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T G Waddell

Publications and source records attributed to T G Waddell.

At least 19 recordsLinked to original sources
PubMed2001

A new method for assembling metabolic networks, with application to the Krebs citric acid cycle.

To understand why a molecular network has a particular connectivity one can generate an ensemble of alternative networks, all of which meet the same performance criteria as the real network. We have generated alternatives to the Krebs cycle, allowing group transfers and B(12)-mediated shifts that were excluded in previous work. Our algorithm does not use a reaction list, but determines the reactants and products in generic reactions. It generates networks in order of increasing number of reaction steps. We find that alternatives to the Krebs cycle are very likely to be cycles. Many of the alternatives produce toxic or unstable compounds and use group transfer reactions, which have unfavorable consequences. Although alternatives are better than the Krebs cycle in some respects, the Krebs cycle has the most favorable combination of traits.

Algorithms↗
PubMed2001

Explaining photodermatosis: cyclopentenone vs. alpha-methylene-gamma-lactone natural products.

The possible role of cyclopentenone-containing sesquiterpene lactones in the cause of photochemical chronic actinic dermatitis (CAD) is examined in light of recent reports that the alpha-methylene-gamma-lactone group of these natural products forms 2+2 photoadducts with the DNA base thymine. Neither cyclopentenone nor tenulin (a cyclopentenone-containing sesquiterpene lactone) form such photoadducts with thymine either with sunlight or a UV lamp (300 nm). In contrast, alpha-methylenebutyrolactone readily forms the 2+2 photoadduct with thymine in sunlight. Thus, the photochemical role of the alpha-methylene-gamma-lactone group (rather than cyclopentenone) is strongly implicated in the CAD disease.

Asteraceae↗
PubMed2000

Prebiotic methylation and the evolution of methyl transfer reactions in living cells.

An hypothesis is presented for the prebiotic origin of methyl groups and the evolution of methyl transfer reactions in living cells. This hypothesis, described in terms of prebiotic and early biotic chemical evolution, is based on experimental observations in our lab and in those of others, and on the mechanisms of enzymatic methyl transfer reactions that occur in living cells. Of particular interest is our demonstration of the reductive methylation of ethanolamine and glycine in aqueous solution by excess formaldehyde. These reactions, involving prebiotic compounds and conditions, are mechanistically analogous to the de novo origin of methyl groups in modern cells by reduction of methylene tetrahydrofolate. Furthermore, modern cellular methyl transfers from S-adenosylmethionine to amine nitrogen may involve formaldehyde as an intermediate and subsequent reductive methylation, analogous to the prebiotic chemistry observed herein.

Betaine↗
PubMed2000

Synergistic insecticidal mode of action between sesquiterpene lactones and a phototoxin, alpha-terthienyl.

The synergistic insecticidal action of characteristic defensive substances produced by the plant family Asteraceae was investigated under controlled laboratory conditions. Sesquiterpene lactones isolated from Asteraceae that may form, through a Michael addition process, conjugates with glutathione were administered in a meridic diet to a herbivorous insect, Manduca sexta. By administering sesquiterpenes, variable in vivo reduced glutathione levels were observed in the insect larvae. When the Asteraceae-derived photooxidant alpha-terthienyl was co-administered, lipid peroxidation and larval mortality were significantly enhanced in the treated groups of insects with lowered in vivo glutathione levels.

Animals↗
PubMed1999

Prebiotic synthesis of vitamin B6-type compounds.

Heating a dilute solution of NH3 and glycoaldehyde gives a large family of pyridines substituted with the same functional groups as occur in the forms of vitamin B6. Thus, vitamin B6-like molecules could have been present on the early Earth and could have been available for catalysis of primitive transamination reactions. Ethanolamine and N-methylethanolamine are also formed as major products. These are choline-like molecules, the latter of which is apparently formed by a prebiotic methylation process.

Ammonia↗
PubMed1997

Theoretical approaches to the evolutionary optimization of glycolysis--chemical analysis.

