Mechanistic interpretation of the genotoxicity of nitrofurans (antibacterial agents) using quantitative structure-activity relationships and comparative molecular field analysis

In silico prediction of the mutagenicity of nitroaromatic compounds using a novel two-QSAR approach

Certain drugs are nitroaromatic compounds, which are potentially toxic. As such, it is of practical importance to assess and predict their mutagenic potency in the process of drug discovery. A classical quantitative structure-activity relationship (QSAR) model was developed using the linear partial least square (PLS) scheme to understand the underline mutagenic mechanism and a non-classical QSAR model was derived using the machine learning-based hierarchical support vector regression (HSVR) to predict the mutagenicity of nitroaromatic compounds based on a series of mutagenicity data (TA98-S9). It was observed that HSVR performed better than PLS as manifested by the predictions of the samples in the training set, test set, and outlier set as well as various statistical validations. A mock test designated to mimic real challenges also confirmed the better performance of HSVR. Furthermore, HSVR exhibited superiority in predictivity, generalization capabilities, consistent performance, and robustness when compared with various published predictive models. PLS, conversely, revealed some mechanistically interpretable relationships between descriptors and mutagenicity. Thus, this two-QSAR approach using the predictive HSVR and interpretable PLS models in a synergistic fashion can be adopted to facilitate drug discovery and development by designing safer drug candidates with nitroaromatic moiety.

Copper/P(tBu)3 -Mediated Regiospecific Synthesis of Fused Furans and Naphthofurans

A novel [3+2] cycloaddition between a variety of cyclic ketones and diverse olefins or alkynes can be effectively promoted by copper in combination with the tri-tert-butylphosphine [P(tBu)₃ ] ligand. This protocol exhibits excellent selectivity and provides an exemplary set of fused heterocycles in good to excellent yields. Present strategy also represents an extremely simple and atom-economic way to construct substituted fused furans and naphthofurans from readily available starting materials under mild reaction conditions. The utility of the method is further demonstrated by the synthesis of chiral furans from (R)-(-)-carvone and (S)-(+)-carvone. A plausible mechanism involving the oxidative radical cyclization has been suggested based on experimental observations.

Facile synthesis of benzoindoles and naphthofurans through carbonaceous material-catalyzed cyclization of naphthylamines/naphthols with nitroolefins in water

A facile and efficient approach has been established for the synthesis of benzoindole and naphthofuran derivatives via the metal-free cyclization reaction of nitroolefins with naphthylamines/naphthols.

Four-component reaction between naphthols, substituted β-nitrostyrenes, substituted benzaldehydes and ammonium acetate in water–PEG-400: an approach to construct polysubstituted naphthofuranamines

The diversity-oriented synthesis of naphtho[b]furans via a four-component reaction between naphthanols, substituted β-nitrostyrenes, substituted benzaldehydes and ammonium acetate has been developed.

Crystal structure of 7-bromo-2-(3-fluorophenyl)-1-(methylsulfinyl)naphtho[2,1-b]furan

In the title compound, C₁₉H₁₁BrFO₂S, the dihedral angle between the plane of the naphtho­furan ring system [r.m.s. deviation = 0.043 (2) Å] and that of the 3-fluoro­benzene ring is 39.32 (8)°. In the crystal, mol­ecules are linked by C—H⋯O and C—Br⋯π [3.835 (1) Å] inter­actions into stacks along the c axis, forming a three-dimensional network. The F atom is disordered over two positions, with site-occupancy factors of 0.851 (3) and 0.149 (3).

