DFT‐based QSAR study and molecular design of AHMA derivatives as potent anticancer agents

A quantitative structure–activity relationship (QSAR) of 3‐(9‐acridinylamino)‐5‐hydroxymethylaniline (AHMA) derivatives and their alkylcarbamates as potent anticancer agents has been studied using density functional theory (DFT), molecular mechanics (MM+), and statistical methods. In the best established QSAR equation, the energy (E_NL) of the next lowest unoccupied molecular orbital (NLUMO) and the net charges (Q_FR) of the first atom of the substituent R, as well as the steric parameter (MR₂) of subsituent R₂ are the main independent factors contributing to the anticancer activity of the compounds. A new scheme determining outliers by “leave‐one‐out” (LOO) cross‐validation coefficient (q) was suggested and successfully used. The fitting correlation coefficient (R²) and the “LOO” cross‐validation coefficient (q²) values for the training set of 25 compounds are 0.881 and 0.829, respectively. The predicted activities of 5 compounds in the test set using this QSAR model are in good agreement with their experimental values, indicating that this model has excellent predictive ability. Based on the established QSAR equation, 10 new compounds with rather high anticancer activity much greater than that of 34 compounds have been designed and await experimental verification. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Theoretical studies on QSAR and mechanism of 2‐indolinone derivatives as tubulin inhibitors

The theoretical studies on three‐dimensional quantitative structure activity relationship (3D‐QSAR) and action mechanism of a series of 2‐indolinone derivatives as tubulin inhibitors against human breast cancer cell line MDA‐MB‐231 have been carried out. The established 3D‐QSAR model from the comparative molecular field analysis (CoMFA) shows not only significant statistical quality but also predictive ability, with high correlation coefficient (R² = 0.986) and cross‐validation coefficient (q² = 0.683). In particular, the appropriate binding orientations and conformations of these 2‐indolinone derivatives interacting with tubulin are located by docking study, and it is very interesting to find that the plot of the energy scores of these compounds in DOCK versus the corresponding experimental pIC₅₀ values exhibits a considerable linear correlation. Therefore, the inhibition mechanism that 2‐indolinone derivatives were regarded as tubulin inhibitors can be theoretically confirmed. Based on such an inhibition mechanism along with 3D‐QSAR results, some important factors improving the activities of these compounds were discussed in detail. These factors can be summarized as follows: the H atom adopted as substituent R₁, the substituent R₂ with higher electropositivity and smaller bulk, the substituents R₄–R₆ (on the phenyl ring) with higher electropositivity and larger bulk, and so on. These results can offer useful theoretical references for understanding the action mechanism, designing more potent inhibitors, and predicting their activities prior to synthesis. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

The ambident electrophilic behavior of 5‐nitro‐3‐X‐thiophenes in σ‐complexation processes

Kinetics of the reactions of 3,5‐dinitrothiophene 1 and 3‐cyano‐5‐nitrothiophene 2 with a series of parasubstituted phenoxide anions 3a–c have been investigated in aqueous solution at 20°C. Two unsubstituted electrophilic centers (C(2) and C(4)) of the two thiophenes have been identified. The Fukui functions correctly predict the C(2) and C(4) atoms as the most electrophilic centers of these electron‐deficient thiophenes 1 and 2 . Analysis of the experimental data in terms of Brønsted relationships reveals that the reaction mechanism likely involves a single‐electron transfer (SET) process. The excellent correlations upon plotting the rate constants versus the oxidation potentials E^o values is an additional evidence that reactions between thiophenes and phenoxide anions are proceeding through an initial electron transfer. It is of particular interest to note that the systems studied in this paper provide a rare example of a SET mechanism in σ‐complexation reactions. According to the free energy relationship log k = s(N + E) (Angew. Chem., Int. Ed. Engl., 1994, 33, 938–957), the electrophilicity parameters E of the C‐4 and C‐2 positions of the thiophenes have been determined and compared with the reactivities of other ambident electrophiles. On the other hand, the second‐order rate constants for the reactions of these thiophenes with the hydroxide ion has been measured in water and 50% water–50% acetonitrile and found to agree with those calculated theoretically using Mayr's equation from the E values determined in this work and from the previously published N and s parameters of OH⁻.     