In the first part of this work [Heinrich, R., Montero, F., Klipp, E., Waddell, T. G. & Melendez-Hevia, E. (1997) Eur. J. Biochem. 243, 191-201] the kinetic and thermodynamic constraints under which an optimal glycolysis must be designed have been analysed. In this second part, we present a chemical analysis of the glycolytic pathway in order to determine if its design is chemically optimized according the possibilities that a glycolytic design can have. Our results demonstrate that glycolysis in modern-day cells (from glucose to lactate) has an optimized design for maximizing the flux of ATP production, and a thermodynamic profile which guarantees a high kinetic efficiency. We also discuss some cases of paleometabolism for this pathway as alternative metabolic pathways, less optimized, that exist in some bacteria. Our analysis relates mainly to metabolism designed under constant chemical affinity (substrates and products of the pathway constant), where the target of optimization can be the flux of ATP production. We also discuss the case of an externally imposed input flux, whose target of optimization is the stoichiometric yield of ATP.

Adenosine Triphosphate↗
PubMed1997

Theoretical approaches to the evolutionary optimization of glycolysis: thermodynamic and kinetic constraints.

It is analyzed whether the structural design of contemporary glycolysis can be explained theoretically on the basis of optimization principles originating from natural selection during evolution. Particular attention is paid to the problem of how the kinetic and thermodynamic properties of the glycolytic pathway are related to its stoichiometry with respect to the number and location of ATP-coupling sites. The mathematical analysis of a minimal model of unbranched energy-converting pathways shows that the requirement of high ATP-production rate favours a structural design that includes not only ATP-producing reactions (P-sites) but also ATP-consuming reactions (C-sites). It is demonstrated that, at fixed overall thermodynamic properties of a chain, the ATP-production rate may be enhanced by kinetic optimization. The ATP-production rate is increased if the C-sites are concentrated at the beginning and all the P-sites at the end of the pathway. An optimum is attained, which is characterized by numbers of coupling sites corresponding to those found in glycolysis. Various extensions of the minimal model are considered, which allow the effects of internal feedback-regulations, variable enzyme concentrations, and the symmetric branching of glycolysis at the aldolase step to be considered.

Adenosine Triphosphate↗
PubMed1997

Prebiotic transamination.

Biological amino acids and alpha keto acids directly condense with decarboxylation and transamination to yield product amino acids. This process is closely related to unusual amino acid decarboxylase enzymes in certain microorganisms and may represent a primordial mode of amino acid metabolism.

Alanine↗
PubMed1996

The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution.

The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained? A number of speculative studies have been carried out that have reached the conclusion that the Krebs cycle evolved from pathways for amino acid biosynthesis, but many important questions remain open: Why and how did the full pathway emerge from there? Are other alternative routes for the same purpose possible? Are they better or worse? Have they had any opportunity to be developed in cellular metabolism evolution? We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of this metabolic pathway as it occurs in living cells is the best chemical solution: It has the least possible number of steps and it also has the greatest ATP yielding. Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into a single-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.

Acetates↗
PubMed1993

Optimization of molecular design in the evolution of metabolism: the glycogen molecule.

The animal glycogen molecule has to be designed in accordance with its metabolic function as a very effective fuel store allowing quick release of large amounts of glucose. In addition, the design should account for a high capacity of glucose storage in the least possible space. We have studied the optimization of these variables by means of a mathematical model of the glycogen molecule. Our results demonstrate that the structure is optimized to maximize (a) the total glucose stored in the smallest possible volume, (b) the proportion of it that can be directly released by phosphorylase before any debranching occurs, and (c) the number of non-reducing ends (points of attack for phosphorylase), which maximizes the speed of fuel release. The optimization of these four variables is achieved with appropriate values for two key parameters in glycogen design: the degree of branching and the length of the chains. The optimal values of these two parameters are precisely those found in cellular glycogen.

Animals↗
PubMed1980

Mode of action of sesquiterpene lactones as anti-inflammatory agents.

