Cellular automata modelling of biomolecular networks dynamics.

The modelling of biological systems dynamics is traditionally performed by ordinary differential equations (ODEs). When dealing with intracellular networks of genes, proteins and metabolites, however, this approach is hindered by network complexity and the lack of experimental kinetic parameters. This opened the field for other modelling techniques, such as cellular automata (CA) and agent-based modelling (ABM). This article reviews this emerging field of studies on network dynamics in molecular biology. The basics of the CA technique are discussed along with an extensive list of related software and websites. The application of CA to networks of biochemical reactions is exemplified in detail by the case studies of the mitogen-activated protein kinase (MAPK) signalling pathway, the FAS-ligand (FASL)-induced and Bcl-2-related apoptosis. The potential of the CA method to model basic pathways patterns, to identify ways to control pathway dynamics and to help in generating strategies to fight with cancer is demonstrated. The different line of CA applications presented includes the search for the best-performing network motifs, an analysis of importance for effective intracellular signalling and pathway cross-talk.

Database organization and searching with E-State indices.

The electrotopological state (E-State) and its extension, the atom-type E-State, is presented as a representation of atom and molecular fragment structure useful for chemical database organization and management. An approach to database organization, using substituted esters and benzene derivatives as examples, reveals the descriptive power of the E-State paradigm. With a database, organized on the basis of structural relationships as described here, it is possible to search for similar molecular structures with potential for comparable activity. The searches using the atom-type E-State indices are demonstrated with several examples.

Issues in representation of molecular structure the development of molecular connectivity.

Significant issues in the representation of molecular structure and the development of the molecular connectivity paradigm are presented. In the molecular connectivity paradigm, molecular structure is represented directly. Kier and Hall developed the method by creating ways to encode electronic information based on the paradigm developed from the Randic branching index. The simple and valence delta values were created to encode atomic and valence-state electronic information through counts of sigma, pi, and lone pair electrons. A family of indices was created to provide a wide range of structure information. The key aspects of the development are presented and discussed in such a way as to reveal, at least in part, the imaginative thinking involved in the process. Possible future roles for molecular connectivity chi indices are discussed.

Molecular connectivity: intermolecular accessibility and encounter simulation.

The simple molecular connectivity indices are interpreted as summations of bond accessibilities to bimolecular encounters with another, identical molecule. To transcend this model, a molecule is treated as disjecta membra with each bond modeled as a discrete cell in a dynamic simulation of many molecules. Each bond accessibility is transformed into a cellular automata rule. The dynamics are run for each of 38 alkanes, recording the average number of cell encounters, beta. The beta values show a high correlation with the boiling points. The significance of the bond accessibilities and the concept of intermolecular encounters explaining the molecular connectivity indices is supported by these findings.

A cellular automata model of chromatography.

Dynamic models of the behavior of solvent and solute molecules can be made using cellular automata. A chromatographic column was represented by use of a cellular automata grid of 43 x 200 spaces. Solvent (mobile phase), solute and stationary phase cells were designated to simulate the chromatographic situation. The movements of solute and solvent cells down the grid were monitored for different numbers of iterations, different flow rates and different affinities of the solutes for the stationary phase and the solvent for itself. The cellular automata dynamics were successfully able to model expected chromatographic behavior except in a few cases where the number of cells was not large enough to provide an average value reflective of the molecular situation.

A cellular automata model of an anticipatory system.

An anticipatory system has been modeled using the dynamic characteristics of cellular automata. Rules governing the steps in an enzymatic conversion of substrates to products are operative in the system. A concentration of an intermediate product influences the creation of a supplemental enzyme that enhances the competence of an enzyme down stream. This anticipation of the future event creates a condition in which the concentration of a later substrate is suppressed, a property characteristic of the system. The model presents a useful opportunity to study a variety of aspects of this fascinating phenomena.

Cellular automata models of chemical systems.

This paper describes the use of kinematic, asynchronous, stochastic cellular automata to model liquid properties, solution phenomena and kinetic phenomena encountered in complex biological systems. Cellular automata models of dynamic phenomena represent in silico experiments designed to assess the effects of competing factors on the physical and chemical properties of solutions and other complex systems. Specific applications include solution behavior, separation of immiscible liquids, micelle formation, diffusion, membrane passage, first- and second-order chemical kinetics, enzyme activity and acid dissociation. Cellular automata is thus considered as providing an exploratory method for the analysis of dynamic phenomena and the discovery and understanding of new, unexpected phenomena.