Comparative QSTR studies for predicting mutagenicity of nitro compounds

Mutagenicity and carcinogenicity are toxicological endpoints which pose a great concern being the major determinants of cancers and tumours. Nitroarenes possess genotoxic properties as they can form various electrophilic intermediates and adducts with biological systems. Different QSTR techniques were employed to develop models for the prediction of mutagenicity of nitroarenes using a diverse set of 197 nitro aromatic and hetero aromatic molecules. The 2D and 3D QSTR methods used for model development gave statistically significant results. The alignment for 3D methods was obtained by maximum common substructures (MCS) approach, by taking the most mutagenic molecule of the dataset as the template. All the QSTR models were developed with the same set of training and test set molecules. The 3D contours and 2D contribution maps along with molecular fingerprints provide useful information about the mutagenic potentials of the molecules. The GFA based model shows thermodynamic and topological descriptors play an important role in characterizing mutagenicity of nitroarenes. Atomic-level thermodynamic descriptor namely AlogP throws light on hydrophobic features and helps to understand the bilinear model. Topological aspects of these classes of compounds were depicted by the fragment fingerprints and Balaban indices obtained from HQSAR and GFA models, respectively. The predictive abilities of 2D and 3D QSTR models may be useful as a vibrant predictive tool to screen out mutagenic nitroarenes and design safer non-mutagenic nitro compounds.

Stability studies of the metabolites of nitrofuran antibiotics during storage and cooking

Nitrofuran antibiotics cannot be used in food production within the European Union because of their potential health risks to consumers. The recent discovery of their widespread use in global food industries and the finding of semicarbazide in baby food as a result of packaging contamination have focused attention on the toxicity and stability of these drugs and their metabolites. The stability of the nitrofuran marker residues 3-amino-2-oxazolidinone (AOZ), 3-amino-5-morpholinomethyl-2-oxazolidone (AMOZ), 1-aminohydantoin (AHD) and semicarbazide (SEM) were tested. Muscle and liver of nitrofuran treated pigs were cooked by frying, grilling, roasting and microwaving. Between 67 and 100% of the residues remained after cooking, demonstrating that these metabolites are largely resistant to conventional cooking techniques and will continue to pose a health risk. The concentration of metabolites in pig muscle and liver did not drop significantly during 8 months of storage at -20 degrees C. Metabolite stock and working standard solutions in methanol were also stable for 10 months at 4 degrees C. Only a 10 ng ml(-1) solution of SEM showed a small drop in concentration over this extended storage period.

In vivo genotoxic evaluation of the furylethylene derivative 1-(5-bromofur-2-yl)-2-nitroethene in mouse bone marrow

The genotoxic potential of the compound 1-(5-bromofur-2-yl)-2-nitroethene (2-βNF) has been tested by using the in vivo mouse bone marrow micronucleus assay. Its ability to induce clastogenicity or aneugenicity, through the induction of micronucleated polychromatic erythrocytes (MNPCE) in the bone marrow cells has been evaluated. Treatment groups of five CD-1 male mice were administered once intraperitoneally at the doses of 10, 20, and 30mg/kg, and their bone marrows were sampled at 24 and 48h after the administration, at the first sampling time animals administered with the three doses were used, and in the second sampling time, only animals administered with the highest dose were used. All animals treated with the highest dose of the test compound (30mg/kg) showed evident clinical symptoms of toxicity such as irritation, hunched posture, slight ataxia, dyspnoea, piloerection, and palpebral ptosis. However, no marked depression of bone marrow cell proliferation was observed, and no significant increases in the frequency of MNPCE were obtained in any of the concentrations tested at any sampling times. The positive control treated-animals were administered with cyclophosphamide at the dose of 40mg/mL. The compound caused a significant increase in the number of MNPCE in all treated animals, demonstrating the sensitivity of the mouse strain used. From the results obtained, it is concluded that the compound 2-βNF is neither clastogenic nor aneugenic in the erythrocytes from the bone marrow of treated mice at the doses tested.

Quantitative structure-activity relationships from optimised ab initio bond lengths: steroid binding affinity and antibacterial activity of nitrofuran derivatives

The present day abundance of cheap computing power enables the use of quantum chemical ab initio data in Quantitative Structure-Activity Relationships (QSARs). Optimised bond lengths are a new such class of descriptors, which we have successfully used previously in representing electronic effects in medicinal and ecological QSARs (enzyme inhibitory activity, hydrolysis rate constants and pKas). Here we use AM1 and HF/3-21G* bond lengths in conjunction with Partial Least Squares (PLS) and a Genetic Algorithm (GA) to predict the Corticosteroid-Binding Globulin (CBG) binding activity of the classic steroid data set, and the antibacterial activity of nitrofuran derivatives. The current procedure, which does not require molecular alignment, produces good r2 and q2 values. Moreover, it highlights regions in the common steroid skeleton deemed relevant to the active regions of the steroids and nitrofuran derivatives.

