C(4)取代紫杉醇类似物的定量构效关系研究

用量子化学B3LYP／6-31G方法计算了23个C（4）取代紫杉醇类似物的结构,用遗传算法（GFA）对能量、电性、拓扑及热力学等类型的278个结构描述符进行筛选,并回归建立其抑制人体结肠癌细胞HCT-116活性的定量构效关系（QSAR）．QSAR方程含分子体积Vm、分子分支度指数CHI-O、分子中带正电荷原子的溶剂可积面积与其所带电荷之积的加和值Jurs-PPSA-3以及分子表面积S4个结构描述符．方程的拟合相关系数的平方R^0及交叉验证系数Q^2分别为0．956和0．913,所得QSAR具有可信的预报能力．由优化后的几何构型知,C（4）取代基、C（13）侧链和2-OBz三基团共同形成疏水腔,C（4）取代基的改变影响C（13）侧链的电子结构．C（13）连接的18号O原子的负电荷越大、3’位连接的NHBz基团的极性越小活性越高;C（4）取代基若为吸电子基对活性不利;适当增大分子体积、表面积和疏水性,保持一定的分支度对活性有利．     

Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods

Summary Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte> MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the phenyl ring rotational barrier for neutral MP and gave results very similar to those of the HF/6-31G* method.     

Synthesis and structure-activity relationships of fenbufen amide analogs

The previous discoveries of butyl fenbufen amide analogs with antitumor effects were further examined. The amide analogs with 1, 3, 4 and 8 carbons chains were prepared in 70-80% yield. Fenbufen had no cytotoxic effects at concentrations ranging from 10 to 100 μM. Methyl fenbufen amide had significant cytotoxic effects at a concentration of 100 μM. As the length of the alkyl amide side chain increased, the cytotoxic effects increased, and the octyl fenbufen amide had the greatest cytotoxic effect. After treatment with 30 μM octyl fenbufen amide, nearly seventy percent of the cells lost their viability. At the concentration of 10 μM, fenbufen amide analogs did not show cytotoxicity according to the MTT assay results. The NO scavenging activities of the fenbufen amide analogs were not significantly different from those of fenbufen.     

4-取代Fentanyl类化合物电子结构及构效关系研究

本文对十一个4-取代Fentanyl类化合物进行了量子化学(INDO)计算, 研究了它们的电子结构及构效关系. 结果表明, 这些化合物同其他Fentanyl类化合物在主要活性部位和电子结构趋势上基本相同. 酰胺氧原子是最重要的负电中心, 哌啶氮原子在季铵化后发挥正电中心作用. 4-取代基的极性基团可能以电荷转移作用或氢键接受体形式与受体极性部位结合, 并能影响其他活性部位电子密度. 另外, 4-取代基的立体因素与疏水因素同生物活性相关.     

Electronic structure of brain: structure-activity relationships between electronic structure and neurotransmitters based on molecular hardness concept

In order to understand the relation between the electronic structure of neurotransmitters and the brain, a model of the brain based on absolute hardness (eta) and absolute electronegativity (chi) is described. It was found that the coordinate r(chi, eta) of electronic structures of neurotransmitters obtained using the parameters eta and chi can be graphically classified into three groups: catecholamine type (group I), gamma-aminobutanoic acid (GABA) type (group II), and acetylcholine (ACh) type (group III) in the eta-chi diagram. The results suggest that the brainstem and neocortex in the brain are chemically soft and hard, respectively, because they show that the myelinated nerve is chemically soft and the unmyelinated nerve is chemically hard. If one calculates the r(chi, eta) to understand which group a drug belongs to, one can predict the target receptors of the drug from the eta-chi diagram. Using eta-chi maps, one is then able to design medications like antidepressants, tranquilizers, and ACh agonists.     

New hybrid method for reactive systems from integrating molecular orbital or molecular mechanics methods with analytical potential energy surfaces

A computational approach to calculating potential energy surfaces for reactive systems is presented and tested. This hybrid approach is based on integrated methods where calculations for a small model system are performed by using analytical potential energy surfaces, and for the real system by using molecular orbital or molecular mechanics methods. The method is tested on a hydrogen abstraction reaction by using the variational transition-state theory with multidimensional tunneling corrections. The agreement between the calculated and experimental information depends on the quality of the method chosen for the real system. When the real system is treated by accurate quantum mechanics methods, the rate constants are in excellent agreement with the experimental measurements over a wide temperature range. When the real system is treated by molecular mechanics methods, the results are still good, which is very encouraging since molecular mechanics itself is not at all capable of describing this reactive system. Since no experimental information or additional fits are required to apply this method, it can be used to improve the accuracy of molecular orbital methods or to extend the molecular mechanics method to treat any reactive system with the single constraint of the availability of an analytical potential energy surface that describes the model system.     

