分子亲脂-亲水性的量子化学描述II. 氨基酸侧链的亲水指标和亲脂指标

在启发式亲脂势HMLP(heuristicmolecularlipophilicitypotential)的基础上提出了分子、分子片段和原子的亲水指标和亲脂指标.计算出了20个天然氨基酸侧链的亲水、亲脂指标和亲水、亲脂表面积,并用线性自由能函数表达氨基酸侧链的溶剂化自由能,?Gsol,=b0 b1Li b2Hi b3Si b4Si.应用线性自由能函数和氨基酸侧链的亲水和亲脂! -i指标,计算了20个氨基酸残基的3种相转移自由能(蒸气-水、蒸气-正辛醇、正辛醇-水)和正辛醇-水分配系数logPow,取得了与实验值高度一致的良好效果.HMLP的亲水和亲脂指标是HMLP的指标化,扩展了这一方法的使用范围.氨基酸侧链的亲水、亲脂指标和线性自由能函数有望用于生物大分子受体与配体的结合自由能的估算、蛋白质的结构与功能、蛋白-蛋白相互作用和识别的研究.     

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.     

分子亲脂-亲水性的量子化学描述II. 氨基酸侧链的亲水指标和亲脂指标

在启发式亲脂势HMLP (heuristic molecular lipophilicity potential)的基础上提出了分子、分子片段和原子的亲水指标和亲脂指标. 计算出了20个天然氨基酸侧链的亲水、亲脂指标和亲水、亲脂表面积, 并用线性自由能函数表达氨基酸侧链的溶剂化自由能, ΔG_sol,i^θ＝b₀＋b₁L_i＋b₂H_i＋b₃S_i^＋＋b₄S_i^－. . 应用线性自由能函数和氨基酸侧链的亲水和亲脂指标, 计算了20个氨基酸残基的3种相转移自由能(蒸气-水、蒸气-正辛醇、正辛醇-水)和正辛醇-水分配系数logP_ow, 取得了与实验值高度一致的良好效果. HMLP的亲水和亲脂指标是HMLP的指标化, 扩展了这一方法的使用范围. 氨基酸侧链的亲水、亲脂指标和线性自由能函数有望用于生物大分子受体与配体的结合自由能的估算、蛋白质的结构与功能、蛋白-蛋白相互作用和识别的研究.     

Heuristic lipophilicity potential for computer-aided rational drug design

In this contribution we suggest a heuristic molecular lipophilicitypotential (HMLP), which is a structure-based technique requiring noempirical indices of atomic lipophilicity. The input data used in thisapproach are molecular geometries and molecular surfaces. The HMLP is amodified electrostatic potential, combined with the averaged influences fromthe molecular environment. Quantum mechanics is used to calculate theelectron density function (r) and the electrostatic potential V(r), andfrom this information a lipophilicity potential L(r) is generated. The HMLPis a unified lipophilicity and hydrophilicity potential. The interactions ofdipole and multipole moments, hydrogen bonds, and charged atoms in amolecule are included in the hydrophilic interactions in this model. TheHMLP is used to study hydrogen bonds and water–octanol partitioncoefficients in several examples. The calculated results show that the HMLPgives qualitatively and quantitatively correct, as well as chemicallyreasonable, results in cases where comparisons are available. Thesecomparisons indicate that the HMLP has advantages over the empiricallipophilicity potential in many aspects. The HMLP is a three-dimensional andeasily visualizable representation of molecular lipophilicity, suggested asa potential tool in computer-aided three-dimensional drug design.     

Structure-Lipophilicity and Structure-Polarity relationships of amino acids and peptides

The objectives of this study were to gain insights into the structure-lipophilicity relationships of peptides and to propose an improved model for estimating their lipophilicity. First, existing databases were extended to obtain the distribution coefficients of a total of 208 free or protected peptides (di- to pentapeptides). The polarity parameters (Λ) of 23 free amino acids and 19 protected amino acids (AcNH? CHR? CONH₂) and of their side chains were calculated from experimental distribution coefficients and computed molecular volumes. An analysis of the polarity parameters revealed that the hydrophobicity of the amino-acid side chains is largely reduced due to the polar field of the backbone. The polarity parameters of the peptides were then obtained in a similar manner and shown to be highly correlated with the sum of the polarity parameters of their side chains, i.e., the lipophilicity of peptides can be calculated from their molecular volume and the sum of their side-chain polarities using the regression established for each individual series of peptides (Fig. 1). This last restriction is essential since the polarity and lipophilic increment of a NH? C*H? CO unit were shown to decrease with increasing length of backbone.     