A comparative study of quantitative structure-activity relationship methods based on gallic acid derivatives

By using hologram quantitative structure-activity relationship (HQSAR) and comparative molecular field analysis (CoMFA) methods, the relationships between the structures of 49 gallic acid derivatives and their analgesic activity have been investigated to yield statistically reliable models with considerable predictive power. The best HQSAR model was generated using atoms, bond and connectivity as fragment distinction parameters and fragment size 5-7 from a hologram length of 307 with 3 components. High conventional r2 (r2 = 0.825) and cross-validation r2 (r2(cv) = 0.726) values were obtained. CoMFA analyses varying lattice size and location, grid spacing, probe charges and using, Tripos standard and Indicator force field were performed. The best model was developed with 4 components using sp3-hybridized carbon atom with +1.0 charge as probe, grid spacing (2 A), lattice offset (1.0, 3.0, -2.5). The CoMFA model showed a conventional correlation coefficient r2 of 0.889 and across-validation r2(cv) equals to 0.633. The robustness and predictive ability of the HQSAR and CoMFA models have been validated by means of an external test set. The results indicate that both models possess high statistical quality in the prediction of analgesic potency of novel gallic acid analogs.

Genotoxicity testing of the furylethylene derivative 1-(5-bromofur-2-yl)-2-bromo-2-nitroethene in cultured human lymphocytes

The genotoxic potential of the compound 1-(5-bromofur-2-yl)-2-bromo-2-nitroethene (G-1) was evaluated in peripheral blood lymphocytes cultured in vitro, at concentrations ranging from 1 to 20 microg/ml. Micronuclei (MN) and sister-chromatid exchanges (SCE) were scored as biomarkers of genotoxic effects. To detect the role of metabolic enzymes on the genotoxicity of this furylethylenic derivative, cultures for MN and SCE demonstrations were treated for 3 h with and without the S9 microsomal fraction as well as for 48 h without S9. Under the conditions of the study, the test agent did not induce significant increases in the frequency of micronucleated cells, irrespective of the presence/absence of the metabolic fraction. Nevertheless, a slight/moderate increase in the SCE frequency was observed in those cultures treated without the S9 mix. In addition, cytotoxic/cytostatic effects of the G-1 compound were observed mainly in cultures without S9 fraction, as indicated by the reduction of cell proliferation measured by the cytokinesis block proliferation index (CBPI) and the proliferative rate index (PRI).

Genotoxic evaluation of the furylethylene derivative 1-(5-bromofur-2-yl)-2-nitroethene in cultured human lymphocytes

The genotoxicity of the 2-furylethylene derivative 1-(5-bromofur-2-yl)-2-nitroethene (2-betaNF) has been evaluated in cultured human peripheral blood lymphocytes at concentrations ranging from 0.5 to 15microg/ml. The frequencies of micronuclei (MN) and sister-chromatid exchanges (SCEs) were used and scored as indicators of genetic damage. To asses the role of the metabolism mediated by the enzymes present in the S9 mix, over the possible genotoxic potential of the test agent, the cultures for MN and SCE demonstrations were treated for 3h in presence and in absence of rat liver microsomal fraction. The results indicate that, under the experimental conditions used, the test agent does not induce significant increases in the frequency of micronucleated cells, irrespective of the presence/absence of metabolic fraction. Nevertheless, a slight increase in the SCE frequency was observed in those cultures treated without the S9 mix; although this slight increase disappeared in the experiments carried out with the microsomal fraction. In addition, cytotoxic/cytostatic effects of (2-betaNF) were observed mainly in the cultures treated without the S9 fraction.

