Bioactivity landscape modeling: Chemoinformatic characterization of structure-activity relationships of compounds tested across multiple targets

Characterizing structure-activity relationships (SAR) of sets of compounds screened across different targets is crucial in several drug discovery endeavors. To this end, chemoinformatic approaches are emerging to characterize SARs using the concept of multi-target activity landscapes. Herein, we present the Structure multiple Activity Similarity (SmAS) maps and the Structure multiple Activity Landscape Index (SmALI) as general approaches to navigate through and quantify the most informative regions of multi-target activity landscapes. These methods are extensions of SAS maps and SALI metric used for single targets. To illustrate the use of these methods, SmAS maps and SmALI values were employed for characterizing the SAR of three benchmark sets of compounds screened with different target families. As a follow up of our work, we employed four 2D and 3D structure representations to obtain consensus models for each data set. For the three data sets, we identified pairs of compounds with high structure similarity but very different bioactivity profile across the corresponding targets of each family that is, multi-target activity cliffs. Also, we identified pairs of compounds with low structure similarity but similar bioactivity profile across the different targets that is, multi-target scaffold hops. The consensus SmAS maps and mean SmALI metric are complementary chemoinformatic tools to systematically describe multi-target activity landscapes.     

Quantitative structure-activity relationships of phenolic compounds causing apoptosis

A study of a variety of phenolic compounds (simple phenols, estradiol, bisphenol A, diethylstilbesterol) on their action on L1210 leukemia cells led to the formulation of the following QSAR for apoptosis:log 1/C=-3.16 Clog P+2.77 CMR-3.76n=11, r(2)=0.939, s=0.630, q(2)=0.892C is the molar concentration causing 25% apoptosis, Clog P is the calculated octanol/water partition coefficient and CMR is the calculated molecular refractivity. Our results imply the significance of characterization of the phenolic compounds with apoptotic activity and the development of new agents for cancer therapy.     

Synthesis and structure-activity relationships of 1,5-diazaanthraquinones as antitumour compounds

1,5-Diazaanthraquinone derivatives were synthesized employing single and double hetero Diels-Alder strategies. Their in vitro antitumour activity was assayed using three cell lines. Some of these compounds, specially those bearing methyl or ethyl groups at the C-3,7 positions or chloro at C-4 and methyl at C-7, showed IC(50) values in the 10(-8)M range for human lung carcinoma and human melanoma, which makes them attractive candidates for further development as anticancer agents.     

Biological activities of marine sesquiterpenoid quinones: structure-activity relationships in cytotoxic and hemolytic assays

Sesquiterpenoid quinones from marine sponges and their semisynthetic derivatives were compared for cytotoxicity on developing eggs of sea urchin Strongylocentrotus nudus and Ehrlich carcinoma cells, and for hemolytic activities on mice red blood cells. Structure-activity studies showed that activities of these compounds with a hydroxyl group at C-20 ((2), (7)) were higher than their methoxyl ((1), (8)) and amino ((4), (5)) derivatives at this position. Sesquiterpenoid quinones containing a dihydropyran ring ((10)-(12)) had lower activity than noncyclic compounds. The structure of the terpenoid moieties of the compounds had no significant influence on biological activity. There was a direct correlation between cytotoxic and hemolytic activities. This report discusses the mechanism of action employed by these compounds against cell membranes.     

Evidence for hormesis in mutagenicity dose-response relationships

This study assessed the occurrence of hormetic dose responses from three previously published data sets [1-3] with 825 chemicals in three Ames assay tester strains (i.e., TA97, TA98, TA100) with and without the S9 fraction, using a five dose protocol and semi-log dose spacing. Ninety-five (95) (11.5%) chemicals satisfied the multiple a priori entry criteria, with a total of 107 assays. Of the assays satisfying the entry criteria, 61 involved TA100, a strain that detects base-pair substitution mutations. 29.5% (18/61) satisfied the statistical evaluative criteria for hormesis, exceeding that predicted by chance by 4.0-fold (p<0.001). The remaining 46 assays involved TA97 and TA98, strains that detect frameshift mutations. Of these 46 assays, the overall responses for the lowest two doses closely approximated the control response (e.g., 101.77% of the control for TA98; 99.20% for TA97). Only 2.2% (1/46) of the assays satisfied the evaluative criteria for hormesis. In conclusion, these data support a hormetic model for TA100, whereas the responses for TA97 and TA98 are consistent with a threshold dose-response model.     

Radiation-induced mutagenicity and lethality in ames tester strains of salmonella

Mutation and killing induced by X radiation and 60CO gamma radiation were studied in six different histidine-requiring auxotrophs of Salmonella typhimurium. Strain TA100, which is sensitive to base-pair substitutions, and strains TA2637 and TA98, which are sensitive to frameshifts, carry the pKM101 plasmid and exhibit significantly higher radiation-induced mutations compared to their plasmidless parent strains TA1535, TA1537, and TA1538, respectively. Among the plasmid-containing strains, TA98 and TA2637 are much more sensitive to the mutagenic action of radiation than is TA100 based on a comparison with their respective spontaneous mutation rates; however, no uniformity was observed in the responses of the strains to the lethal action of ionizing radiation. The pKM101 plasmid provides partial protection against lethality in TA100 and TA2637, whereas the same plasmid enhances the lethal action of ionizing radiation in TA98. The following conclusions are consistent with these observations: (1) the standard Ames Salmonella assay correctly identifies ionizing radiation as a mutagenic agent; (2) frameshift-sensitive parent strains are more sensitive to the mutagenic effects of ionizing radiation than is the only strain studied that is sensitive to base-pair substitutions; and (3) enhancement of mutagenesis and survival is related to plasmid-mediated repair of DNA damage induced by ionizing radiation and does not involve damage induced by Cerenkov-generated uv radiation which is negligible for our irradiation conditions.     

beta-Endorphin: structure-activity relationships in the guinea pig ileum and opiate receptor binding assays.

