Improved Lipophilicity and Aqueous Solubility Prediction with Composite Graph Neural Networks

The accurate prediction of molecular properties, such as lipophilicity and aqueous solubility, are of great importance and pose challenges in several stages of the drug discovery pipeline. Machine learning methods, such as graph-based neural networks (GNNs), have shown exceptionally good performance in predicting these properties. In this work, we introduce a novel GNN architecture, called directed edge graph isomorphism network (D-GIN). It is composed of two distinct sub-architectures (D-MPNN, GIN) and achieves an improvement in accuracy over its sub-architectures employing various learning, and featurization strategies. We argue that combining models with different key aspects help make graph neural networks deeper and simultaneously increase their predictive power. Furthermore, we address current limitations in assessment of deep-learning models, namely, comparison of single training run performance metrics, and offer a more robust solution.     

A Comparative Study of the Lipophilicity of Metformin and Phenformin

The results presented in this paper confirm the beneficial role of an easy-to-use and low-cost thin-layer chromatography (TLC) technique for describing the retention behavior and the experimental lipophilicity parameter of two biguanide derivatives, metformin and phenformin, in both normal-phase (NP) and reversed-phase (RP) TLC systems. The retention parameters (R_F, R_M) obtained under different chromatographic conditions, i.e., various stationary and mobile phases in the NP-TLC and RP-TLC systems, were used to determine the lipophilicity parameter (R_MW) of metformin and phenformin. This study confirms the poor lipophilicity of both metformin and phenformin. It can be stated that the optimization of chromatographic conditions, i.e., the kind of stationary phase and the composition of mobile phase, was needed to obtain the reliable value of the chromatographic lipophilicity parameter (R_MW) in this study. The fewer differences in the R_MW values of both biguanide derivatives were ensured by the RP-TLC system composed of RP2, RP18, and RP18W plates and the mixture composed of methanol, propan-1-ol, and acetonitrile as an organic modifier compared to the NP-TLC analysis. The new calculation procedures for logP of drugs based on topological indices ⁰χ^ν, ⁰χ, ¹χ^ν, M, and M^ν may be a certain alternative to other algorithms as well as the TLC procedure performed under optimized chromatographic conditions. The knowledge of different lipophilicity parameters of the studied biguanides can be useful in the future design of novel and more therapeutically effective metformin and phenformin formulations for antidiabetic and possible anticancer treatment. Moreover, the topological indices presented in this work may be further used in the QSAR study of the examined biguanides.     

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.     

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.     

Experimental Examination of Solubility and Lipophilicity as Pharmaceutically Relevant Points of Novel Bioactive Hybrid Compounds

The important physicochemical properties of three novel bioactive hybrid compounds with different groups (-CH₃, -F and -Cl) were studied, including kinetic and thermodynamic solubility in pharmaceutically relevant solvents (buffer solutions and 1-octanol) as well as partition coefficient in system 1-octanol/buffer pH 7.4. The aqueous solubility of these chemicals is poor and ranged from 0.67 × 10⁻⁴ to 1.98 × 10⁻³ mol·L⁻¹. The compounds studied are more soluble in the buffer pH 2.0, simulating the gastrointestinal tract environment (by an order of magnitude) than in the buffer pH 7.4 modelling plasma of blood. The solubility in 1-octanol is significantly higher; that is because of the specific interactions of the compounds with the solvent. The prediction solubility behaviour of the hybrid compounds using Hansen’s three-parameter approach showed acceptable results. The experimental solubility of potential drugs was successfully correlated by means of two commonly known equations: modified Apelblat and van’t Hoff. The temperature dependencies of partition coefficients of new hybrids in the model system 1-octanol/buffer pH 7.4 as a surrogate lipophilicity were measured by the shake flask method. It was found that compounds demonstrated a lipophilic nature and have optimal values of partition coefficients for oral absorption. Bioactive assay manifested that prepared compounds showed antifungal activities equal to or greater than fluconazole. In addition, the thermodynamic aspects of dissolution and partition processes have been examined. Bioactive assay manifested that prepared compounds showed antifungal activities equal to or greater than the reference drug.     

柚皮素三乙胺盐一水合物的制备、晶体结构及溶解度

柚皮素是一种天然黄酮类化合物,几乎不溶于水。利用晶体工程学原理可以有效改善天然产物的溶解性。本文合成了柚皮素和三乙胺的有机盐一水合物[C_(15)H_(11)O_5]-·[C_6H_(16)N]+·H_2O,测定了其晶体结构。解析结果表明,有机盐水合物属于单斜晶系,P2_1/n空间群。柚皮素7取代位的羟基上的质子转移到了三乙胺的N原子上,并形成了N~+—H....O~-氢键。羟基阴离子与4'取代位上的羟基形成了O—H....O~-氢键,产生了一维的氢键链状结构。水分子通过两种氢键作用将一维的氢键链连接成二维的氢键网络。形成三乙胺盐一水合物后,柚皮素在水中的溶解度增加了20倍。     

