Identification of the structural requirements for mutagencitiy, by incorporating molecular flexibility and metabolic activation of chemicals. II. General Ames mutagenicity model

The tissue metabolic simulator (TIMES) modeling approach is a hybrid expert system that couples a metabolic simulator together with structure toxicity rules, underpinned by structural alerts, to predict interaction of chemicals or their metabolites with target macromolecules. Some of the structural alerts representing the reactivity pattern-causing effect could interact directly with the target whereas others necessitated a combination with two- or three-dimensional quantitative structure-activity relationship models describing the firing of the alerts from the rest of the molecules. Recently, TIMES has been used to model bacterial mutagenicity [Mekenyan, O., Dimitrov, S., Serafimova, R., Thompson, E., Kotov, S., Dimitrova, N., and Walker, J. (2004) Identification of the structural requirements for mutagenicity by incorporating molecular flexibility and metabolic activation of chemicals I: TA100 model. Chem. Res. Toxicol. 17 (6), 753-766]. The original model was derived for a single tester strain, Salmonella typhimurium (TA100), using the Ames test by the National Toxicology Program (NTP). The model correctly identified 82% of the primary acting mutagens, 94% of the nonmutagens, and 77% of the metabolically activated chemicals in a training set. The identified high correlation between activities across different strains changed the initial strategic direction to look at the other strains in the next modeling developments. In this respect, the focus of the present work was to build a general mutagenicity model predicting mutagenicity with respect to any of the Ames tester strains. The use of all reactivity alerts in the model was justified by their interaction mechanisms with DNA, found in the literature. The alerts identified for the current model were analyzed by comparison with other established alerts derived from human experts. In the new model, the original NTP training set with 1341 structures was expanded by 1626 proprietary chemicals provided by BASF AG. Eventually, the training set consisted of 435 chemicals, which are mutagenic as parents, 397 chemicals that are mutagenic after S9 metabolic activation, and 2012 nonmutagenic chemicals. The general mutagenicity model was found to have 82% sensitivity, 89% specificity, and 88% concordance for training set chemicals. The model applicability domain was introduced accounting for similarity (structural, mechanistic, etc.) between predicted chemicals and training set chemicals for which the model performs correctly.     

Identifying the structural requirements for chromosomal aberration by incorporating molecular flexibility and metabolic activation of chemicals

Modeling the potential of chemicals to induce chromosomal damage has been hampered by the diversity of mechanisms which condition this biological effect. The direct binding of a chemical to DNA is one of the underlying mechanisms that is also responsible for bacterial mutagenicity. Disturbance of DNA synthesis due to inhibition of topoisomerases and interaction of chemicals with nuclear proteins associated with DNA (e.g., histone proteins) were identified as additional mechanisms leading to chromosomal aberrations (CA). A comparative analysis of in vitro genotoxic data for a large number of chemicals revealed that more than 80% of chemicals that elicit bacterial mutagenicity (as indicated by the Ames test) also induce CA; alternatively, only 60% of chemicals that induce CA have been found to be active in the Ames test. In agreement with this relationship, a battery of models is developed for modeling CA. It combines the Ames model for bacterial mutagenicity, which has already been derived and integrated into the Optimized Approach Based on Structural Indices Set (OASIS) tissue metabolic simulator (TIMES) platform, and a newly derived model accounting for additional mechanisms leading to CA. Both models are based on the classical concept of reactive alerts. Some of the specified alerts interact directly with DNA or nuclear proteins, whereas others are applied in a combination of two- or three-dimensional quantitative structure-activity relationship models assessing the degree of activation of the alerts from the rest of the molecules. The use of each of the alerts has been justified by a mechanistic interpretation of the interaction. In combination with a rat liver S9 metabolism simulator, the model explained the CA induced by metabolically activated chemicals that do not elicit activity in the parent form. The model can be applied in two ways: with and without metabolic activation of chemicals.     

