The role of hydrophobic properties of chemicals in promoting allosteric reactions

Mild and efficient synthesis of benzothiazolopyrimidine derivatives via CuAAC/ring cleavage/cyclization reaction

An operationally mild and efficient synthesis of benzothiazolopyrimidine is achieved by a three-component reaction of 2-aminebenzo[d]thiazoles, sulfonyl azides and terminal ynones. This cascade process involved a CuAAC/ring cleavage/cyclization reaction. Particularly, most of the benzothiazolopyrimidine derivatives could be isolated by filtration without further purification.

Outliers in SAR and QSAR: 4. effects of allosteric protein-ligand interactions on the classical quantitative structure-activity relationships

Effects of allosteric interactions on the classical structure-activity relationship (SAR) and quantitative SAR (QSAR) have been investigated. Apprehending the outliers in SAR and QSAR studies can improve the quality, predictability, and use of QSAR in designing unknown compounds in drug discovery research. We explored allosteric protein-ligand interactions as a possible source of outliers in SAR/QSAR. We used glycogen phosphorylase as an example of a protein that has an allosteric site. Examination of the ligand-bound x-ray crystal structures of glycogen phosphorylase revealed that many inhibitors bound at more than one binding site. The results of QSAR analyses of the inhibitors included a QSAR that recognized an outlier bound at a distinctive allosteric binding site. The case provided an example of constructive use of QSAR identifying outliers with alternative binding modes. Other allosteric QSARs that captured our attention were the inverted parabola/bilinear QSARs. The x-ray crystal structures and the QSAR analyses indicated that the inverted parabola QSARs could be associated with the conformational changes in the allosteric interactions. Our results showed that the normal parabola, as well as the inverted parabola QSARs, can describe the allosteric interactions. Examination of the ligand-bound X-ray crystal structures of glycogen phosphorylase revealed that many inhibitors bound at more than one binding site. The results of QSAR analyses of the inhibitors included a QSAR that recognized an outlier bound at a distinctive allosteric binding site.

Understanding tubulin/microtubule-taxane interactions: a quantitative structure-activity relationship study

For years, the microtubule-stabilizing agents paclitaxel and docetaxel (progenitors of the family of taxanes) have been the most successful anticancer drugs currently used in clinics. However, both drugs are associated with notorious side effects, drug resistance, and cross resistance with other chemotherapeutic agents. These limitations have led to the search for new drugs with improved biological activity. In the present paper, we discuss the interaction of taxanes with the tubulin/microtubule system by the formulation of 6 QSARs. Hydrophobicity of the substituents (pi) is found to be one of the most important determinants of the activity followed by steric parameters. Parabolic correlations (eqs 3 and 7) with B5 and pi are the most encouraging examples, where the optimum values of these parameters are well defined. We believe that these two QSARs may prove to be adequate predictive models that can help to provide guidance in design/synthesis and subsequently yield very specific compounds (IV and VIII) that may have high biological activities. On the basis of these two QSARs 3 and 7, 18 compounds (IV-12- IV-22 and VIII-16- VIII-22) are suggested as potential synthetic targets. Cross-validation, quality factor (Q), Fischer statistics (F), and Y-randomization tests have validated all the QSAR models.

Evaluation of electronic, lipophilic and membrane affinity effects on antiproliferative activity of 5-substituted-2-(2,4-dihydroxyphenyl)-1,3,4-thiadiazoles against various human cancer cells

The QSAR studies of 5-substituted-2-(2,4-dihydroxyphenyl)-1,3,4-thiadiazoles set of antiproliferative activity against human cancer cell lines have been performed. Electronic properties of compounds were estimated by the Hartree-Fock method at 6-31G** level. Lipophilicity and membrane affinity parameters were determined by the chromatographic methods RP-8 OPLC and IAM HPLC, respectively. Mono- and multivariable regression analyses were performed. The principle factor for determination of activity of compounds is partial charge of nitrogen (q(N3), q(N4)) and carbon (q(C5)) atoms of the 1,3,4-thiadiazole ring. Biological effect is also connected with molar refractivity (CMR) and lipophilicity of derivatives obtained by RP-8 chromatography. The analysis of the QSAR equations for individual cell lines indicates both similarities and differences of electron, steric factors and hydrophobic-hydrophilic character of the analogues of the tested set affecting the antiproliferative activity.