Peptide reagent design based on physical and chemical properties of amino acid residues

It has tremendous values for both drug discovery and basic research to develop a solid bioinformatical tool for guiding peptide reagent design. Based on the physical and chemical properties of amino acids, a new strategy for peptide reagent design, the so-called AABPD (amino acid based-peptide design), is proposed. The peptide samples in a training dataset are described by a series of HMLP (heuristic molecular lipophilicity potential) parameters and other physicochemical properties of amino acid residues that form a three-dimensional data matrix where each component is defined by three indexes: the first index refers to the peptide samples, the second to the amino acid positions, and the third to the amino acid parameters. The binding free energy between a peptide ligand and its protein receptor is calculated by a linear free energy equation through the physicochemical parameters, resulting in a set of simultaneous linear equations between the bioactivity of the peptides and the physicochemical properties of amino acids. An iterative double least square technique is developed for the solution of the three-dimensional simultaneous linear equation set to determine the amino acid position coefficients of peptide sequence and the physicochemical parameter coefficients of amino acid residues alternately. The two sets of coefficients thus obtained are used for predicting the bioactivity of other query peptide reagents. Two calculation examples, the peptide substrate specificity of the SARS coronavirus 3C-like proteinase and the affinity prediction for epitope-peptides with Class I MHC molecules are studied by using the peptide reagent design strategy.     

分子亲脂-亲水性的量子化学描述(Ⅰ)——分子的亲脂和亲水表面

给出基于分子结构的“启发式”亲脂-亲水势HMLP(Heuristic molecular lipophilicity-hydrophilicity potential)的理论分析和有说服力的算例.用量子化学计算其分子表面的静电势V(r)的分布,通过与周围原子表面静电势的比较,构造表达分子静电势的极性和大小的函数L(r).亲脂势L(r)保留了静电势V(r)描述分子静电作用的能力,并把应用范围扩展到疏水性的描述.HMLP不使用原子的经验参数,但在L(r)的构造中使用了经验的函数形式.经参数化和指标化后,HMLP有望用于蛋白质结构与功能的研究和药物分子配体与生物大分子受体结合自由能的估算.     

Effect of analyte lipophilicity on the resolution of α‐ and β‐amino acids on liquid chromatographic ligand exchange chiral stationary phases

Separation of the two enantiomers of racemic α‐ and β‐amino acids on two ligand exchange chiral stationary phases (CSPs) prepared previously by covalently bonding sodium N‐((S)‐1‐hydroxymethy‐3‐methylbutyl)‐N‐undecylaminoacetate or sodium N‐((R)‐2‐hydroxy‐1‐phenylethyl)‐N‐undecylaminoacetate on silica gel was studied with variation of the organic modifier (methanol) concentration in the aqueous mobile phase. In particular, the variation of retention factors with changing organic modifier concentration in the aqueous mobile phase was found to be strongly dependent on both the analyte lipophilicity and the stationary phase lipophilicity. In general, the retention factors of relatively lipophilic analytes on relatively lipophilic CSPs tend to increase with increasing organic modifier concentration in the aqueous mobile phases while those of less lipophilic or hydrophilic analytes tend to increase. However, only highly lipophilic analytes show decreasing retention factors with increasing organic modifier concentration in the aqueous mobile phase on less lipophilic CSPs. The contrasting retention behaviors on the two CSPs were rationalized by the balance of the two competing interactions, viz. hydrophilic interaction of analytes with polar aqueous mobile phase and the lipophilic interaction of analytes with the stationary phase.     

Multivariate analysis of chromatographic retention data and lipophilicity of phenylacetamide derivatives

One of the most important physicochemical parameters of a molecule that determines its bioactivity is its lipophilicity. Cluster analysis (CA), principal component analysis (PCA), and sum of ranking differences (SRD) were used to compare the lipophilic parameters of twenty phenylacetamide derivatives, obtained experimentally as chromatographic retention data in the presence of different solvents and calculated by different mathematical methods. All the applied methods of multivariate analysis gave approximately similar grouping of the studied lipophilic parameters. In the attempt to group the investigated compounds in respect of their lipophilicity, the obtained results appeared to be dependent on the applied chemometric method. The CA and PCA, grouped the compounds on the basis of the nature of the substituents R₁ and R₂, indicating that they determine to a great extent the lipophilicity of the investigated molecules. Unlike them, the SRD method could not be used to group the studied compounds on the basis of their lipophilic character.     