Resolution of dose-response toxicity data for chemicals requiring metabolic activation: example--vinyl chloride

The toxicity of many chemicals results from biotransformation products formed from the chemical rather than from the chemical per se. In such cases, the incremental response may become diminishingly smaller with increasing dose or exposure because activation of the chemical to the toxic form follows apparent Michaelis—Menten rather than apparent first-order kinetics. To illustrate this concept, rats were exposed to concentrations ranging from 1.4 to 4600 ppm of vinyl chloride for 6 hr, and the total amount metabolized was determined. The amount metabolized followed apparent Michaelis—Menten kinetics. For rats, the logarithmic probability incidence of angiosarcoma versus the amount of vinyl chloride metabolized rather than the exposure concentration of vinyl chloride is linear. Assuming no threshold in spite of evidence to the contrary, extrapolation of the data below the range of doses causing experimentally observable responses predicted an incidence of 0.01% hepatic angiosarcoma in rats exposed to 4.6 ppm of vinyl chloride. Theoretical extension of the extrapolation to humans after adjusting for metabolic and body mass differences was undertaken. The theoretical extrapolation for man exposed daily for 8 hr to 1 ppm suggests an incidence of 1.5 per 100,000,000. This theoretical incidence, although a likely overestimate because of a less than predicted incidence in men exposed to 200 ppm and greater, as well as evidence for a threshold in rats, is less than that expected to occur spontaneously. The concepts evolved from this analysis reveals why pharmacokinetics must be considered in designing toxicology experiments as well as in interpretation of the resulting data.     

Separation of the structural requirements for agonist-promoted activation and sequestration of the beta-adrenergic receptor

The deletion of residues 222-229 from the hamster beta 2-adrenergic receptor (beta AR) resulted in an inability of the mutant receptor to couple to the guanine nucleotide-binding protein (G protein) Gs and to undergo the agonist-mediated sequestration response that is associated with desensitization [Mol. Pharmacol. 34:132-138 (1989)]. Replacement of this region of the beta AR with the analogous region of the M1-muscarinic acetylcholine receptor restored the sequestration response but not the G protein activation. These data suggest that there is a structural, rather than a functional, relationship between these two processes and demonstrate that G protein coupling is not a prerequisite for receptor sequestration.     

Substance P: structural requirements for the activation of brain catecholamine synthesis and locomotor activity in rats

Intracerebroventricularly administered Arg-Pro-Lys-Pro-Gln-Gln-Phe-Gly-Leu-Met-NH2 (substance P, SP) enhanced the accumulation of DOPA after inhibition of the aromatic L-amino acid decarboxylase in the rat brain. SP also stimulated locomotor activity in a dose-dependent manner. A total of 31 structural analogues of SP were evaluated with respect to the action on brain monoamine synthesis as well as on locomotor activity. Catecholamine synthesis: SP1-10 was inactive which indicated that the [Met11]-NH2 terminal is essential for biological activity; [Leu10], [Phe7] and [Gln6] were also essential for activity; the minimum length requirement for activity was a hexapeptide amide structure. D-Amino acids in positions 8 or 9 increased activity. [D-Pro2]p-SP and [pGlu5, Gly7]-SP5-11 were active in the dopamine-rich areas, but inactive in the noradrenaline (norepinephrine)-predominant parts of the brain. The inactive [Ile7]-SP potentiated the effect of SP. Neither SP nor its analogues, with the exception of [Lys5,D-Leu8,D-Phe9]-SP5-11, increased the synthesis of 5-hydroxytryptophan (5-HTP). Locomotor activity: SP1-10 and [D-Phe9]-SP were as active as SP; [Ile7]-SP and [Ile7, Ile8]-SP were inactive and they did not antagonize the effect of SP. The results indicate that after chemical manipulation of the SP molecule it is possible to obtain great variation in activity and to dissociate to some extent the behavioural effects from those on brain catecholamine synthesis.     

Immunosuppression induced by chemicals requiring metabolic activation in mixed cultures of rat hepatocytes and murine splenocytes

Primary cultures of adult rat hepatocytes (Fischer 344) were used as an in vitro metabolic activation system in immunotoxicological assays. Rat hepatocytes were isolated by a collagenase perfusion technique and cultured for 20 to 24 hr to allow the formation of a monolayer on collagen-coated plastic petri dishes. Spleen cells isolated from (C57BL/6 X C3H)F1 mice were cocultured with the hepatocytes along with the chemicals. Cyclophosphamide (CP) and Aflatoxin B1 (AFB1) were effectively activated in this coculture system and produced a dose-related suppression of the in vitro antibody responses to LPS, DNP-Ficoll, and SRBC in 3 hr. Neither CP (1 mM) nor AFB1 (10(-4) M) cultured with spleen cells alone produced any effects. Both CP and AFB1 also produced a dose-related suppression of the proliferative responses to LPS, Con A, and PHA. In contrast, up to 100 mM of N-nitrosodimethylamine (DMN) did not suppress any of these assays after a 3-hr incubation in the coculture system. These results indicate that a coculture system can be used to characterize the activity of immunosuppressive chemicals requiring metabolic activation.     