Investigation of 5-nitrofuran derivatives: synthesis, antibacterial activity, and quantitative structure-activity relationships

Three sets of antibacterial nitrofuran derivatives [set I, 5-R-substituted (Z)-2-(5-nitrofuran-2-ylmethylene)-3(2H)-benzofuranones (R = OCH(3), H, CH(3), C(2)H(5), nC(3)H(7), Cl, Br, CN, and NO(2)) and their 2-hydroxyphenyl and 2-acetoxyphenyl analogues; set II, 5-R-substituted (E)-1-(2-hydroxyphenyl)-3-(5-nitrofuryl)-2-propen-1-ones (R = H, CH(3), C(2)H(5), Cl, and NO(2)); and set III, 5-R-substituted (E)-1-(2-acetoxyphenyl)-3-(5-nitrofuryl)-2-propen-1-ones (R = H, CH(3); C(2)H(5), Cl, and NO(2))] were prepared and tested against a Gram-positive (Staphylococcus aureus, strain ATCC-25923) and a Gram-negative bacterium (Caulobacter crescentus, strain NA 1000). QSAR equations derived for the IC(50) values against both bacteria show negative contributions of two terms: an electronic one, expressed either by sigma, the Hammett substituent constant, or by E, the cyclic voltametric reduction potential. Another term described by an indicator variable, I(abs), is assigned the value of 0 for set I compounds and the value of 1 for sets II and III. No important contribution of the hydrophobic factor was found. For the three sets, the QSAR regressions suggest that the same structural features describe the activities for both bacteria and that, although reduction is a necessary step, it should not be the determining one. These results agree with those found for the QSAR of 5-nitroimidazole analogues.

Genotoxic evaluation of the furylethylene derivative 2-furyl-1-nitroethene in cultured human lymphocytes

The compound 2-furyl-1-nitroethene (G-0) was evaluated for genotoxicity in cultured human peripheral blood lymphocytes, at concentrations ranging from 1 to 15microg/ml. Micronuclei (MN) and sister-chromatid exchanges (SCEs) were scored as genetic endpoints. In order to detect the role of metabolic enzymes on the genotoxicity of this furylethylenic derivative, the cultures for MN and SCE demonstrations were also treated with S9 microsomal fraction. The results indicate that, under the conditions of the study, the test agent does not seem to induce significant increases in the frequency of micronucleated cells, irrespective of the presence of metabolic activation. Nevertheless, a slight increase in the SCE frequency was observed in those cultures treated without the S9 mix; although this increase disappeared in presence of the microsomal fraction. In addition, cytostatic effects of 2-furyl-1-nitroethene were observed mainly in cultures without S9 fraction, as indicated by the reduction of cell proliferation.

Structure-based drug design approaches for predicting binding affinities of HIV1 protease inhibitors

Computational assessment of the binding affinity of enzyme inhibitors prior to synthesis is an important component of computer-assisted drug design (CADD) paradigms. The free energy perturbation (FEP) methodology is the most accurate means of estimating relative binding affinities between two inhibitors. However, due to its complexity and computation-intensive nature, practical applications are restricted to analysis of structurally-related inhibitors. Accordingly, there is a need for methods that enable rapid assessment of large number of structurally-unrelated molecules in a suitably accurate manner. In this review, the FEP method is compared with regression-based methods that employ multivariate models to assess the advantages of each in the estimation of relative binding affinities of inhibitors to an enzyme. Semiquantitative predictions of relative binding free energies of human immunodeficiency virus 1 (HIV1) protease inhibitors are also presented and compared with the corresponding FEP results. The results indicate that the regression-based methods and the FEP method are useful in the semi-quantitative and quantitative assessment of relative binding affinities of enzyme inhibitors, respectively, prior to synthesis.