Cationic Poly([R]‐3‐hydroxybutyrate) Copolymers as Antimicrobial Agents

Poly([R]‐3‐hydroxybutyrate) (PHB), a natural biodegradable polyester, has attracted much attention as a new biomaterial because of its sustainability and good biocompatibility. In this study, it is discovered that PHB can be conveniently functionalized to obtain a number of platform chain architectures that may provide a wide range of functional copolymers. In a transesterification reaction, linear (di‐hydroxylated) and star shaped (tri‐ and tetra‐hydroxylated) PHB oligomers are synthesized, followed by copolymerization with 2‐(dimethylamino)ethyl methacrylate and quaternization with benzyl bromide to afford antimicrobial properties. The antimicrobial activities of the quaternary salts against clinically relevant pathogens on the interactions with outer and cytoplasmic membranes, lethal mechanisms, multipassage resistance, and synergy effect with antibiotics are investigated. Cationic PHB copolymers show effectiveness as antimicrobial agents, with minimum inhibitory concentration values 0.24–0.65 µm (or µmol dm^?3) (or 32–128 µg mL^?1) against Gram‐positive and Gram‐negative bacteria. Modifying the copolymer architectures into star shapes results in enhanced effectiveness to disrupt the membrane integrity. Synergistic effects are attained for all the quaternized PHB derivatives when they are used together with tobramycin. Multipassage resistance does not occur in both the linear and star derivatives against Gram‐negative bacteria after 20 passages.     

An alignment‐free methodology for modelling field‐based 3D‐structure activity relationships using inductive logic programming

Traditional 3D‐quantitative structure–activity relationship (QSAR)/structure–activity relationship (SAR) methodologies are sensitive to the quality of an alignment step which is required to make molecular structures comparable. Even though many methods have been proposed to solve this problem, they often result in a loss of model interpretability. The requirement of alignment is a restriction imposed by traditional regression methods due to their failure to represent relations between data objects directly. Inductive logic programming (ILP) is a class of machine‐learning methods able to describe relational data directly. We propose a new methodology which is aimed at using the richness in molecular interaction fields (MIFs) without being restricted by any alignment procedure. A set of MIFs is computed and further compressed by finding their minima corresponding to the sites of strongest interaction between a molecule and the applied test probe. ILP uses these minima to build easily interpretable rules about activity expressed as pharmacophore rules in the powerful language of first‐order logic. We use a set of previously published inhibitors of factor Xa of the benzamidine family to discuss the problems, requirements and advantages of the new methodology. Copyright © 2007 John Wiley & Sons, Ltd.     

A Facile Synthesis of New 4,6‐Dichloropyridine Derivatives,Their Biological Evaluation for Antimicrobial and Antioxidant Activity,and Docking Studies

A facile synthesis of new 4,6‐dichloropyridine derivatives 5 ( a–f ), 6 ( a–c ), and 7 ( a–c ) were synthesized using both conventional heating and solvent‐free microwave irradiation techniques. The results revealed that the latter method is superior to the conventional heating method. The easy work‐up of the products, rapid reaction, and mild conditions are noticeable features of this protocol. Structural elucidation of the synthesized compounds was made on the basis of various spectroscopic methods. The synthesized compounds were evaluated for their in vitro antimicrobial activity (minimum inhibitory concentration; MIC) against various microbial strains using the agar well‐diffusion method. Among the compounds, 5c showed best antimicrobial activity against most of the employed strains, especially against Staphylococcus aureus, Escherichia coli, Rhizopus arrhizus, and Candida albicans. Compounds 5a , 6a , 6c , 7a , and 7c showed significant antioxidant activity when compared to the other compounds. In addition to this, theoretical docking studies were performed for the highly potent compounds 5a , 6a , 6c , 7a , and 7c against three different drug targets belonging to the oxidoreductase family, and the results were found to be highly satisfactory.     

Reactivity Controlling Factors for an Aromatic Carbon‐Centered σ,σ,σ‐Triradical: The 4,5,8‐Tridehydroisoquinolinium Ion

