Searching for allosteric effects via QSAR. Part II

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.

Novel antibacterial active quinolone-fluoroquinolone conjugates and 2D-QSAR studies

Novel, quinolone-fluoroquinolone conjugates 10a-f, 11a-f, 13a-f and 14a-f with amino acid linkers were synthesized in good yields utilizing benzotriazole chemistry. Antibacterial bioassay showed the synthesized bis-conjugates exhibit anti-bacterial properties comparable with the parent drugs.

Insights into the structure of urea-like compounds as inhibitors of the juvenile hormone epoxide hydrolase (JHEH) of the tobacco hornworm Manduca sexta: analysis of the binding modes and structure-activity relationships of the inhibitors by docking and CoMFA calculations

Substituted urea compounds are well-known as potent inhibitors of juvenile hormone epoxide hydrolase (JHEH) of the tobacco hornworm Manduca sexta. Docking simulations of 47 derivatives inside JHEH were performed to gain insight into the structural characteristics of these complexes. The obtained orientations show a strong similitude with the observed in the known X-ray crystal structures of human soluble epoxide hydrolase (sEH) complexed with dialkylurea inhibitors. In addition, the predicted inhibitor concentration (IC₅₀) of the above-mentioned compounds as JHEH inhibitors were obtained by a quantitative structure-activity relationship (QSAR) method by using comparative molecular field analysis (CoMFA) applied to aligned dataset. The best models included steric and electrostatic fields and had adequate predictive abilities. In addition, these models were used to predict the activity of an external test set of compounds that was not used for building the model. Furthermore, plots of the CoMFA fields allowed conclusions to be drawn for the choice of suitable inhibitors.

Computer-aided drug discovery and development

Computer-aided approaches have been widely used in pharmaceutical research to improve the efficiency of the drug discovery and development pipeline. To identify and design small molecules as clinically effective therapeutics, various computational methods have been evaluated as promising strategies, depending on the purpose and systems of interest. Both ligand and structure-based drug design approaches are powerful technologies, which can be applied to virtual screening for lead identification and optimization. Here, we review the progress in this field and summarize the application of some new technologies we developed. These state-of-the-art tools have been used for the discovery and development of active agents for various diseases, in particular for cancer therapies. The described protocols are appropriate for all drug discovery stages, but expertise is still needed to perform the studies based on the targets of interest.

Dual Allosteric Effect in Glycine/NMDA Receptor Antagonism: A Comparative QSAR Approach

A comparative Hansch type QSAR study was conducted using multiple regression analysis on various sets of quinoxalines, quinoxalin-4-ones, quinazoline-2-carboxylates, 4-hydroxyquinolin-2(1H)-ones, 2-carboxytetrahydroquinolines, phenyl-hydroxy-quinolones, nitroquinolones and 4-substituted-3-phenylquinolin-2(1H)-ones as selective glycine/NMDA site antagonists. Ten statistically validated equations were developed, which indicated the importance of CMR, Verloop’s sterimol L1 and ClogP parameters in contributing towards biological activity. Interestingly, normal and inverse parabolic relationships were found with CMR in different series, indicating a dual allosteric binding mode in glycine/NMDA antagonism. Equations reveal an optimum CMR of 10 ± 10% is required for good potency of antagonists. Other equations indicate the presence of anionic functionality at 4-position of quinoline/quinolone ring system is not absolutely required for effective binding. The observations are laterally validated and in accordance with previous studies.

Discriminant analysis as a tool to identify compounds with potential as transdermal enhancers

Structure-activity relationships were sought for 73 enhancers of hydrocortisone permeation from propylene glycol across hairless mouse skin. Enhancers had chain lengths (CC) from 0 to 16 carbon atoms, 1 to 8 H-bonding atoms (HB), molecular weight 60 to 450, log P (calculated) −1.7 to 9.7 and log S (calculated) −7.8 to 0.7. These predictive properties were chosen because of their ready availability. Enhancement ratio (ER) was defined as hydrocortisone transferred after 24 h relative to control. Values for the ER ranged from 0.2 to 25.3. Multiple regression analysis failed to predict activity; ER values for the ‘good’ enhancers (ER>10) were underestimated. Simple guidelines suggested that high ER was associated with CC>12 and HB 2–5. This was refined by multivariate analysis to identify significant predictors. Discriminant analysis using CC, HB, and molecular weight correctly assigned 11 of the 12 ‘good’ enhancers (92%). The incorrectly assigned compound was a known, idiosyncratic Br compound. Seventeen of the 61 ‘poor’ enhancers (28%) were incorrectly assigned but four could be considered marginal (ER>8). The success of this simple approach in identifying potent enhancers suggested its potential in predicting novel enhancer activity.

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.

The role of hydrophobic properties of chemicals in promoting allosteric reactions

An allosteric reaction has been found in a variety of instances where an inverted parabolic relationship between biological activity and hydrophobicity is apparent, that is the activity first decreases as hydrophobicity increases and after a certain point, activity begins to increase. This could be attributed to the ligands causing a change in the receptor structure. In this report, the role of hydrophobic properties of chemicals in promoting allosteric reactions have been discussed in term of hydrophobicity (logP) by the formulation of a total number of 50 QSAR equations. The QSAR model of this type may be represented by Eq. I.

Understanding topoisomerase I and II in terms of QSAR

A variety of antitumor agents currently used in chemotherapy or evaluated in clinical trials are known to inhibit DNA topoisomerase I or II. We have developed sixteen quantitative structure-activity relationships (QSAR) for different sets of compounds that are camptothecin analogs, 1,4-naphthoquinones, unsaturated acids, benzimidazoles, quinolones, and miscellaneous fused heterocycles to understand chemical-biological interactions governing their inhibitory activities toward topoisomerase I and II.

Synthesis, Biological Activity, and Quantitative Structure−Activity Relationship Study of Azanaphthalimide and Arylnaphthalimide Derivatives

A series of quinoline derivatives as aza analogues of the naphthalene chromophore and a series of "nonfused" tricyclic aromatic systems, in particular 5-arylquinolines and 5- or 6-aryl and heteroaryl naphthalene systems, were synthesized and evaluated for growth-inhibitory properties in several human cell lines. The analysis of quantitative structure-antitumor activity relationships for the growth-inhibitory properties is also reported. Findings suggest that these compounds may not express their cytotoxicity via interaction on DNA.