Frontier orbital energies, hydrophobicity and steric factors as physical QSAR descriptors of molecular mutagenicity. A review with a case study: MX compounds

A review on QSARs (Quantitative Structure-Activity Relationships) in modelling molecular mutagenicity is given. The importance of hydrophobicity, frontier orbital (HOMO and LUMO) energies and steric factors as physical descriptors of mutagenicity is emphasized. In addition, some possible connections between QSAR models and the general electrophilic theory of genotoxic activity are discussed. As a detailed example, QSARs for the Ames Salmonella typhimurium TA100 mutagenicity of halogenated hydroxyfuranones including MX, one of the most potent bacterial mutagens ever identified, are discussed and a plausible mechanism for their mutagenic activity is proposed.

Synthesis, biochemical evaluation, and classical and three-dimensional quantitative structure-activity relationship studies of 7-substituted-1,2,3,4-tetrahydroisoquinolines and their relative affinities toward phenylethanolamine N-methyltransferase and the alpha2-adrenoceptor

7-Substituted-1,2,3,4-tetrahydroisoquinolines (7-substituted-THIQs) are potent inhibitors of phenylethanolamine N-methyltransferase (PNMT, EC 2.1.1.28), the enzyme involved in the biosynthesis of epinephrine. Unfortunately, most of these compounds also exhibit strong affinity for the alpha2-adrenoceptor. To design a selective (PNMT vs alpha2-adrenoceptor affinity) inhibitor of PNMT, the steric and electrostatic factors responsible for PNMT inhibitory activity and alpha2-adrenoceptor affinity were investigated by evaluating a number of 7-substituted-THIQs. A classical quantitative structure-activity relationship (QSAR) study resulted in a three-parameter equation for PNMT (PNMT pKi = 0.599pi - 0.0725MR + 1. 55sigmam + 5.80; n = 27, r = 0.885, s = 0.573) and a three-parameter equation for the alpha2-adrenoceptor (alpha2 pKi = 0.599pi - 0. 0542MR - 0.951sigmam + 6.45; n = 27, r = 0.917, s = 0.397). These equations indicated that steric effects and lipophilicity play a similar role at either active site but that electronic effects play opposite roles at either active site. Two binding orientations for the THIQs were postulated such that lipophilic and hydrophilic 7-substituents would not occupy the same region of space at either binding site. Using these two binding orientations, based on the lipophilicity of the 7-substituent, comparative molecular field analysis (CoMFA) models were developed that showed that the steric and electrostatic interactions at both sites were similar to those previously elaborated in the QSAR analyses. Both the QSAR and the CoMFA analyses showed that the steric interactions are similar at the PNMT active site and at the alpha2-adrenoceptor and that the electrostatic interactions were different at the two sites. This difference in electrostatic interactions might be responsible for the selectivity of THIQs bearing a nonlipophilic electron-withdrawing group at the 7-position. These QSAR and CoMFA results will be useful in the design of potent and selective (PNMT vs alpha2-adrenoceptor affinity) inhibitors of PNMT.

Ligand binding to I2 imidazoline receptor: the role of lipophilicity in quantitative structure-activity relationship models

A series of 2-trans-styryl-imidazoline (tracizoline) congeners were designed and tested to develop 2-D and 3-D QSAR models for their binding to imidazoline (I2) receptor. The important role of lipophilicity was assessed by classical 2-D QSAR study (Hansch approach) and by comparative molecular field analysis (CoMFA) with the inclusion of the molecular lipophilicity potential (MLP), as an additional descriptor, besides standard steric and electrostatic fields. Results from these studies were compared to those obtained in a previous modeling study of I2 receptor ligands and integrated into a new, comprehensive model, based on about sixty I2 receptor ligands. This model revealed, at the three-dimensional level, the most significant steric, electrostatic, and lipophilic interactions accounting for high I2 receptor affinity.