Genome resequencing analysis of Salmonella typhimurium LT‐2 strains TA98 and TA100 for the establishment of a next‐generation sequencing‐based mutagenicity assay

Next‐generation sequencing (NGS) is a potentially useful technology to achieve a more precise evaluation of chemical mutagenicity. To establish NGS‐based mutagenicity assays, which enable the direct detection of chemically induced mutations in a whole genome manner, the selection of appropriate biological resources and their precise genome sequences are essential. Here, we performed genome re‐sequencing analyses of Salmonella typhimurium LT‐2 strains TA98 and TA100, which have been frequently used in mutagenicity assays. We identified several strain‐specific mutations including those that were relevant to their known phenotypes (his , ΔuvrB and rfa ). The details of rfa mutations were first clarified in this study, which was a frameshift variant in rfaF and a missense variant in rfaC in TA98 and TA100, respectively. The uvrB deletion in TA98 was larger than that in TA100, which suggested differences in defects of lipopolysaccharide synthesis between these strains. The re‐sequenced genome data of TA98 and TA100 will help us establish NGS‐based bacterial mutagenicity assays and understand the biological events seen in them. Copyright © 2017 John Wiley & Sons, Ltd.     

Mutagenic activity of various chemicals in Salmonella strain TA100 and glutathione-deficient derivatives. On the role of glutathione in the detoxification or activation of mutagens inside bacterial cells

Several mutants with decreased levels of reduced glutathione (GSH) were isolated from the sensitive mutagen tester strain Salmonella typhimurium TA100 after treatment with u.v. and selection for resistance to N-ethyl-N'-nitro-N-nitrosoguanidine (ENNG) and its methyl analogue MNNG. Estimation of the GSH concentration and GSH S-transferase activity in extracts of these strains and of TA100 indicates that the GSH- derivatives contain 10-30% of the GSH level found in TA100, and that they exhibit normal GSH S-transferase activity. The mutagenic activities of 7 chemicals, namely, MNNG, ENNG, 1,2-dibromoethane (DBE), 1-chloro-2,4-dinitrobenzene (CDNB), styrene-7,8-oxide (STOX), N-ethyl-N-nitrosourea (ENU) and methyl methane sulphonate (MMS) were compared in TA100 and in one representative GSH- strain, denominated NG-57. MNNG, ENNG, DBE and CDNB are potent to extremely potent mutagens in TA100, but induce very low levels of His+ mutants in NG-57. Pretreatment of NG-57 with 1 mM GSH (partially) restores the mutant yields to the levels usually found in TA100. The mutagenic activities of STOX, ENU and MMS are similar in both strains. These results support some previous findings, namely that ENNG, MNNG and DBE, but not ENU are activated to mutagens inside the test bacteria, and also suggest that CDNB is activated by bacterial GSH. The latter finding is in contrast with the current view that CDNB is detoxified by GSH, as is also presently evidenced by a strong reduction of the compound's mutagenicity in the presence of extracts of rat liver, which contains GSH and GSH S-transferase activity. The results with STOX indicate that GSH plays in bacteria a much less important role in the detoxification of xenobiotics than in mammalian tissue, presumably due to a much lower GSH S-transferase activity in the first organism.     

Small atrial natriuretic peptide analogues: design, synthesis, and structural requirements for guanylate cyclase activation.

Structure/activity studies on atrial natriuretic peptide ANP (1-28) have highlighted three portions of the native molecule as necessary for its biological responses. We have linked these three regions and excised the remaining segments to produce a family of small analogues (less than half the size of the parent) which demonstrate the full range of ANP's actions. Importantly, these compounds act at both major types of ANP receptor. Two critical modifications lead to more potent analogues; both involve expanding the cyclic portion of the molecule. Further optimization of one of these modified structures leads to A68828, a full ANP agonist which shows promise as a preventative agent against acute renal failure.     