An evaluation of the carcinogenic potential of the herbicide alachlor to man.

Chronic bioassays have revealed that alachlor caused nasal, thyroid, and stomach tumours in rats but was not carcinogenic in mice. Significant increases in thyroid and stomach tumours were observed only at doses that exceeded the maximum tolerated dose (MTD). While nasal tumours were found at doses below the MTD, they were small and benign in nature. This publication describes the work undertaken by Monsanto to understand the carcinogenic mode of action of alachlor in the rat and to investigate the relevance to humans. The genetic toxicity of alachlor has been investigated in an extensive battery of in vitro and in vivo test systems. In addition, target-specific mutagenicity tests, such as the COMET assay and DNA binding in nasal tissue, were carried out to investigate any possible in-situ genotoxic action. The weight-of-evidence analysis of all available data clearly demonstrates that alachlor exerts its carcinogenicity in the rat by non-genotoxic mechanisms. In the rat, alachlor is initially metabolised primarily in the liver through the P-450 pathway and by glutathione conjugation. The glutathione conjugates and their metabolites undergo enterohepatic circulation with further metabolism in the gastrointestinal tract, liver, and then nasal tissue where they can be converted to a diethyliminoquinone metabolite (DEIQ). This electrophilic species binds to the cysteine moiety of proteins leading to cell damage and increased cell turnover. When comparisons of in vitro nasal metabolic capability were made, the rat's capacity to form DEIQ from precursor metabolites was 38 times greater than for the mouse, 30-fold higher than monkey, and 751 times greater than that of humans. This data is consistent with the results of studies showing in vivo formation of DEIQ-protein adducts in the nasal tissue of rats but not mice or monkeys. The lack of DEIQ nasal adducts in mice is consistent with the lack of nasal tumours in that species. When the differences between rat and humans in the capacity for initial glutathione conjugation by the liver and nasal tissue are also taken into account, the rat is found to be even more susceptible to DEIQ formation than man. Based on this, it is clear that the potential for DEIQ formation and nasal tumour development in humans is negligible. The mechanism of stomach tumour formation has been studied in the rat. The results demonstrated that the mechanism is threshold-sensitive and involves a combination of regenerative cell proliferation and a gastrin-induced tropic effect on enterochromaffin-like (ECL) cells and stem cells of the mucosal epithelium. The absence of a carcinogenic effect in mice and of any preneoplastic effect in monkeys treated with very high doses is indicative ofthe species-specific aspect of this mechanism of action. The results of studies on thyroid tumour production indicate that alachlor is acting indirectly through the pituitary-thyroid axis by increasing the excretion of T4 by enhanced glucuronidation and subsequent biliary excretion. The increased excretion reduces plasma T4 levels and a feedback mechanism leads to increased synthesis of TSH by the pituitary. Chronic stimulation of the follicular epithelium of the thyroid by TSH produces hyperplasia and ultimately tumour formation. This non-genotoxic, threshold-based mechanism is well established and widely considered to be not relevant to humans. In this work, the modes of action for the three types of tumours elicited in the rat by alachlor were investigated. All are based on non-genotoxic, threshold-sensitive processes. From all the data presented it can be concluded that the tumours detected in the rat are not relevant to man and that alachlor presents no significant cancer risk to humans. This conclusion is supported by the lack of mortality and tumours in an epidemiology study of alachlor manufacturing workers.

Revolution through genomics in investigative and discovery toxicology.

The remarkable technologic and methodologic advances spurred on by the Human Genome Project are being applied throughout the life sciences. In the field of toxicology, high-resolution assays now make it possible to discover virtually all the differences in gene expression brought on by exposure to a particular xenobiotic. There are 2 principal approaches used to build a catalog of changes in gene expression: hybridization microarrays and gel-based methods, such as differential display and AFLP-based mRNA finger-printing. The power of such approaches is exemplified by the identification of more than 300 genes that differ in expression level by at least 2-fold in response to the nongenotoxic rodent liver carcinogen phenobarbital.

QSAR modeling with the electrotopological state indices: corticosteroids.

A structure-activity analysis of a series of steroids binding to corticosteroid-binding globulin was made using the electrotopological state index for each atom in the molecule. Two indices were found to correlate well with the binding affinity. The indices encode structural characteristics in the A and the D rings of the steroids in the study. One of the indices was formulated as the difference between two indices in the A ring. The two were not intercorrelated, suggesting that the composite index signals the influence of structure changes in or near the A ring that can be monitored by the composite index. This is a new observation using this structure-activity method. It is suggested that this model makes some contributions towards detection of the pharmacophore.

