reliable limits.     

Molecular structure-activity relationships for the oxidation of organic compounds using mesoporous silica catalysts derivatised with bis(halogeno)dioxomolybdenum(VI) complexes

Mo K-edge XAFS spectra have been measured for ordered mesoporous silica MCM-41 grafted with the complexes [MoO2X2(thf)2] (X=Cl, Br). For grafting reactions in the absence of triethylamine, materials with 1 wt. % Mo are obtained; the Mo K-edge EXAFS results indicate the co-existence of isolated surface-fixed monomeric species [MoO2[(-O)3SiO]2(thf)(n)] and [MoO2[(-O)3SiO]X(thf)(n)]. When Et3N is used in the grafting reactions, materials with 4 wt. % Mo are obtained. The EXAFS data for the material prepared using [MoO2Cl2(thf)2] and Et3N indicate the presence of dinuclear species with two Mo(VI) centres, each with two Mo=O groups and each linked by one or two oxo bridges (Mo...Mo 3.27 A). The molybdenum centres in the material prepared using the dibromo complex comprise mainly isolated four-coordinate dioxomolybdenum(VI) and trioxomolybdenum(VI) monomeric species, with a small contribution from dimeric species. All materials were further characterised in the solid state by powder X-ray diffraction, N2 adsorption analysis, MAS NMR (13C, 29Si) and FTIR spectroscopy. The derivatised MCMs perform differently as catalysts in the liquid-phase oxidation of various olefins and alcohols with tert-butyl hydroperoxide. The highest alkene epoxidation activity was recorded for the catalysts with low metal loading, whereas the material containing oxo-bridged dimers had the highest activity for oxidation of alcohols. The recyclability of all the catalysts was tested: the catalytic activity of the derivatised materials tended to stabilize with ageing.     

A cytotoxic constituent of Lysimachia japonica THUNB. (Primulaceae) and the structure-activity relationships of related compounds

A cytotoxic alkylresorcinol was isolated from Lysimachia japonica THUNB. (Primulaceae) and identified as grevillol (2). It was tested for cytotoxicity against KB, B-16, PC-13, L-5178Y, P-388, and HEp-2 cells in vitro. Synthetic related compounds were also tested for cytotoxicity against the KB cell line, and the structure-activity relationships are discussed.     

Heuristic molecular lipophilicity potential (HMLP): a 2D-QSAR study to LADH of molecular family pyrazole and derivatives

The quantum chemical and structure-based technique heuristic molecular lipophilicity potential (HMLP) is used in the liver alcohol dehydrogenase (LADH) study of molecular family pyrazole and derivatives. The molecular lipophilic index LM, molecular hydrophilic index HM, lipophilic indices lss, and hydrophilic indices hss of the substitutes (fragments), and atomic lipophilicity indices las are constructed and used in QSAR study. The HMLP indices are correlated with bioactivities of 18 pyrazole derivatives according to the 2D QSAR procedure. The multiple linear regression equation between the bioactivities of pyrazole derivatives and HMLP indices are built using partial least square (PLS) with the optimal statistical quantity (r=0.987, s=0.479, F=47.19). The inhibition mechanism of LADH of the pyrazole derivatives is explained according to the physical meaning of HMLP indices. During the HMLP calculations for the 2D QSAR, the only input parameters are the atomic van der Waals radius without the need to resort to any empirical parameters. Accordingly, HMLP can provide a rigorous theoretical approach with a crystal clear physical meaning for the 2D QSAR.     

Identification of potential CRAC channel inhibitors: Pharmacophore mapping, 3D-QSAR modelling,and molecular docking approach

Upregulation of store-operated Ca²⁺ influx via ORAI1, an integral component of the CRAC channel, is responsible for abnormal cytokine release in active rheumatoid arthritis, and therefore ORAI1 has been proposed as an attractive molecular target. In this study, we attempted to predict the mechanical insights of ORAI1 inhibitors through pharmacophore modelling, 3D-QSAR, molecular docking and free energy analysis. Various hypotheses of pharmacophores were generated and from that, a pharmacophore hypothesis with two hydrogen bond acceptors, one hydrogen bond donor and two aromatic rings (AADRR) resulted in a statistically significant 3D-QSAR model (r² = 0.84 and q² = 0.74). We believe that the obtained statistical model is a reliable QSAR model for the diverse dataset of inhibitors against the IL-2 production assay. The visualization of contours in active and inactive compounds generated from the 3D-QSAR models and molecular docking studies revealed major interaction with GLN108, HIS113 and ASP114, and interestingly, these residues are located near the Ca²⁺ selectivity filter region. Free energy binding analysis revealed that Coulomb energy, van der Waals energy and non-polar solvation terms are more favourable for ligand binding. Thus, the present study provides the physical and chemical requirements for the development of novel ORAI1 inhibitors with improved biological activity.     