Comparison of CoMFA models for Salmonella typhimurium TA98, TA100, TA98 + S9 and TA100 + S9 mutagenicity of nitroaromatics

Comparative Molecular Field Analysis (CoMFA) was applied to a comprehensive data set of heterogeneous nitroaromatics tested in Salmonella typhimurium TA98 and TA100 with and without S9 microsomal activation. The four CoMFA models developed agree with postulated mechanisms of mutagenicity, and explain over 70% of the corresponding mutagenic variance The standard deviation coefficient contours common in the four models included high electronic density regions equivalent to C4-C5 in the pyrene ring, and an electron deficient site equivalent to C6. These areas are associated with high mutagenicity. Electron deficient areas may be related with the nitroreductive bioactivation of nitroaromatics. Electron rich sites may be involved with oxidative mechanisms analogous to the bioactivation pathway of polycyclic aromatic hydrocarbons. The contribution of steric factors to mutagenicity follows the order TA98 + S9 > TA98 > TA100 + S9 > TA100. The models indicated that increasing bulk perpendicular to the aromatic plane would decrease mutagenicity, but increasing the aromatic ring system along a region corresponding to C6-C7 in 1-nitropyrene would increase mutagenicity.

The mutational specificity of furazolidone in the lacI gene of Escherichia coli

The mutational specificity of the 5-nitrofuran derivative furazolidone was determined in the lacI gene of Escherichia coli. E. coli strain TC3960 (delta uvrB, pKM101) was treated with 10 microM furazolidone, yielding an induced mutation frequency of 30 times over the spontaneous frequency. Mutations from 88 furazolidone-induced mutants were analyzed by DNA sequencing: 74 were base substitutions, 7 were frameshift mutations, 3 were tandem base substitutions, 3 were complex mutations and 1 deletion was detected. The specificity of mutation was compared to that of furylfuramide (AF2). Differences were observed in both the site specificity and the mutagenic specificity of the two 5-nitrofuran derivatives. (1) Furazolidone-induced point mutations were observed at both G:C and A:T base pairs; 93% of AF2-induced point mutations were targeted to G:C sites. (2) At G:C sites approximately equal numbers of G:C-->T:A transversions and G:C-->A:T transversions and G:C-->A:T transitions were induced by furazolidone; AF2-induced G:C-->T:A transversions outnumbered G:C-->A:T transitions 76:49. (3) There was no observable preference for particular sequences of furazolidone-induced mutations; the prominent hotspots for AF2-induced G:C-->T:A transversions, G:C-->A:T transitions and -(G:C) frameshifts were at 5'-TGC-3' sequences in the lacI gene. (4) Furazolidone-induced frameshifts occurred at homopolymeric sequences suggesting that the mutations arose through a strand slippage mechanism; AF2-induced frameshifts occurred at a nonreiterated G:C base pair and could be templated, through formation of a palindrome, by a sequence 110 base pairs upstream from the site of mutation. The significant differences that we observe between the two spectra do not support the notion that structurally different 5-nitrofuran derivatives might react in a similar manner with DNA to produce premutational lesions with similar characteristics.

Antitumor agents. 163. Three-dimensional quantitative structure-activity relationship study of 4'-O-demethylepipodophyllotoxin analogs using the modified CoMFA/q2-GRS approach

Analogs of 4'O-demethylepipodophyllotoxin are considered as potential anticancer agents. We have applied comparative molecular field analysis (CoMFA) and a novel CoMFA/q2-GRS technique recently developed in our group to identify the essential structural requirements for increasing the ability of these compounds to form cellular protein-DNA complex. In addition, a new method to incorporate different types of probe atoms as part of q2-GRS routine has been developed. The best final model with 101 compounds using a combination of four different sets of probe atoms and charges [C (sp3, +1), C (sp3, 0), H (+1), and O (sp3, -1)] yielded a q 2 of 0.584 and the standard error of prediction of 0.660 at 5 principal components. The steric and electrostatic contour plots of the final model were compared with the DNA phosphate backbone environment of the DNA-4'O-demethylepipodophylltoxin analog complex, which was generated using the X-ray structure of the DNA-nogalamycin complex. The comparison reveals that the CoMFA steric and electrostatic fields are compatible with stereochemical properties of the DNA backbone. The results obtained from this study shall guide our future synthetic efforts.