Sesquiterpene lactones containing an alpha-methylene-gamma-lactone moiety were shown to be potent inhibitors of carrageenan-induced edema and chronic adjuvant-induced arthritis in rodents at 2.5 mg/kg/day. The mode of action of sesquiterpene lactones as anti-inflammatory agents appeared to be at multiple sites; for example, at 5 X 10(-4) M, the sesquiterpene lactones effectively uncoupled the oxidative phosphorylation of human polymorphonuclear neutrophils and elevated the cyclic adenosine monophosphate levels of rat neutrophils and rat and mouse liver cells. Free and total lysosomal enzymatic activity was inhibited by these agents at 5 X 10(-4) M in both rat and mouse liver and rat and human neutrophils. Furthermore, the structure-activity relationships for the stabilization of lysosomal membrane for rat liver cathepsin activity followed the same structural requirement necessary for anti-inflammatory activity; i.e., the alpha-methylene-gamma-lactone moiety contributed the most activity, whereas the beta-unsubstituted cyclopentenone and alpha-epoxycyclopentanone contributed only minor activity. Human polymorphonuclear neutrophil chemotaxis was inhibited at low concentrations (i.e., 5 X 10(-5) and 5 X10(-6) M), whereas prostaglandin synthetase activity was inhibited at a higher concentration (i.e., 10(-3) M) by the sesquiterpene lactones.

Acid Phosphatase↗
PubMed1980

Antihyperlipidemic activity of sesquiterpene lactones and related compounds.

Some naturally occurring pseudoguaianolides and germacranolides as well as synthetic related compounds were observed to be antihyperlipidemic agents in mice. Several of these compounds at a dose of 20 mg/kg/day resulted in lowering of serum cholesterol by approximately 30% and of serum triglycerides by approximately 25%. Thiol-bearing enzymes of lipid synthesis, i.e., acetyl-CoA, citrate-lyase, acetyl-CoA synthetase, and beta-hydroxy-beta-methylglutaryl-CoA reductase, were inhibited by these agents in vitro, supporting the premise that these agents alkylate thiol nucleophiles by a Michael-type addition. The alpha-methylene-gamma-lactone moiety, the beta-unsubstituted cyclopentenone ring, and the alpha-epoxycyclopentanone system of these compounds appeared to be responsible for the lowering of serum lipids.

Animals↗
PubMed1979

Anti-inflammatory activity of sesquiterpene lactones and related compounds.

Some sesquiterpene lactones and related compounds were tested for anti-inflammatory activity in rodents. In the edema-induced carrageenan inflammation screen, the alpha-methylene-gamma-lactone moiety of the sesquiterpene lactones was required for inhibitory activity. The 6-hydroxy group of helenalin also was required for potency. In the tenulin series, the 2,3-epoxy derivatives were marginally active. The same structure was required for inhibition of the writhing reflex. In the chronic adjuvant arthritic screen, compounds containing the alpha-methylene-gamma-lactone moiety, the beta-unsubstituted cyclopentenone ring, and the alpha-epoxy cyclopentenone system afforded significant inhibition at 2.5 mg/kg/day. The sesquiterpene lactones were marginally effective against induced pleurisy. The delayed hypersensitivity was suppressed by these agents whereas immunoglobulin synthesis was slightly stimulated. No delerious side effects were observed with these agents from the limited tests performed.

Anaphylaxis↗
PubMed1979

Antitumor agents: structure--activity relationships in tenulin series.

Systematic structural modifications were performed on the natural sesquiterpene lactone tenulin to define those groupings essential to, or significant in, its in vivo antitumor activity. Accordingly, the following tenulin analogs were prepared: dihydrotenulin, 2,3-epoxytenulin, isotenulin, dihydroisotenulin, 2,3-epoxyisotenulin, and tetrahydrodeacetylisotenulin. Both the cyclopentenone and the hemiketal units in tenulin were necessary for high in vivo activity.

Animals↗
PubMed1977

Sesquiterpene antitumor agents: inhibitors of cellular metabolism.

Helenalin and tenulin injected into CF1 male mice bearing Ehrlich ascites tumors inhibit DNA synthesis and DNA polymerase enzymatic activity in the tumor cells. Helenalin inhibited protein synthesis. Both drugs increased the concentration of adenosine 3',5'-monophosphate, and interfered with glycolytic and mitochondrial energy processes. Cholesterol synthesis was also inhibited, resulting in lower serum cholesterol levels in tumor-bearing animals. Data obtained in vitro indicate that the cyclopentenone-bearing sesquiterpene lactone and related compounds do not alkylate puring bases of nucleic acids but rather undergo a Michael-type addition reaction with the sulfhydryl groups of reduced glutathione and l-cysteine. Thus, the inhibition of cellular enzyme activities and metabolism that has been observed with these drugs might be explained by the occurrence of a Michael-type teaction.

Alkylation↗