The opiate activities of some derivatives and enzymatic digests of camel and human β-endorphin were determined in the guinea pig ileum and rat brain opiate receptor binding assays. Derivatives of β-endorphins altered within the amino-terminal five residues showed pronounced losses in activity. Anisylation of the C-terminal glutamic acid residue of β_h-endorphin produced only small reductions in activity. Chymotryptic digestion greatly weakened the opiate activities of β_h-endorphin, whereas carboxypeptidase A, tryptic and leucine aminopeptidase digests showed only small losses in potency. The C-terminus of β-endorphin appears to contribute little directly to opiate activity. Amino acid analysis and assay of the leucine aminopeptidase digests suggest that the larger potency of β-endorphin relative to Met-enkephalin may be a consequence of its greater resistance to exopeptidase attack.     

Novel lopinavir analogues incorporating heterocyclic replacements of six-member cyclic urea--synthesis and structure-activity relationships

The HIV protease inhibitor ABT-378 (lopinavir) has a six-member cyclic urea in the P-2 position. A series of analogues in which the six-member cyclic urea is replaced by various heterocycles was synthesized and the structure-activity relationships explored.     

The use of marine bacteria in mutagenicity assays

Mutagenic pollution of environment is a global and important problem. This includes marine environment. Although many mutagenicity assays have been developed, there are specific problems with testing marine water and sediments for mutagenic contamination. One of them is the fact that most of genetically modified strains used in commonly available microbiological mutagenicity assays, like Escherichia coli or Salmonella, survive relatively poorly in marine waters, especially those of higher salinity. Thus, alternative assays have been developed, in which bacteria occurring naturally in marine habitats are employed. These assays, reviewed in this article, appear to be useful in testing not only marine samples but also can be used in other approaches, which involve detection and estimation of the amount of mutagenic compounds.     

Genotoxicity of zinc in 4 short-term mutagenicity assays

The genotoxicity of zinc was examined in 4 short-term mutagenicity assays. Zinc acetate produced dose-related positive responses in the L5178Y mouse lymphoma assay and an in vitro cytogenetic assay with Chinese hamster ovary cells, but was negative in the Salmonella mutation assay and did not induce unscheduled DNA synthesis in primary cultures of rat hepatocytes. Zinc-2,4-pentanedione produced frameshift mutations in Salmonella tester strains TA1538 and TA98, but did not induce unscheduled DNA synthesis in primary cultures of rat hepatocytes. The effect of ligand binding of zinc in the in vitro test systems is discussed.     

Definitive relationships among chemical structure, carcinogenicity and mutagenicity for 301 chemicals tested by the U.S. NTP.

An analysis is presented in which are evaluated correlations among chemical structure, mutagenicity to Salmonella, and carcinogenicity to rats and mice among 301 chemicals tested by the U.S. NTP. Overall, there was a high correlation between structural alerts to DNA reactivity and mutagenicity, but the correlation of either property with carcinogenicity was low. If rodent carcinogenicity is regarded as a singular property of chemicals, then neither structural alerts nor mutagenicity to Salmonella are effective in its prediction. Given this, the database was fragmented and new correlations sought between the derived sub-groups. First, the 301 chemicals were segregated into six broad chemical groupings. Second, the rodent cancer data were partially segregated by target tissue. Using the previously assigned structural alerts to DNA reactivity (electrophilicity), the chemicals were split into 154 alerting chemicals and 147 non-alerting chemicals. The alerting chemicals were split into three chemical groups; aromatic amino/nitro-types, alkylating agents and miscellaneous structurally-alerting groups. The non-alerting chemicals were subjectively split into three broad categories; non-alerting, non-alerting containing a non-reactive halogen group, and non-alerting chemical with minor concerns about a possible structural alert. The tumor data for all 301 chemicals are re-presented according to these six chemical groupings. The most significant findings to emerge from comparisons among these six groups of chemicals were as follows: (a) Most of the rodent carcinogens, including most of the 2-species and/or multiple site carcinogens, were among the structurally alerting chemicals. (b) Most of the structurally alerting chemicals were mutagenic; 84% of the carcinogens and 66% of the non-carcinogens. 100% of the 33 aromatic amino/nitro-type 2-species carcinogens were mutagenic. Thus, for structurally alerting chemicals, the Salmonella assay showed high sensitivity and low specificity (0.84 and 0.33, respectively). (c) Among the 147 non-alerting chemicals less than 5% were mutagenic, whether they were carcinogens or non-carcinogens (sensitivity 0.04).     

Dimethylglycine and chemically related amines tested for mutagenicity under potential nitrosation conditions

Dimethylglycine (DMG) and the chemically related amino acids glycine, sarcosine (monomethylglycine) and betaine (trimethylglycine) were tested in Salmonella typhimurium strain TA100 after treatment with sodium nitrite under acidic conditions using a modified Ames Salmonella/microsome assay as reported by Colman et al. (1980). The increase in the number of revertants observed both with and without metabolic activation was also induced in the control mixtures without adding the amines. From the subsequent testing of the individual components of the mixtures, we concluded that non-consumed nitrite was responsible for the mutagenic responses observed in the different reaction mixtures, and not the amines themselves. There were no consistent indications of mutagenic activity of the DMG test mixture as compared to the control mixture which exhibited both consistent mutagenic activity and a toxic effect which was not increased by the addition of DMG. In fact, DMG seemed to decrease the toxicity of the control reaction solution to the Salmonella which was clearly observed at the higher doses. DMG cannot be considered mutagenic under the test conditions employed. The same can be said of the other amino acids as well.