An empirical and theoretical study on mechanisms of mutagenic activity of hydrazine compounds

Hydrazine compounds are important industrial and laboratory chemicals. Many of them are carcinogenic in animal tests. Although the carcinogenicity is well established, the results of mutagenicity tests performed on alkylhydrazines vary greatly in different studies. In an attempt to clarify the situation we have applied Salmonella typhimurium TA102 tests to hydrazine and its mono- and dimethyl derivatives. These compounds were also tested by an Escherichia coli DNA repair-assay. The results of the repair tests indicate that unsymmetrically alkylated hydrazines can cause DNA-lesions which are lethal in repair-deficient strains. Finally QSAR (Quantitative Structure Activity Relationships) was used to develop a model to describe the genotoxic mechanism of hydrazine compounds, taking advantage of the results of previous mutagenicity studies. Energy of the lowest unoccupied molecular orbital together with octanol-water partition coefficient explains nearly completely the mutagenic activity of alkylated hydrazine compounds included in the analysis. The mutagenic activity of unsubstituted hydrazine is apparently based on different mechanisms.

A new procedure for improving the predictiveness of CoMFA models and its application to a set of dihydrofolate reductase inhibitors

A new automated procedure to improve the predictive quality of CoMFA models for both training and test sets is described. A model of greater consistency is generated by performing small reorientations of the underlying molecules for which too low activities are calculated. In order to predict activities of test compounds, the most similar molecules in the previously optimized model are identified and used as a basis for the prediction. This method has been applied to two independent sets of dihydrofolate reductase inhibitors (80 compounds each, serving as training sets), resulting in a significant increase of the cross-validated r2 value. For both models, the predictive r2 value for a test set consisting of 70 compounds was improved substantially.

Calculation of hydrophobic parameters directly from three-dimensional structures using comparative molecular field analysis

Capacity ratio (log k') values, which are a measure of hydrophobicity, were calculated directly from the three-dimensional structures of 17 furans and 54 triazines using the comparative molecular field analysis approach. The H2O probe and the GRID force field, including hydrogen-bond potentials, yielded excellent correlations with the log k' values. Moreover, the predicted values of log k' from 14 additional triazine analogs showed excellent agreement with log k' values reported in the literature. Similar results were obtained for the octanol-water partition coefficients (log P) of 17 furans.

Replacement of steric 6-12 potential-derived interaction energies by atom-based indicator variables in CoMFA leads to models of higher consistency

The steric descriptors commonly used in CoMFA--Lennard-Jones 6-12 potential-derived interaction energies calculated between a probe atom and the molecules under investigation--have been replaced by variables indicating the presence of an atom of a particular molecule in predefined volume elements (cubes) within the region enclosing the ensemble of superimposed molecules. The resulting 'atom indicator vectors' were used as steric fields in the subsequent PLS analyses, with and without inclusion of electrostatic Coulomb interaction-derived fields. Application of this method to five training sets (80 compounds each) and five test sets (60 compounds each), randomly selected from an ensemble of 256 dihydrofolate reductase inhibitors, leads to models of significantly higher consistency, as indicated by the cross-validated r2 values for the training sets and the predictive r2 values for the test sets.

Shape-dependent effects in a series of aromatic nitro compounds acting as mutagenic agents on S. typhimurium TA98

The steric properties modulating the mutagenic activity on S. typhimurium TA98 of a set of nitroaromatic compounds have been investigated using the CoMFA method. In addition to steric probe-ligand interaction energies, the overall lipophilicity and the energy of the lowest occupied molecular orbital have been employed as molecular descriptors.

Comparative QSAR in toxicology: examples from teratology and cancer chemotherapy of aniline mustards

During the past 30 years, thousands of quantitative structure-activity relationships (QSAR) have been published for all sorts of chemicals acting on many forms of life or parts thereof (DNA, enzymes, organelles, etc.). Very little effort has been made to show the relationship among these equations. In this report, we discuss two examples, the toxicity of phenols to rats and the effect of aniline mustards on a variety of living systems, where the electronic effects in the QSAR can be correlated to QSAR from physical organic chemistry. This enables one to make better mechanistic deductions about the biological structure-activity relationships. From this, it is concluded that radicals formed from the phenols cause birth defects.