Study of structure-activity relationships in a series of alkaloids ofAconitum zeravschanicum and their analogs

The toxic and antiarrhythmic activities of diterpene alkaloids fromAconitum zeravschanicum and their synthetic analogs have been investigated. It has been established that, in the series of compounds studied, activity and toxicity depend on the type of skeleton, the nature and positions of substituents, and the basicity of the nitrogen atom.Institute of the Chemistry of Plant Substances, Academy of Sciences of the Republic of Uzbekistan, Tashkent, fax (3712) 89 14 75. Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 384–387, May–June, 1996. Original article submitted February 26, 1996.     

Comparison of different partial least-squares methods in quantitative structure-activity relationships

In this paper, the partial least-squares (PLS) is discussed. A new hybrid method combining PLS with GAGP, in which selection of variables, selection of functions and optimization of parameters were carried at the same time without any foreknowledge, was studied. A number of PLS algorithms (linear PLS, QPLS, SPL-PLS, NPLSNGA) that have appeared were compared from a theoretical viewpoint. Eight practical results with all the compared methods indicated that nonlinear models are better than linear model. In nonlinear methods, GAGP-PLS is significant.     

Theory and range of modern semiempirical molecular orbital methods

Semiempirical molecular orbital methods have a long history. They serve to tackle large systems and complicated processes beyond the reach of ab initio or density functional methods. Although their setup is derived from Hartree–Fock theory, the design of approximate energy expressions and the empirical parameters are used to achieve higher accuracy than the underlying ab initio theory. In this way the effect of larger basis sets or correlation can be partially simulated. All widely used semiempirical methods establish their accuracy by error statistics for molecular properties with experimental and high-level ab initio or density functional theory calculations as a reference. Their computational efficiency makes them suitable for the study of biochemical systems and solid materials. The present review presents a variety of applications which demonstrate the need for and success of semiempirical methods.     

Structural analysis of porphyrin molecular squares using molecular mechanics and density-functional methods

"Molecular squares" formed from Re(CO)(3)Cl corners and porphyrin sides have potential applications as hosts for catalytic sites and as building blocks for membranes. In these materials, knowledge of the conformations of the squares is important. Molecular-mechanics (MM) and density-functional (DF) calculations have been used iteratively in this work to find the minimum-energy configurations of several porphyrin molecular squares. MM predicts that the steric and torsional interactions at connecting junctures of the square framework determine the overall geometry. Torsional degrees of freedom around these junctures were therefore analyzed using DF methods, giving further insight and helping choose among MM force-field options. Single-point DF calculations on the entire squares showed that the energy and conformation of the entire square could be reliably obtained by performing DF calculations on the critical elements of the square and then piecing them together. This "piecewise" strategy allows for both the major torsional motions and the most important local relaxations of large supramolecular species such as molecular squares.     

Comparison of DFT methods for molecular orbital eigenvalue calculations

We report how closely the Kohn-Sham highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) eigenvalues of 11 density functional theory (DFT) functionals, respectively, correspond to the negative ionization potentials (-IPs) and electron affinities (EAs) of a test set of molecules. We also report how accurately the HOMO-LUMO gaps of these methods predict the lowest excitation energies using both time-independent and time-dependent DFT (TD-DFT). The 11 DFT functionals include the local spin density approximation (LSDA), five generalized gradient approximation (GGA) functionals, three hybrid GGA functionals, one hybrid functional, and one hybrid meta GGA functional. We find that the HOMO eigenvalues predicted by KMLYP, BH&HLYP, B3LYP, PW91, PBE, and BLYP predict the -IPs with average absolute errors of 0.73, 1.48, 3.10, 4.27, 4.33, and 4.41 eV, respectively. The LUMOs of all functionals fail to accurately predict the EAs. Although the GGA functionals inaccurately predict both the HOMO and LUMO eigenvalues, they predict the HOMO-LUMO gap relatively accurately (approximately 0.73 eV). On the other hand, the LUMO eigenvalues of the hybrid functionals fail to predict the EA to the extent that they include HF exchange, although increasing HF exchange improves the correspondence between the HOMO eigenvalue and -IP so that the HOMO-LUMO gaps are inaccurately predicted by hybrid DFT functionals. We find that TD-DFT with all functionals accurately predicts the HOMO-LUMO gaps. A linear correlation between the calculated HOMO eigenvalue and the experimental -IP and calculated HOMO-LUMO gap and experimental lowest excitation energy enables us to derive a simple correction formula.     