Aminoglutethimide-induced leucopenia in a mouse model: effects of metabolic and structural determinates

A model of human leucopenia has been developed further in the female mouse. Following daily administration to female mice of 50 mg/kg of the aromatase inhibitor aminoglutethimide, significant falls in platelet and white cell counts occurred after 2 and 3 weeks. At week 4, drug dosage was stopped and the cell counts recovered at the end of that week, although on rechallenge at the beginning of week 5, both platelet and white cell counts fell rapidly. Administration to the mice of structural analogues of aminoglutethimide, such as WSP-3, glutethimide and 4-nitroglutethimide, showed no reductions in platelet and white cell counts. The haemotoxicity of aminoglutethimide over 21 days was unaffected by the presence of either the P-450 inhibitor SKF-525A or the hepatic P-450 inducer phenobarbitone. However, the co-administration of cimetidine abolished the haemotoxicity of aminoglutethimide in terms of platelet and white cell levels. In in vitro studies, both aminoglutethimide and WSP-3 were oxidised to cytotoxic species, although aminoglutethimide was significantly more cytotoxic than WSP-3. The NADPH-dependent covalent binding of (14)C aminoglutethimide to mouse microsomes in vitro was significantly reduced by the presence of cimetidine. The activation of the compound to reactive species in vitro, the inhibitory effects of cimetidine in vivo and in vitro, as well as the rapid fall in the in vivo white cell count on rechallenge with aminoglutethimide suggest that this model illustrates a form of leucopenia which may be related to hapten formation and subsequent immune-mediated platelet and white cell lysis.     

Study of the structural requirements for dopa potentiation and oxotremorine antagonism by L-prolyl-L-leucylglycinamide.

A number of analogs of the tripeptide L-prolyly-L-leucylglycinamide (1) were synthesized and evaluated in the Dopa potentiation and oxotremorine antagonism tests. The replacement of the glycinamide residue with either the glycine methylamide, glycine, aminoacetonitrile, amino-2-propanone, semicarbazide, or beta-alaninamide residues resulted in a loss of activity in both tests. A 1:1 mixture of L-prolyl-L-leucyl-(-)-thiazolidine-2-carboxamide (8) and L-prolyl-L-leucyl-(+)-thiazolidine-2-carboxamide (9) showed marked activity in the Dopa potentiation test but was unable to antagonize the tremors induced by oxotremorine. L-Prolyl-L-leucyl-L-prolinamide (11), on the other hand, was active in the oxotremorine antagonism test but inactive in the Dopa potentiation test. The replacement of the pyrrolidine ring of 1 with either a thiazolidine or cyclopentane ring system caused a loss of activity. The cyclopentanecarboxylic acid analogue 13, however, was found to have moderate activity in the serotonin potentiation test.     

Building new function into glycine receptors: a structural model for the activation of the glycine-gated chloride channel

1. The glycine receptor chloride channel mediates inhibitory neurotransmission and is a member of the ligand-gated ion channel superfamily, which includes the nicotinic acetylcholine receptor channel. 2. Activation of these channels involves a movement of the pore-lining second membrane-spanning domain with respect to the remainder of the protein. 3. The present review considers the evidence that the loops that connect this domain with the rest of the protein act as crucial components of the channel activation mechanism.     

Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy

The key to success for computational tools used in structure-based drug design is the ability to accurately place or "dock" a ligand in the binding pocket of the target of interest. In this report we examine the effect of several factors on docking accuracy, including ligand and protein flexibility. To examine ligand flexibility in an unbiased fashion, a test set of 41 ligand-protein cocomplex X-ray structures were assembled that represent a diversity of size, flexibility, and polarity with respect to the ligands. Four docking algorithms, DOCK, FlexX, GOLD, and CDOCKER, were applied to the test set, and the results were examined in terms of the ability to reproduce X-ray ligand positions within 2.0A heavy atom root-mean-square deviation. Overall, each method performed well (>50% accuracy) but for all methods it was found that docking accuracy decreased substantially for ligands with eight or more rotatable bonds. Only CDOCKER was able to accurately dock most of those ligands with eight or more rotatable bonds (71% accuracy rate). A second test set of structures was gathered to examine how protein flexibility influences docking accuracy. CDOCKER was applied to X-ray structures of trypsin, thrombin, and HIV-1-protease, using protein structures bound to several ligands and also the unbound (apo) form. Docking experiments of each ligand to one "average" structure and to the apo form were carried out, and the results were compared to docking each ligand back to its originating structure. The results show that docking accuracy falls off dramatically if one uses an average or apo structure. In fact, it is shown that the drop in docking accuracy mirrors the degree to which the protein moves upon ligand binding.     