Matrix metalloproteinases (MMPs): chemical-biological functions and (Q)SARs

Matrix metalloproteinases (MMPs) are a large family of calcium-dependent zinc-containing endopeptidases, which are responsible for the tissue remodeling and degradation of the extracellular matrix (ECM), including collagens, elastins, gelatin, matrix glycoproteins, and proteoglycan. They are regulated by hormones, growth factors, and cytokines, and are involved in ovarian functions. MMPs are excreted by a variety of connective tissue and pro-inflammatory cells including fibroblasts, osteoblasts, endothelial cells, macrophages, neutrophils, and lymphocytes. These enzymes are expressed as zymogens, which are subsequently processed by other proteolytic enzymes (such as serine proteases, furin, plasmin, and others) to generate the active forms. Matrix metalloproteinases are considered as promising targets for the treatment of cancer due to their strong involvement in malignant pathologies. Clinical/preclinical studies on MMP inhibition in tumor models brought positive results raising the idea that the development of strategies to inhibit MMPs may be proved to be a powerful tool to fight against cancer. However, the presence of an inherent flexibility in the MMP active-site limits dramatically the accurate modeling of MMP-inhibitor complexes. The interest in the application of quantitative structure-activity relationships (QSARs) has steadily increased in recent decades and we hope it may be useful in elucidating the mechanisms of chemical-biological interactions for this enzyme. In the present review, an attempt has been made to explore the in-depth knowledge from the classification of this enzyme to the clinical trials of their inhibitors. A total number of 92 QSAR models (44 published and 48 new formulated QSAR models) have also been presented to understand the chemical-biological interactions. QSAR results on the inhibition of various compound series against MMP-1, -2, -3, -7, -8, -9, -12, -13, and -14 reveal a number of interesting points. The most important of these are hydrophobicity and molar refractivity, which are the most important determinants of the activity.

Guanidinium derivatives bind preferentially and trigger long-distance conformational changes in an engineered T4 lysozyme

The binding of guanidinium ion has been shown to promote a large-scale translation of a tandemly duplicated helix in an engineered mutant of T4 lysozyme. The guanidinium ion acts as a surrogate for the guanidino group of an arginine side chain. Here we determine whether methyl- and ethylguanidinium provide better mimics. The results show that addition of the hydrophobic moieties to the ligand enhances the binding affinity concomitant with reduction in ligand solubility. Crystallographic analysis confirms that binding of the alternative ligands to the engineered site still drives the large-scale conformational change. Thermal analysis and NMR data show, in comparison to guanidinium, an increase in protein stability and in ligand affinity. This is presumably due to the successive increase in hydrophobicity in going from guanidinium to ethylguanidinium. A fluorescence-based optical method was developed to sense the ligand-triggered helix translation in solution. The results are a first step in the de novo design of a molecular switch that is not related to the normal function of the protein.

A QSAR study on influenza neuraminidase inhibitors

Influenza is a major respiratory infection associated with significant morbidity in the general population and mortality in elderly and high-risk patients. It is an RNA virus that contains two major surface glycoproteins, neuraminidase and hemagglutinin. These proteins are essential for infection. Neuraminidase has been found to be a potential target to control influenza virus. In this paper, we have developed 17 quantitative structure-activity relationships (QSAR) for different sets of compounds to understand chemical-biological interactions governing their activities toward influenza neuraminidase.

A QSAR review on melanoma toxicity

Melanoma is one of the most aggressive forms of skin cancer and is currently attracting our attention particularly in the area of quantitative structure-activity relationships (QSAR). In the present review, an attempt has been made to collect the data for different sets of compounds and to discuss their toxicities toward melanoma cells by the formulation of a total number of 36 QSAR.

An approach toward the problem of outliers in QSAR

Compounds that have unexpected biological activity and are unable to fit in a QSAR model are known as outliers. These are valuable in defining the limitations under which compounds act by a common molecular mechanism modeled by one or more descriptors, and also in defining the experimental limitations of the biological test data. Thus, the outliers should be submitted to particular attention to see if the reason for their peculiarity can be determined. Separating these outliers from the main data set and formulating another QSAR can resolve the problem. Our result shows that these outliers may be acting by a different mechanism or interacting with the receptor in different modes.