Evaluation of the mutagenicity of acetochlor to male rat germ cells.

Male rat dominant lethal (DL) assays conducted on the herbicide acetochlor are described. Single dose studies conducted at the maximum tolerated dose (MTD, < or = 1000 mg/kg) produced no effects on any of the DL assay parameters at any of the ten weekly sampling periods. It is concluded that acetochlor is non-mutagenic to rat germ cells. Due to initial limited knowledge of the MTD of acetochlor it was also evaluated in the DL assay at a dose level of 2000 mg/kg. At this high dose level severe bodyweight loss and some deaths occurred among the treated animals. In addition, reduced implantations and reduced pregnancy rates were observed at the third sampling period (18-25 days post dosing) in the absence of an increase in early post-implantation deaths. These results indicated that the use of supra-MTD doses of acetochlor had reduced the fertility of the treated males leading to the production of a pseudo-DL assay response, as alerted to and defined by Ehling. Although several such pseudo-DL assay responses have been described, none have been explained mechanistically. It was therefore decided to pursue the effects seen in the DL assay when using supra-MTD doses of acetochlor. Ova analysis of female rats mated with male rats exposed to 2000 mg/kg acetochlor revealed unfertilized ova at the critical third sampling time. Normal fertilization of ova was observed at the first and fifth sampling period and, for a dose of 200 mg/kg acetochlor, at the third sampling period. The magnitude and temporal nature of these effects confirmed the induction of a pseudo-DL assay response, and studies were then undertaken to probe its genesis. Rats treated with 2000 mg/kg acetochlor had normal testicular and epididymal pathology and normal sperm numbers and sperm motility at the critical third sampling period. Despite a small reduction in testicular and epididymal glutathione levels 12 h after exposure to 2000 mg/kg acetochlor, testicular LDH and LDH-X enzyme levels were unaffected. Further, no reduction in the level of free sulphydryl groups (-SH) were observed in epididymal caput sperm heads isolated 0.5, 7 or 14 days after treatment of male rats with 2000 mg/kg acetochlor. The only sperm parameter affected by treatment with 2000 mg/kg acetochlor was an increase in epididymal cauda sperm with head abnormalities. The non-specific nature of this effect was considered inadequate to explain fully the high dose fertility effects seen in the DL assays, which therefore remain unexplained. The present data establish that acetochlor is non-mutagenic to rat germ cells. They also confirm the importance of segregating mutagenic and fertility effects in the DL assay, and emphasize the need for appropriate dose-setting studies prior to the conduct of rodent genetic toxicity assays.

The tetratricopeptide repeat containing Tg737 gene is a liver neoplasia tumor suppressor gene.

The Tg737 gene was investigated for gross alterations in a series of rodent/human liver tumors and human tumorigenic cell lines. The Tg737 gene was found to be altered in approximately 40% of the rodent chemically-induced liver tumors, 40% of the human liver tumors, and in liver, kidney and pancreatic human tumor cell lines. Ectopic re-expression of the Tg737 gene in a Tg737 deleted mouse liver tumor cell line resulted in suppression of tumorigenic growth, without altering in vitro cell culture growth. Treatment of mice which are either homozygous normal or heterozygous deleted at the Tg737 locus with the carcinogen diethylnitrosamine resulted in an increase in preneoplastic foci formation in the Tg737 heterozygous deleted mice. Ectopic expression of the Tg737 gene results in multinucleated cells, loss of Tg737 gene expression results in the proliferation of liver stem cells (oval cells) without concomitant differentiation, and reexpression of the Tg737 gene reestablished responsiveness to external differentiation factors. We believe this is the first report demonstrating tumor suppression activity for a tetratricopeptide repeat gene family member and provides insights into the function of this family of genes in mammalian cells.

A cellular automata model of diffusion in aqueous systems.

A cellular automata model of a solute diffusing in water has been created and studied for the influential attributes. The results with this model are in agreement with experimental results; that is, that lipophilic solutes diffuse faster than do polar solutes. The model reveals that a solution composed of a relatively lipophilic solute permits a greater extent of diffusion of another solute. This observation is in agreement with the model showing a diffusion preference of a solute between two solutions made up of differing polarities. The solute diffuses farther into the lipophilic solution. A temperature-lipophilicity phase diagram shows the influence of these two attributes on the rate of diffusion. A model of diffusion through solutions containing stationary ingredients reveals a faster rate when the ingredient is lipophilic. We are led to a conclusion that the relative lipophilicity of solutes or stationary ingredients in a solution has a direct influence on the rates of diffusion of other solutes in their midst.