Identification of ssDNA aptamers specific for anti-neuroexcitation peptide III and molecular modeling studies: Insights into structural interactions

Twelve ssDNA aptamers specific for a novel recombinant anti-neuroexcitation peptide (ANEPIII) were identified using the SELEX method from a 79-nucleotide ssDNA pool to purify ANEPIII in a more efficient way. To further understand the binding modes between ssDNA and ANEPIII, fully flexible dinucleotides were docked onto the homology-modeled ANEPIII structure. AutoDocking identified favorable binding sites on ANEPIII for nucleotides, which was valuable for designing more potent ligands.     

A molecular model for an anionic opiate mu-receptor: affinity and activation of morphine conformers.

In this study, the minimal neglect of differential overlap, hydrogen bonding corrected (MNDO/H) method was used to construct an explicit three component mu-opioid receptor binding site composed of formate (Glu-, Asp-), H2O (Ser, Thr) and NH4+ (Lys+, Arg+) which has optimum interactions with the protonated amine and polar oxygen regions of morphine, respectively. These moieties are common to most classes of opioids and are thought to be involved in key interactions of the protonated form with the receptor leading to recognition and activation. Two predominant conformers of morphineH+, N-Me (equatorial) and N-Me (axial) were used as templates for construction of the binding site. In these studies, a plausible recognition mechanism involving electrostatic interaction between the protonated amine and an anionic receptor site, together with a proton-donating phenolic group and proton-accepting polar oxygens was characterized. The role of hydration of both the receptor site and morphine in determining affinity was also explicitly considered. The results strongly indicate that the high-affinity binding of morphineH+ to an 'anionic' receptor site is due mainly to a large entropy term resulting from expulsion of H2O from the receptor site upon introduction of morphine. A possible mechanism of receptor activation was also explored involving proton transfer from morphine to the receptor. Two results obtained support the plausibility of this mechanism: the barrier to proton transfer is reduced by receptor interaction with the polar oxygens and a conformational change occurs in the model receptor during this process.     

Inhibition of prostaglandin biosynthesis by clidanac and related compounds: structural and conformational requirements for PG synthetase inhibition

The inhibition of prostaglandin (PG) biosynthesis by clidanac (6-chloro-5-cyclohexyl-1-indancarboxylic acid, TAI-284), its metabolites and some analogues has been examined using various microsomal preparations as enzyme source. Clidanac and some analogues were among the most potent inhibitors. The (+)-isomer of clidanac was shown to be 1000 times more potent than the (-)-isomer in inhibiting PG synthetase activity. The cis-3'-hydroxyl metabolite which retains anti-inflammatory activity comparable to that of clidanac had much less inhibitory activity. Structure-activity studies with clidanac analogues showed that the position of halogen substitution in 1-indancarboxylic acid is of considerable significance for the conformational requirement for binding to the enzyme.     

Genotoxicity and mutagenicity of melanoidins isolated from a roasted glucose-glycine model in human lymphocyte cultures, intestinal Caco-2 cells and in the Salmonella typhimurium strains TA98 and TA102 applying the AMES test.

Melanoidins are formed during household cooking procedures and are part of our daily diet, but data on their toxicological potential are still scarce. Therefore, the mutagenic, cytotoxic and genotoxic activity of the water soluble total fraction (sol A), the water soluble high molecular weight fraction (HMW; Molecular weight>12,400 Da) and the remaining water soluble low molecular weight fraction (LMW) isolated from a glucose-glycine model system roasted at 125 degrees C was comprehensively studied in human lymphocytes (genetic end point: sister chromatid exchange (SCE)), Caco-2 cells (SCE, cell viability, cell proliferation) and in the Salmonella typhimurium strains TA98 and TA102 (Ames test). Tests were performed in a dose- and time-dependent manner. The results indicate a significant increase in SCE formation in human lymphocytes after the exposure to 0.05% and 0.1% of the melanoidin fractions. In Caco-2 cells, only the exposure to LMW increased the SCE formation as a matter of concentration. Cell's proliferation and viability decreased significantly after exposure to melanoidins. In the AMES test, melanoidins did not show a mutagenic potential, neither using the TA98 nor the TA102 strain. These results show that melanoidins isolated from the glucose-glycine mixture exhibited modest but significant genotoxic effects in human lymphocytes and, in particular the LMW, in Caco-2 cells, but they induce neither in low nor in very high concentrations mutagenicity in bacteria strains.