The fragment molecular orbital and systematic molecular fragmentation methods applied to water clusters

Two electronic structure methods, the fragment molecular orbital (FMO) and systematic molecular fragmentation (SMF) methods, that are based on fragmenting a large molecular system into smaller, more computationally tractable components (fragments), are presented and compared with fully ab initio results for the predicted binding energies of water clusters. It is demonstrated that, even when explicit three-body effects are included (especially necessary for water clusters due to their complex hydrogen-bonded networks) both methods present viable, computationally efficient alternatives to fully ab initio quantum chemistry.     

Higher-order correlated calculations based on fragment molecular orbital scheme

We have developed a new module for higher-order correlated methods up to coupled-cluster singles and doubles with perturbative triples (CCSD(T)). The matrix-matrix operations through the DGEMM routine were pursued for a number of contractions. This code was then incorporated into the ABINIT-MPX program for the fragment molecular orbital (FMO) calculations. Intra-fragment processings were parallelized with OpenMP in a node-wise fashion, whereas the message passing interface (MPI) was used for the fragment-wise parallelization over nodes. Our new implementation made the FMO-based higher-order calculations applicable to realistic proteins. We have performed several benchmark tests on the Earth Simulator (ES2), a massively parallel computer. For example, the FMO-CCSD(T)/6-31G job for the HIV-1 protease (198 amino acid residues)?Clopinavir complex was completed in 9.8?h with 512 processors (or 64 nodes). Another example was the influenza neuraminidase (386 residues) with oseltamivir calculated at the full fourth-order M?ller?CPlesset perturbation level (MP4), of which job timing was 10.3?h with 1024 processors. The applicability of the methods to commodity cluster computers was tested as well.     

Mechanism based structure-activity relationships for skin sensitisation--the carbonyl group domain

The biological activity of skin-sensitising chemicals is related to their ability to react either directly or after metabolic activity with appropriate skin proteins. For direct-acting electrophilic compounds, this ability can be modelled by the Relative Alkylation Index (RAI) by a combination of electrophilicity and hydrophobicity parameters. Several SARs based on this approach are reported. In this present work, electrophilicity parameters based on Taft substituent constants are used together with Leo and Hansch log P fragment values to calculate RAI values for hard electrophiles having a reactive carbonyl group. These are then applied to analysis of sensitisation data obtained in the murine Local Lymph Node Assay (LLNA) for two series of diketones as well as a homologous series of alpha, beta-unsaturated aldehydes. The sensitisation potentials of these reactive electrophiles show good correlations with the RAI. These findings re-affirm the view that physicochemical parameters are the key to eliciting the relationship between chemical structure and a toxic endpoint. They provide further evidence of the value of SAR studies in identifying mechanisms of sensitisation and aiding risk assessments without the need for extensive animal testing.     

Mechanism based structure-activity relationships for skin sensitisation--the carbonyl group domain

The biological activity of skin-sensitising chemicals is related to their ability to react either directly or after metabolic activity with appropriate skin proteins. For direct-acting electrophilic compounds, this ability can be modelled by the Relative Alkylation Index (RAI) by a combination of electrophilicity and hydrophobicity parameters. Several SARs based on this approach are reported. In this present work, electrophilicity parameters based on Taft substituent constants are used together with Leo and Hansch log P fragment values to calculate RAI values for hard electrophiles having a reactive carbonyl group. These are then applied to analysis of sensitisation data obtained in the murine Local Lymph Node Assay (LLNA) for two series of diketones as well as a homologous series of alpha, beta-unsaturated aldehydes. The sensitisation potentials of these reactive electrophiles show good correlations with the RAI. These findings re-affirm the view that physicochemical parameters are the key to eliciting the relationship between chemical structure and a toxic endpoint. They provide further evidence of the value of SAR studies in identifying mechanisms of sensitisation and aiding risk assessments without the need for extensive animal testing.