Selective ATP competitive leads of CDK4: Discovery by 3D-QSAR pharmacophore mapping and molecular docking approach

The discovery of ATP competitive CDK4 inhibitors is an on-going challenging task in cancer therapy. Here, an attempt has been made to develop new leads targeting ATP binding site of CDK4 by applying 3D-QSAR pharmacophore mapping and molecular docking methods The outcome of 6 leads offers a significant contribution for selective CDK4 inhibition, since they show potential binding interactions with Val⁹⁶, Arg¹⁰¹, and Glu¹⁴⁴ residues of CDK4, that are unique and from other kinases. It is worth noting that there is a striking similarity in binding interactions of the leads and known CDK4 inhibitors, namely Abemaciclib, Palbociclib and Ribociclib. Further key features, including high dock score value, good predicted activity, scaffold diversity, and the acceptable ADME profile of leads, provide a great opportunity for the development of highly potent and selective ATP competitive inhibitors of CDK4.     

Molecular field analysis and 3D-quantitative structure-activity relationship study (MFA 3D-QSAR) unveil novel features of bile acid recognition at TGR5

Bile acids regulate nongenomic actions through the activation of TGR5, a membrane receptor that is G protein-coupled to the induction of adenylate cyclase. In this work, a training set of 43 bile acid derivatives is used to develop a molecular interaction field analysis (MFA) and a 3D-quantitative structure-activity relationship study (3D-QSAR) of TGR5 agonists. The predictive ability of the resulting model is evaluated using an external set of compounds with known TGR5 activity, and six bile acid derivatives whose unknown TGR5 activity is herein assessed with in vitro luciferase assay of cAMP formation. The results show a good predictive model and indicate a statistically relevant degree of correlation between the TGR5 activity and the molecular interaction fields produced by discrete positions of the bile acid scaffold. This information is instrumental to extend on a quantitative basis the current structure-activity relationships of bile acids as TGR5 modulators and will be fruitful to design new potent and selective agonists of the receptor.     

Predicted binding rate of new cephalosporin antibiotics by a 3D-QSAR method: a new approach

Abstract  

Antibiotics are chemotherapeutic agents with activity against microorganisms, for example bacteria, fungi, or protozoa, used for the treatment of many types of diseases. Binding of antibiotics to serum proteins in human plasma is a major determinant of their pharmacodynamic and pharmacokinetic behavior and, consequently, can affect their systemic distribution in the body. Here, the predicted binding rates of ceftazidime and 13 other pharmacological agents classified as antibiotics to plasma proteins (percentage fraction bound; PFB) were evaluated by use of 3D-QSAR models. We attempted to establish the contribution of hydrogen bond donor/acceptor and hydrophobic properties supplied by electrostatic fields to the PFB. Significant cross-validated correlation q ² (0.5–0.7) and the fitted correlation r ² (0.7–0.97) coefficients revealed that these models have reasonable power to predict the design 19 new antibiotics using ceftazidime as template, these compounds being our suggestion for further studies.     

三维含时量子散射研究H + CIH体系

用三维含时量子散射理论模拟了H+CIH体系在BW2,mBW2,G3势能面上的动力学行为,其计算结果表明,振动量子态对反应几率影响很大;势能面的地形对转动量子态如何影响反应几率起重要作用;反应几率表现出“黄金规则”,此外,BW2,mBW2势能面上的反应几率几乎相同,而G3势能面上的反应几率较前者低,大概由于G3的势垒高的缘故。     

The story of silica-supported Os3(CO)12 a molecular approach to heterogeneous catalysis

The surface organometallic chemistry can be defined as the study of the reactivity of organometallic complexes, in particular molecular metals carbonyl clusters, with the surface of microporous metal oxides and, by extension, of zeolites.