The chemical properties of the 4,5,8‐tridehydroisoquinolinium ion (doublet ground state) and related mono‐ and biradicals were examined in the gas phase in a dual‐cell Fourier‐transform ion cyclotron resonance (FT‐ICR) mass spectrometer. The triradical abstracted three hydrogen atoms in a consecutive manner from tetrahydrofuran (THF) and cyclohexane molecules; this demonstrates the presence of three reactive radical sites in this molecule. The high (calculated) electron affinity (EA=6.06 eV) at the radical sites makes the triradical more reactive than two related monoradicals, the 5‐ and 8‐dehydroisoquinolinium ions (EA=4.87 and 5.06 eV, respectively), the reactivity of which is controlled predominantly by polar effects. Calculated triradical stabilization energies predict that the most reactive radical site in the triradical is not position C4, as expected based on the high EA of this radical site, but instead position C5. The latter radical site actually destabilizes the 4,8‐biradical moiety, which is singlet coupled. Indeed, experimental reactivity studies show that the radical site at C5 reacts first. This explains why the triradical is not more reactive than the 4‐dehydroisoquinolinium ion because the C5 site is the intrinsically least reactive of the three radical sites due to its low EA. Although both EA and spin–spin coupling play major roles in controlling the overall reactivity of the triradical, spin–spin coupling determines the relative reactivity of the three radical sites.     

马来酰亚胺类GSK-3β抑制剂的QSAR研究及分子设计

为了研究马来酰亚胺类化合物抑制活性与分子结构的定量构效关系,在分子理论的基础上计算了67个马来酰亚胺类化合物的电性距离矢量,通过最佳变量子集回归的方法,建立了抑制活性的五元线性回归模型,模型的传统相关系数(R2)和交叉验证相关系数(RCV2)分别为0.864和0.825.该模型经过Jackknife法检验、交叉验证、F检验及外部检验法证明具有良好的稳健性和预测能力.根据进入模型的5个变量分析,影响马来酰亚胺类GSK-3β抑制剂抑制活性的主要结构基团是-NH-,=O(或-OH),≡CH,Cl-及-O-(或-S-).同时基于QSAR模型设计了6个抑制活性显著提高的马来酰亚胺类分子,并预测了它们的抑制活性.     

An Optimised Small‐Molecule Stabiliser of the 14‐3‐3–PMA2 Protein–Protein Interaction

Modulation of protein–protein interactions (PPIs) is a highly demanding, but also a very promising approach in chemical biology and targeted drug discovery. In contrast to inhibiting PPIs with small, chemically tractable molecules, stabilisation of these interactions can only be achieved with complex natural products, like rapamycin, FK506, taxol, forskolin, brefeldin and fusicoccin. Fusicoccin stabilises the activatory complex of the plant H⁺‐ATPase PMA2 and 14‐3‐3 proteins. Recently, we have shown that the stabilising effect of fusicoccin could be mimicked by a trisubstituted pyrrolinone (pyrrolidone1, 1 ). Here, we report the synthesis, functional activity and crystal structure of derivatives of 1 that stabilise the 14‐3‐3–PMA2 complex. With a limited compound collection three modifications that are important for activity enhancement could be determined: 1) conversion of the pyrrolinone scaffold into a pyrazole, 2) introduction of a tetrazole moiety to the phenyl ring that contacts PMA2, and 3) addition of a bromine to the phenyl ring that exclusively contacts the 14‐3‐3 protein. The crystal structure of a pyrazole derivative of 1 in complex with 14‐3‐3 and PMA2 revealed that the more rigid core of this molecule positions the stabiliser deeper into the rim of the interface, enlarging especially the contact surface to PMA2. Combination of the aforementioned features gave rise to a molecule ( 37 ) that displays a threefold increase in stabilising the 14‐3‐3–PMA2 complex over 1 . Compound 37 and the other active derivatives show no effect on two other important 14‐3‐3 protein–protein interactions, that is, with CRaf and p53. This is the first study that describes the successful optimisation of a PPI stabiliser identified by screening.     

Carbohydrate Chain of Ganglioside GM1 as a Ligand: Identification of the Binding Strategies of Three 15 mer Peptides and Their Divergence from the Binding Modes of Growth‐Regulatory Galectin‐1 and Cholera Toxin

The branched pentasaccharide chain of ganglioside GM₁ is a prominent cell surface ligand, for example, for cholera toxin or tumor growth‐regulatory homodimeric galectins. This activity profile via protein recognition prompted us to examine the binding properties of peptides with this specificity. Our study provides insights into the mechanism of molecular interaction of this thus far unexplored size limit of the protein part. We used three pentadecapeptides in a combined approach of mass spectrometry, NMR spectroscopy and molecular modelling to analyze the ligand binding in solution. Availability of charged and hydrophobic functionalities affected the intramolecular flexibility of the peptides differently. Backfolding led to restrictions in two cases; the flexibility was not reduced significantly by association of the ligand in its energetically privileged conformations. Major contributions to the interaction energy arise from the sialic acid moiety contacting Arg/Lys residues and the N‐terminal charge. Considerable involvement of stacking between the monovalent ligand and aromatic rings could not be detected. This carbohydrate binding strategy is similar to how an adenoviral fiber knob targets sialylated glycans. Rational manipulation for an affinity enhancement can now be directed to reduce the flexibility, exploit the potential for stacking and acquire the cross‐linking capacity of the natural lectins by peptide attachment to a suitable scaffold.     

