Predicting kinase selectivity profiles using Free-Wilson QSAR analysis

Kinases are involved in a variety of diseases such as cancer, diabetes, and arthritis. In recent years, many kinase small molecule inhibitors have been developed as potential disease treatments. Despite the recent advances, selectivity remains one of the most challenging aspects in kinase inhibitor design. To interrogate kinase selectivity, a panel of 45 kinase assays has been developed in-house at Pfizer. Here we present an application of in silico quantitative structure activity relationship (QSAR) models to extract rules from this experimental screening data and make reliable selectivity profile predictions for all compounds enumerated from virtual libraries. We also propose the construction of R-group selectivity profiles by deriving their activity contribution against each kinase using QSAR models. Such selectivity profiles can be used to provide better understanding of subtle structure selectivity relationships during kinase inhibitor design.     

Joint QSAR Analysis Using the Free-Wilson Approach and Quantum Chemical Parameters

Abstract

A new quantitative structure-activity relationship (QSAR) technique combining the Free-Wilson method and constructed quantum chemical parameters was used to simulate the aqueous solubility (S _w), 1-octanol/water partition coefficient (K _ow) of 14 new synthesized benzanilide derivatives and their 96 h acute toxicity (EC₅₀) to Daphnia magna. The mode of action of the 14 selected compounds to Daphnia magna was shown to be a complex process involving a physical partition stage and a biochemical reaction stage. The results also indicated that the joint (QSAR) analysis was much effective than the original Free-Wilson method and Hansch method not only in predicting properties/toxicity, but also in investigating the mode of action of chemicals.     

Conformational and thermodynamic analysis of the COXIB scaffold using quantum chemical calculations

Selective cyclo‐oxygenase‐2 inhibitors (COXIBs) are prominent members of the nonsteroidal anti‐inflammatory drugs. The neutral and protonated COXIB scaffold has been subjected to molecular computations in the gas phase and implicit solvent to measure the relative changes in the thermodynamic functions, enthalpy (H_rel), potential energy (U_rel), Gibbs free energy (G_rel) and entropy (S_rel) induced by selected substituents. Conformational analysis of the COXIB scaffold indentified four pairs of atropisomeric conformers (from I, I′ to IV, IV′) associated with a molecular structure containing a double rotor system. All conformers had similar stability. Para‐substitution with substituents that cover a wide range of Hammett sigma values did not alter the geometries of the neutral COXIB conformers; however, the protonated COXIB scaffold was showed an increase in structural and thermodynamic perturbations due to inductive effects. Flexibility and structural resilience of the COXIB scaffold under the conditions studied herein could be an important feature of the COXIBs, especially considering the previously proposed flexibility of the cyclo‐oxygenase binding site. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A 3D QSAR pharmacophore model and quantum chemical structure--activity analysis of chloroquine(CQ)-resistance reversal

Using CATALYST, a three-dimensional QSAR pharmacophore model for chloroquine(CQ)-resistance reversal was developed from a training set of 17 compounds. These included imipramine (1), desipramine (2), and 15 of their analogues (3-17), some of which fully reversed CQ-resistance, while others were without effect. The generated pharmacophore model indicates that two aromatic hydrophobic interaction sites on the tricyclic ring and a hydrogen bond acceptor (lipid) site at the side chain, preferably on a nitrogen atom, are necessary for potent activity. Stereoelectronic properties calculated by using AM1 semiempirical calculations were consistent with the model, particularly the electrostatic potential profiles characterized by a localized negative potential region by the side chain nitrogen atom and a large region covering the aromatic ring. The calculated data further revealed that aminoalkyl substitution at the N5-position of the heterocycle and a secondary or tertiary aliphatic aminoalkyl nitrogen atom with a two or three carbon bridge to the heteroaromatic nitrogen (N5) are required for potent "resistance reversal activity". Lowest energy conformers for 1-17 were determined and optimized to afford stereoelectronic properties such as molecular orbital energies, electrostatic potentials, atomic charges, proton affinities, octanol-water partition coefficients (log P), and structural parameters. For 1-17, fairly good correlation exists between resistance reversal activity and intrinsic basicity of the nitrogen atom at the tricyclic ring system, frontier orbital energies, and lipophilicity. Significantly, nine out of 11 of a group of structurally diverse CQ-resistance reversal agents mapped very well on the 3D QSAR pharmacophore model.     

Guidelines proposed for designing organic ferromagnets by using a quantum chemical approach

For predicting the characteristics of organic ferromagnetic substances, we have previously proposed a simple rule for conjugated organic molecules based on molecular orbital coefficients by the simple Hückel??s nonbonding molecular orbital (NBMO) method. In this work, we extended the rule to systems including heteroatoms to become more widely applicable to various magnetic polymers. It was proven that the linkage between molecules having an NBMO conserves the original NBMO levels even for the supermolecule after the linkage. In addition, we have also proposed an index to estimate the amount of possessing ferromagnetic property. The reliability of the rule and index is examined by applying both the density functional theory (DFT) with functional methods, i.e., B3LYP, B3PW91, BLYP, PBEPBE, and PBEP86, and the complete active space SCF (CASSCF) calculations to several model molecules.     

QSAR modeling and chemical space analysis of antimalarial compounds

Generative topographic mapping (GTM) has been used to visualize and analyze the chemical space of antimalarial compounds as well as to build predictive models linking structure of molecules with their antimalarial activity. For this, a database, including ~3000 molecules tested in one or several of 17 anti-Plasmodium activity assessment protocols, has been compiled by assembling experimental data from in-house and ChEMBL databases. GTM classification models built on subsets corresponding to individual bioassays perform similarly to the earlier reported SVM models. Zones preferentially populated by active and inactive molecules, respectively, clearly emerge in the class landscapes supported by the GTM model. Their analysis resulted in identification of privileged structural motifs of potential antimalarial compounds. Projection of marketed antimalarial drugs on this map allowed us to delineate several areas in the chemical space corresponding to different mechanisms of antimalarial activity. This helped us to make a suggestion about the mode of action of the molecules populating these zones.     