Comprehensive evaluation of lipophilicity of biogenic amines and related compounds using different chemically bonded phases and various descriptors

The retention behavior for a series of biogenic amines and related sympathomimetic drugs has been investigated in reversed-phase thin-layer chromatography using RP-2, RP-8, RP-18W, and Diol stationary phase and mixtures of phosphate buffer (pH = 7.10) and methanol in different proportions as mobile phases. Several methodologies like arithmetic mean of experimental retention values, extrapolation to zero methanol concentration procedure and principal component analysis were applied to retention data values (R(M)) in order to determine relevant parameters (mean of R(M) - mR(M), R(M0), and scores corresponding to the first principal component - PC1/R(M) respectively) encoding information on the lipophilic behavior of compounds. High similarities in lipophilicity behavior of investigated amines were highlighted by mR(M) and PC1/R(M) lipophilicity indices for all of the studied stationary phases. The experimental results were compared with some computed lipophilicity parameters expressed as distribution coefficients at working pH (logD), partition coefficients (logP(N), logP(I), and diff(logP(N-I))) concerning both neutral and fully protonated species and difference between both species, and also with various lipophilicity values (logP) generated by different commonly used software. Significant correlations were observed between the experimental lipophilicity indices mR(M) respectively PC1/R(M) and diff(logP(N-I) ) values in all cases.     

Influence of mobile phase composition on evaluation of lipophilicity by partition chromatography.

The problems of the concentration dependence of retention indices and the applicability of extrapolated values in the evaluation of lipophilicity were studied. The reversed-phase high-performance liquid chromatography of arylalkanoic acids were carried out with experimental data for substituted estra-1,3,5 (10)-trienes, benzodiazepines, dermorphine derivatives and dansylamides selected from the literature for this purpose. Fair linear relationships between slopes of concentration dependences and extrapolated and non-extrapolated values of RM and log k' were found. Equivalence of these indices in the evaluation of lipophilicity can be inferred. Statistically significant dependences of log P (sigma pi) values on concentration slopes make it possible to use them as new parameters of lipophilicity. The goodness of fit of these relationships increases when the values of ET(30), as a measure of the solvatochromic solvent polarity of mobile phases, are used instead of the change in modifier concentration.     

The effect of stationary phase on lipophilicity determination of beta-blockers using reverse-phase chromatographic systems

Evaluation of lipophilicity parameters for basic compounds using different chromatographic stationary phases is presented. An HPLC method for determination of lipophilic molecule-stationary phase interactions was based on gradient analysis. Differences in correlation between the lipophilicity of compounds and experimental chromatographic results obtained in pseudo-membrane systems showed a strong influence of stationary phase structure and physico-chemical properties. beta-Blocker drugs with varying lipophilicity and bio-activity were chosen as test compounds. The stationary phases used for the study were monolithic rod-structure C18 and silica gel octadecyl phase SG-C18 as reference material. The second group was silica gel-based polar-embedded alkylamide and cholesterolic phases. The mobile phase was composed of acetonitrile or methanol with ammonium acetate, and a linear gradient of methanol and acetonitrile in mobile phase was performed. A linear correlation of plots of log k(g) = f(log P) was observed, especially for polar-embedded phases, and this allowed log P(HPLC) to be calculated. The behavior of stationary phases in methanol and acetonitrile buffer showed differences between obtained log P(HPLC) values.     

Determination of the lipophilicity of quinolinesulfonamides by reversed-phase HPLC and theoretical calculations

Reversed-phase high-performance liquid chromatography analyses were used for the determination of the retention factor (log k) of a set of quinolinesulfonamides. The analyses utilized a mixture of acetonitrile/water as the mobile phase. The log k values were linearly dependent on the concentration of acetonitrile and extrapolated to 100% water and gave the lipophilicity parameter log k_w. The parameter log P_HPLC was determined from log k_w values using the calibration curve obtained for five standards. The log P_HPLC parameters are discussed in terms of structure–lipophilicity relationships. Furthermore, the theoretical lipophilic parameters (log P_calc) for all compounds were calculated using chemical programs (e.g., Advanced Chemistry Development (ACD/ logP), miLogP, AlogP, ClogP, and Pallas). The determined log P_HPLC and calculated log P_calc values were compared by linear regression analysis.     

Evaluation of the lipophilicity of bile acids and their derivatives by thin-layer chromatography and principal component analysis

The lipophilic character of bile acids and their glyco- and tauro-conjugates was studied. The classical R(Mo) values were measured by means of reversed thin-layer chromatography using a mixture of methanol-water as the solvent system and compared with the factors scores obtained by principal component analysis based also onto the TLC-retention data. The reliability of the factor scores values as lipophilic indices are shown by their high correlation with the classical R(Mo) values. In addition, a better correlation was observed between scores corresponding to the first principal components and the partition coefficients (log P) of bile acids. Finally, the "lipophilicity chart" described by the first two components has the effect of separating compounds from each other most effectively from the congeneric aspect point of view.     