3D‐QSAR studies and molecular design on a novel series of pyrimidine benzimidazoles as Lck inhibitors

The development of selective lymphocyte‐specific kinase (Lck) inhibitors has attracted much attention for the research of the treatment of T‐cell mediated autoimmune and inflammatory diseases. In the present work, three‐dimensional quantitative structure–activity relationship (3D‐QSAR) analyses are performed on a novel series of 4‐amino‐6‐benzimidazole‐pyrimidines acting as Lck inhibitors. The established 3D‐QSAR models show significant statistical quality and satisfactory predictive ability, with high q² and R² values: the comparative molecular field analysis (CoMFA) model (q² = 0.802, R² = 0.991), and the comparative molecular similarity indexes analysis (CoMSIA) model (q² = 0.731, R² = 0.982). The systemic external validation indicates that both CoMFA and CoMSIA models are quite robust and possess high predictive abilities with values of 0.881 and 0.877, values of 0.897 and 0.847, values of 0.897 and 0.850, and values of 0.897 and 0.854, respectively. Several key structural features accounting for the inhibitory activities of these compounds are discussed. Based on established models and design considerations, six new compounds with significantly improved activities are theoretically designed, which still await experimental confirmation and evaluation. These theoretical results may provide a useful reference for understanding the action mechanism and designing novel potential Lck inhibitors. © 2014 Wiley Periodicals, Inc.     

4‐Aryl‐3,5‐bis(arylethynyl)aryl‐4H‐1,2,4‐triazoles: Multitasking Skeleton as a Self‐Assembling Unit

The synthesis of a series of 4‐aryl‐3,5‐bis(arylethynyl)aryl‐4H‐1,2,4‐triazoles derivatives is reported and the influence exerted by peripheral substitution on the morphology of the aggregates generated from these 1,2,4‐triazoles is investigated by SEM imaging. The presence of paraffinic side chains results in long fibrillar supramolecular structures, but unsubstituted triazoles self‐assemble into thinner ribbons and needle‐like aggregates. The crystals obtained from methoxy‐substituted triazoles have been utilised to elaborate a model that helps to justify aggregation of the investigated 1,2,4‐triazoles, in which the operation of arrays of C?H???π non‐covalent interactions plays a significant role. The results presented herein demonstrate the ability of simple molecules to behave as multitasking scaffolds with different properties, depending on peripheral substitution. Thus, although 1,2,4‐triazoles without long paraffinic side chains exhibit optical waveguiding behaviour, triazoles endowed with peripheral paraffinic side chains exhibit hexagonal columnar mesomorphism.     

Energetic N‐Nitramino/N‐Oxyl‐Functionalized Pyrazoles with Versatile π–π Stacking: Structure–Property Relationships of High‐Performance Energetic Materials

N‐Nitramino/N‐oxyl functionalization strategies were employed to investigate structure–property relationships of energetic materials. Based on single‐crystal diffraction data, π–π stacking of pyrazole backbones can be tailored effectively by energetic functionalities, thereby resulting in diversified energetic compounds. Among them, hydroxylammonium 4‐amino‐3,5‐dinitro‐1H‐pyrazol‐1‐olate and dipotassium N,N′‐(3,5‐dinitro‐1H‐pyrazol‐1,4‐diyl)dinitramidate, with unique face‐to‐face π–π stacking, can be potentially used as a high‐performance explosive and an energetic oxidizer, respectively.     

Estimating the lipophilicity of a number of 2‐amino‐1‐cyclohexanol derivatives exhibiting anticonvulsant activity

The lipophilicity of a number of N‐acyl derivatives of trans‐ or cis‐: racemic, (1R,2R)‐ or (1S,2S)‐aminocyclohexanol (1–13) exhibiting anticonvulsant activity was investigated. Their lipophilicity (R_{m 0}) was determined using reversed‐phase thin‐layer chromatography (RP‐TLC) with mixtures of methanol and water as mobile phases. The partition coefficients of compounds 1–13 (log P) were also calculated using two computer programs (Pallas and Chem DU) and compared with R_{m 0}. Copyright © 2009 John Wiley & Sons, Ltd.