Lipophilicity analysis of newly synthetized quinobenzothiazines by use of TLC

Lipophilicity is a very important property of chemical compound taking into consideration in drugs design. Relationships between biological activity, among others lipophilicity, and chemical structure (QSAR) of the compound are very often used by researches. Especially important is the kind of substituents connected to the basic structural fragment and how it changes the lipophilicity of the compound. The aim of this study was to determine the parameters of lipophilicity of quinobenzothiazine derivatives using reversed phase - thin-layer chromatography (RP-TLC), which would enable one to determine the structure–activity relationship. The objective of our work is a series of 15 newly synthetized quinobenzothiazines. They were analyzed by thin-layer chromatography (TLC) with the use of two different mobile phases consisting of methanol or acetone as organic modifiers. For all compounds investigated, the values of lipophilicity obtained from computational method were also determined. Cluster analysis was carried out too for all data of lipophilicity obtained. Low correlation was found between values of experimental lipophilicity and lipophilicity from computational methods for newly synthetized compounds.     

Modeling of Anticancer Sulfonamide Derivatives Lipophilicity by Chemometric and Quantitative Structure-Retention Relationships Approaches

Sulfonamides are a classic group of chemotherapeutic drugs with a broad spectrum of pharmacological action, including anticancer activity. In this work, reversed-phase high-performance liquid chromatography and biomimetic chromatography were applied to characterize the lipophilicity of sulfonamide derivatives with proven anticancer activities against human colon cancer. Chromatographically determined lipophilicity parameters were compared with obtained logP, employing various computational approaches. Similarities and dissimilarities between experimental and computational logP were studied using principal component analysis, cluster analysis, and the sum of ranking differences. Furthermore, quantitative structure–retention relationship modeling was applied to understand the influences of sulfonamide’s molecular properties on lipophilicity and affinity to phospholipids.     

几类醚化物的水溶性、碱水溶解性和酸解活性

本文对几类典型醚类化合物的水溶性、碱水(5%的Na₂SiO₃·9H₂O)溶解性和酸解活性进行了初步研究,查阅了这些醚类化合物的水溶性,并测定了其碱水溶解性、临界碱水不可溶醚当量以及在微量酸存在条件下的酸解活性,研究结果表明,对一般醚类化合物而言,当醚键中不含p-π共轭时其临界水不溶醚当量为116,临界碱水不溶醚当量为102;当醚键中含p-π共轭时其临界水不溶醚当量在56-100之间,临界碱水不溶醚当量在56-72之间,这些数据对光/热成像用活性醚化物阻溶/促溶剂的分子设计以及碱显影成像制版具有重大的指导意义。     

杯芳烃构象的分子力学研究

杯芳烃是对位取代的苯酚与甲醛反应得到的环状缩合物,由于其独特的结构和易于衍生化的特点而受到广泛的关注［１］．杯芳烃中苯酚单元由亚甲基相连,由于酚羟基端可经杯中央翻转而产生多种构象异构体．杯［４］芳烃有４种典型构象：杯式、部分杯式、１,２－交替式和１,...     

Solubility Determination,Hansen Solubility Parameters and Thermodynamic Evaluation of Thymoquinone in (Isopropanol + Water) Compositions

This article studies the solubility, Hansen solubility parameters (HSPs), and thermodynamic behavior of a naturally-derived bioactive thymoquinone (TQ) in different binary combinations of isopropanol (IPA) and water (H₂O). The mole fraction solubilities (x₃) of TQ in various (IPA + H₂O) compositions are measured at 298.2–318.2 K and 0.1 MPa. The HSPs of TQ, neat IPA, neat H₂O, and binary (IPA + H₂O) compositions free of TQ are also determined. The x₃ data of TQ are regressed by van’t Hoff, Apelblat, Yalkowsky–Roseman, Buchowski–Ksiazczak λh, Jouyban–Acree, and Jouyban–Acree–van’t Hoff models. The maximum and minimum x₃ values of TQ are recorded in neat IPA (7.63 × 10⁻² at 318.2 K) and neat H₂O (8.25 × 10⁻⁵ at 298.2 K), respectively. The solubility of TQ is recorded as increasing with the rise in temperature and IPA mass fraction in all (IPA + H₂O) mixtures, including pure IPA and pure H₂O. The HSP of TQ is similar to that of pure IPA, suggesting the great potential of IPA in TQ solubilization. The maximum molecular solute-solvent interactions are found in TQ-IPA compared to TQ-H₂O. A thermodynamic study indicates an endothermic and entropy-driven dissolution of TQ in all (IPA + H₂O) mixtures, including pure IPA and pure H₂O.     

Crystal Structure and Chemical Reactivity of Heme Phenoxide Adducts

Abstract

A simple phenoxide heme compound has been fully structurally characterized for the first time. The crystal structure of a 2,6-dichlorophenoxy Fe(III) 5,10,15,20-tetraphenylporphyrin is reported and compared with the structure of simple aliphatic alkoxy aducts of Fe(III) porphyrins. It is further shown that phenoxy Fe porphyrins can promote regiospecific substitution (cyanation) of the bound phenol ring.     