脂肪醇气相色谱保留指数与结构的相关性研究

在分子图的邻接矩阵基础上,构建了一个化合物均价连接性指数mL,mL=∑(Ai·Aj·Ak…)-0.5,其中一阶指数1L及定位基参数β与25种脂肪醇在6种固定相(SE-30,OV-3,OV-7,OV-11,OV-17和OV-25)上的气相色谱保留指数I显著相关,相关系数均大于0.98。所建定量结 构-保留关系(QSRR)模型具有良好的稳定性和预测能力,较好地揭示了脂肪醇在不同固定相上气相色谱保留指数的变化规律。     

Residual and exploitable fluorescence in micellar self-assembled ON-OFF sensors for copper(II)

A set of new ligands, L2H(2)-L5H(2), containing the 1,4,8,11-tetraaza-5,7-dione framework has been prepared, The ligands feature lipophilic substituents either on the carbon atom in the 6 position or on the amino groups, or on both. The solution behaviour of the ligands when included in TritonX-100 micelles has been investigated by means of potentiometric titrations and protonation and complexation constants for the Cu(2+) cation have been determined in micellar medium. Micellar assemblies containing the ligands and pyrene have been prepared, and coupled pH-metric and fluorimetric titrations allowed the determination of the response of the systems as ON-OFF fluorescent sensors for Cu(2+). A correlation between the effective lipophilicity of the ligand and the residual fluorescence (i.e. the fluorescence of the OFF state) was observed, and with the more lipophilic ligand, L3H(2), we obtained a residual fluorescence as low as 8%, with a significant improvement with respect to other published systems. On the other hand, introduction of functionalities on the amino groups of 1,4,8,11-tetraaza-5,7-dione brings the drawback of a small but significant decrease of the exploitable fluorescence, i.e. the fluorescence of the system in the absence of added Cu(2+), at the pH value suitable for full metal complexation.     

SYNTHESIS OF POSITIVELY CHARGED PHTHALOCYANINES and THEIR ACTIVITY IN THE PHOTODYNAMIC THERAPY OF CANCER CELLS

Positively charged zinc containing or metal free phthalocyanines 6a-c and 7a-c were prepared via a three step procedure starting from 4-nitrophthalonitrile. The phthalocyanines contain alkyl chains of different length in order to influence the hydrophilic vs lipophilic character of the compounds. The partition between a hydrophilic (water) and lipophilic (octanol-1) phase was determined, and the photoredox activities were investigated. Initial results on the photodynamic activity of these compounds were compared with those of Dougherty's Photofrin II on different malignant and non-malignant cell lines (XP 29MAmal, CX1, HeLa, S180 and NO17). Positively charged phthalocyanines in vitro showed a higher photodynamic activity than Photofrin II.     

Ligand design for heterobimetallic single-chain magnets: synthesis, crystal structures, and magnetic properties of MIICuII (M=Mn, Co) chains with sterically hindered methyl-substituted phenyloxamate bridging ligands

Two new series of neutral oxamato-bridged heterobimetallic chains of general formula [MCu(L(x))(2)] m DMSO (m=0-4) (L(1)=N-2-methylphenyloxamate, M=Mn (1 a) and Co (1 b); L(2)=N-2,6-dimethylphenyloxamate, M=Mn (2 a) and Co (2 b); L(3)=N-2,4,6-trimethylphenyloxamate, M=Mn (3 a) and Co (3 b)) have been prepared by reaction between the corresponding anionic oxamatocopper(II) complexes [Cu(Lx)2](2-) with Mn(2+) or Co(2+) cations in DMSO. The crystal structures of [CoCu(L2)2(H2O)2] (2 b') and [CoCu(L3)2(H2O)2]4 H2O (3 b') have been solved by single-crystal X-ray diffraction methods. Compounds 2 b' and 3 b' adopt zigzag and linear chain structures, respectively. The intrachain Cu...Co distance through the oxamate bridge is 5.296(1) A in 2 b' and 5.301(2) A in 3 b', while the shortest interchain Co...Co distance is 5.995(5) A in 2 b' and 8.702(3) A in 3 b', that is, the chains are well isolated in the crystal lattice due to the presence of the bulky methyl-substituted phenyl groups. Although both Mn(II)Cu(II) and Co(II)Cu(II) chains exhibit ferrimagnetic behaviour with moderately strong intrachain antiferromagnetic coupling (-J(Mn,Cu)=24.7-27.9 cm(-1) and -J(Co,Cu)=35.0-45.8 cm(-1); H= Sigma -J(M,Cu)S(M,i)S(Cu,i)), only the Co(II)Cu(II) chains show slow magnetic relaxation at low temperatures (T(B)<3.5 K), which is characteristic of single-chain magnets (SCMs) because of the high magnetic anisotropy of the Co(II) ion. The blocking temperatures T(B) along this series of chains vary according to the steric hindrance of the aromatic substituent of the oxamate ligand in the series L(1)相似文献