QSAR analysis of the catalytic asymmetric ethylation of ketone using physical steric parameters of chiral ligand substituents

We have demonstrated that a validated QSAR (quantitative structure–activity relationship) model can be constructed between sterimol steric parameters of the N-substituents of chiral 1,2-amino-phosphoramide ligands and the enantiomeric ratios of alcohol products produced in the asymmetric additions of diethylzinc to acetophenone, which is powerful for predicting the steric effects of ligand substituents on enantioselectivities and instructive for ligand optimization.     

Local properties of quantum chemical systems: the LoProp approach

A new method is presented, which makes it possible to partition molecular properties like multipole moments and polarizabilities, into atomic and interatomic contributions. The method requires a subdivision of the atomic basis set into occupied and virtual basis functions for each atom in the molecular system. The localization procedure is organized into a series of orthogonalizations of the original basis set, which will have as a final result a localized orthonormal basis set. The new localization procedure is demonstrated to be stable with various basis sets, and to provide physically meaningful localized properties. Transferability of the methyl properties for the alkane series and of the carbon and hydrogen properties for the benzene, naphtalene, and anthracene series is demonstrated.     

QSAR analysis of hypoglycemic agents using the topological indices

The molecular topology model and discriminant analysis have been applied to the prediction of some pharmacological properties of hypoglycemic drugs using multiple regression equations with their statistical parameters. Regression analysis showed that the molecular topology model predicts these properties. The corresponding stability (cross-validation) studies performed on the selected prediction models confirmed the goodness of the fits. The method used for hypoglycemic activity selection was a linear discriminant analysis (LDA). We make use of the pharmacological distribution diagrams (PDDs) as a visualizing technique for the identification and selection of new hypoglycemic agents, and we tested on rats the predictive ability of the model.     

Investigating inclusion complexes using quantum chemical methods

Quantum chemistry has firmly established itself as a reliable method for investigating present-day problems in biological and materials chemistry. Understanding inclusion complexes represents one of the cutting edges of simulation sciences. In this tutorial review, we focus on the role and composition of non-covalent interactions, which are essential when studying inclusion complexes. A selected set of recently developed pragmatic methods used to study inclusion complexes are then surveyed including e.g. dispersion corrected DFT, double-hybrid functionals and spin-component scaled MP2. Finally, three case studies are outlined: (a) endohedral fullerene complexes, (b) buckyball catcher and (c) resorcinarene capsule. These case studies were carefully chosen to help illustrate how one may accurately investigate inclusion complexes, at a modest computational cost, using state-of-the-art quantum chemical methods (67 references).     

A new approach to NMR chemical shift additivity parameters using simultaneous linear equation method

A new approach to NMR chemical shift additivity parameters using simultaneous linear equation method has been introduced. Three general nitrogen-15 NMR chemical shift additivity parameters with physical significance for aliphatic amines in methanol and cyclohexane and their hydrochlorides in methanol have been derived. A characteristic feature of these additivity parameters is the individual equation can be applied to both open-chain and rigid systems. The factors that influence the (15)N chemical shift of these substances have been determined. A new method for evaluating conformational equilibria at nitrogen in these compounds using the derived additivity parameters has been developed. Conformational analyses of these substances have been worked out. In general, the results indicate that there are four factors affecting the (15)N chemical shift of aliphatic amines; paramagnetic term (p-character), lone pair-proton interactions, proton-proton interactions, symmetry of alkyl substituents and molecular association.     

Some quantum chemical aspects of solvent effects on NMR parameters

The non-bonded interactions which occur between solute and solvent molecules are discussed and the various models which describe the interactions are presented. The models are employed, within a quantum chemical framework, to estimate the extent of medium effects on chemical shifts and spin-spin couplings. Comparison between the calculated and available experimental data is provided for some first row nuclei.     

脂肪醇盐离子质子亲和能与量子化学参数的关系

采用半经验量子化学方法（MNDO，AM1和PM3）、从头算（采用STO-3G，3-21G，6-31G，6-31G^*,^6-31G^**,6-311G,6-311G^*和6-311G^**基组）HF方法计算羟基和6种脂肪醇盐离子以获得电子结构数据。通过相关分析发现脂肪醇盐离子中的氧原子净电荷，HOMO能级与质子亲和能之间具有良好的线性的相关性。     

某些含氧酸的酸强度与量化参数的相关性

本文利用从头计算法, 采用STO-3G基集计算了某些含氧酸分子的电子结构, 它们的标准几何构型取自已知的实验数据. 将氢、氧原子上的总电荷密度以及氧原子上的亲电子超离域度与实验测得的酸性离解常数相联系, 应用多元回归法, 得到了较好的线性关系.     

偏最小二乘和量子化学参数预测酯类物质的闪点

基于化合物定量结构与性质的关系,对其中88个酯类化合物进行了B3LYP/6-31G*水平上的结构优化,并在优化结构基础上进行了量子化学结构参数的计算。应用偏最小二乘(PLS)方法对酯类化合物闪点温度这个理化性质与量子化学参数进行了关联。结果表明,分子热力学自由能(ΔG)结合偶极距(μ)可以很好地表达酯类化合物闪点温度与量子化学参数间的定量关系。所建立的QSPR模型具有较强的稳健性和预测能力。