Electronic Structure,Molecular Conformation and Reactivity of Benzonorbornadiene Systems

From the photoelectron spectra of benzonorbornadiene ( 1 ) and its 9-isopropylidene derivative ( 2 ) the energy and an approximate wave function for the highest occupied orbitals is obtained. With these results the differential reactivity of the systems in Diels-Alder additions with ‘inverse electron demand’ is discussed on the basis of frontier orbitals. For the ground state of 2 similar non-bonded interactions between the isopropylidene unit and the double bond or the benzene ring are indicated. Conformational equilibria in 9-aza derivatives of 1 are discussed in view of these findings.     

Improvement in Aqueous Solubility of Retinoic Acid Receptor (RAR) Agonists by Bending the Molecular Structure

Aqueous solubility is a key requirement for many functional molecules, e. g., drug candidates. Decrease of the partition coefficient (log P) by chemical modification, i.e., introduction of hydrophilic group(s) into molecules, is a classical strategy for improving aqueous solubility. We have been investigating alternative strategies for improving the aqueous solubility of pharmaceutical compounds by disrupting intermolecular interactions. Here, we show that introducing a bend into the molecular structure of retinoic acid receptor (RAR) agonists by changing the substitution pattern from para to meta or ortho dramatically enhances aqueous solubility by up to 890‐fold. We found that meta analogs exhibit similar hydrophobicity to the parent para compound, and have lower melting points, supporting the idea that the increase of aqueous solubility was due to decreased intermolecular interactions in the solid state as a result of the structural changes.     

Phase Solubility Analysis of Some Organophosphate Pesticides

Abstract

Phase solubility analysis (PSA) was applied to the determination of azinphos-ethyl and - methyl standards. The presence of 0.5% purity was detected by the method. A linear cumulative effect was obtained when known amounts of two impurities were added to standards of both organophosphate materials which were then analyzed by the phase solubility method.     

Theoretical Study of Molecular Structure, Tautomerism, and Geometrical Isomerism of N-Methyl- and N-Phenyl-Substituted Cyclic Imidazolines, Oxazolines, and Thiazolines

The geometries of various tautomers and isomers of 2-methylamino-2-imidazoline, 2-methylamino-2-oxazoline, 2-methylamino-2-thiazoline, 2-phenylamino-2-imidazoline, 2-phenylamino-2-oxazoline, and 2-phenylamino-2-thiazoline have been studied using the Becke3LYP/6–31+G(d,p) DFT, ONIOM(Becke3LYP/6–31+G(d,p):HF/3–21G^*) and ONIOM(Becke3LYP/6–31+G(d,p):AM1) methods. The optimized geometries indicate that these molecules show a distinctly nonplanar configuration of the cyclic moieties. In the gas phase, the amino tautomers (with exception of 2-phenylamino-2-imidazoline) are computed to be more stable than the imino tautomers. Of the two possible (E and Z) isomers of methyl and phenyl derivatives of imino-oxazolidine and imino-thiazolidine species, the (Z) isomers have the lowest energy. The iminozation free energies in the gas phase were found to be 5 – 15 kJ/mol. Absolute values of K _T depend strongly on the accuracy of the method used for calculation of free energy. Solvation (using the MD simulations) causes, in most cases, a shift in tautomeric preference toward the imino species.     

Theoretical Study of the Structural Stability,Chemical Reactivity,and Protein Interaction for NMP Compounds as Modulators of the Endocannabinoid System

The cannabinoid receptors (CB1/CB2) and the T-type calcium channels are involved in disorders associated with both physiological pain and depressive behaviors. Valuable pharmacological species carbazole derivatives such as the NMP-4, NMP-7, and NMP-181 (Neuro Molecular Production) regulate both biological entities. In this work, DFT calculations were performed to characterize theoretically their structural and chemical reactivity properties using the BP86/cc-pVTZ level of theory. The molecular orbital contributions and the chemical reactivity analysis reveal that a major participation of the carbazole group is in the donor-acceptor interactions of the NMP compounds. The DFT analysis on the NMP compounds provides insights into the relevant functional groups involved during the ligand-receptor interactions. Molecular docking analysis is used to reveal possible sites of interaction of the NMP compounds with the Ca_v3.2 calcium channel. The interaction energy values and reported experimental evidence indicate that the site denominated as “Pore-blocking”, which is formed mainly by hydrophobic residues and the T586 residue, is a probable binding site for the NMP compounds.     

药物水溶解度的QSAR研究和VolSurf参数

药物的水溶解度与其吸收密切相关。本文利用一种新的计算方法,VolSurf,预测药物的水溶解度并测定有利于药物水溶解度的主要分子特征。被测化合物包括26个结构不同的药物,通过偏最小二乘分析法,对药物水溶解度实验值与分子特征进行相关,得到较好的模型(r2=0.90,q2=0.77)。将化合物分为训练集和预测集进行相关分析,结果表明以18个化合物所建立的训练集模型对其余8个化合物有较好的预测能力,预测的标准偏差(SDEP)为0.59。参数分析表明分子与水相互作用的3个局部能量最小值越小,且它们之间的距离越大,对其水溶解度越有利;亲水性占主导因素的分子有高的水溶解度;分子的疏水性越强,在水中的溶解性越弱;大分子的溶解度较小分子溶解度低。