E-state fields: applications to 3D QSAR.

The derivation of a new 3D QSAR field based on the electrotopological state (E-state) formalism is described. A complementary index and its associated field, the HE-state, describing the polarity of hydrogens is also defined. These new fields are constructed from a nonempirical index that incorporates electronegativity, the inductive influence of neighboring atoms, and the topological state into a single atomistic descriptor. The classic CoMFA steroid test data set was examined with models incorporating the E-state and HE-state fields alone and in combination with steric, electrostatic and hydropathic fields. The single best model was the E-state/HE-state combination with q2 = 0.803 (three components) and r2 = 0.979. Using the E-state and/or HE-state fields with other fields consistently produced models with improved statistics, where the E-state fields provided a significant, if not dominant, contribution.

Evaluation of the potential carcinogenicity and genetic toxicity to humans of the herbicide acetochlor.

Comprehensive toxicological studies of the herbicide acetochlor are presented and discussed. Although it gave a negative profile of responses in the many toxicity tests conducted there were some findings that prompted further investigation. First, although non-mutagenic in the Salmonella assay, acetochlor was clastogenic to mammalian cells treated in vitro. This clastogenic potential was not expressed in vivo in four rodent cytogenetic assays (bone marrow and germ cells). Second, although acetochlor gave a negative response in rat liver UDS assays when tested at the acute MTD, gavage administration of a single, supra-MTD dose (2000 mg/kg) gave a weak positive assay response. This dose-level (2000 mg/kg) was necrotic to the liver, depressed hepatic glutathione levels by up to approximately 80%, altered the metabolism of acetochlor, and was associated with up to 33% lethality. In contrast, reference liver genotoxins such as DMN, DMH and 2AAF were shown to elicit UDS in the absence of such effects, and at approximately 400 x lower dose-levels. Finally, microscopic nasal polypoid adenomas were induced in the rat when acetochlor was administered for two years at the maximum tolerated dose (MTD). The tumours were not life-threatening, they did not metastasize, and no DNA damage was induced in the nasal cells of rats maintained on a diet containing the MTD of acetochlor for either 1 or 18 weeks (comet assay). In order to probe the mechanism of action of these high dose toxicities a series of chemical and genetic toxicity studies was conducted on acetochlor and a range of structural analogues. These revealed the chloroacetyl substructure to be the clastogenic species in vitro. Although relatively inert, this substituent is preferentially reactive to sulphydryl groupings, most evidently, to glutathione (GSH). Similar chemical reactivity and clastogenicity in vitro was observed for two related chemicals bearing a chloroacetyl group, both of which have been defined as non-carcinogens in studies reported by the US.NTP. These collective observations indicate that the source of the clastogenicity of acetochlor in vitro is also the source of its rapid detoxification in the rat in vivo, via reaction with GSH. Metabolic studies of acetochlor are described which reveal the formation of a series of GSH-associated biliary metabolites in the rat that were not produced in the mouse. The metabolism of acetochlor in the rat changes with increasing dose-levels, probably because of depletion of hepatic GSH. It is most likely that a rat-specific metabolite is responsible for the rat nasal tumours observed uniquely at elevated dose-levels. The absence of genetic toxicity to the nasal epithelium of rats exposed acutely or subchronically to acetochlor favours a non-genotoxic mechanism for the induction of these adenomas. The observation of a time- and dose-related increase in S-phase cells in the nasal epithelium is consistent with this conclusion. Despite some confusion caused by the early use of perilethal gavage administrations of acetochlor to rodents, and supra-MTD dietary concentrations in some of the chronic studies, the available MTD data are consistent with acetochlor not posing a genetic or carcinogenic hazard to humans.

A cellular automata model of enzyme kinetics.

We have developed a cellular automata model of an enzyme reaction with a substrate in water. The model produces Michaelis-Menten kinetics with good Lineweaver-Burk plots. The variation in affinity parameters predicts that, in general, hydrophobic substrates are more reactive with enzymes, this attribute being more important than the relationship between enzyme and substrate. The ease of generation and the illustrative value of the model lead us to believe that cellular automata models have a useful role in the study of dynamic phenomena such as enzyme kinetics.