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Pathophysiology Nodes

6
6 shared nodes are defined in this module.
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Cell Types

2
cardiomyocyte CL:0000746 Cell Ontology (CL) Relation: this mechanism module involves this cell type This mechanism module involves cardiomyocyte (CL:0000746). CL:0000746 is a cell type from the Cell Ontology. neuron CL:0000540 Cell Ontology (CL) Relation: this mechanism module involves this cell type This mechanism module involves neuron (CL:0000540). CL:0000540 is a cell type from the Cell Ontology.
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Biological Processes

7
electron transport chain GO:0022900 ↓ DECREASED Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves decreased electron transport chain (GO:0022900). GO:0022900 is a biological process from the Gene Ontology. oxidative phosphorylation GO:0006119 ↓ DECREASED Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves decreased oxidative phosphorylation (GO:0006119). GO:0006119 is a biological process from the Gene Ontology. ATP biosynthetic process GO:0006754 ↓ DECREASED Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves decreased ATP biosynthetic process (GO:0006754). GO:0006754 is a biological process from the Gene Ontology. glycolytic process GO:0006096 ↑ INCREASED Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves increased glycolytic process (GO:0006096). GO:0006096 is a biological process from the Gene Ontology. reactive oxygen species metabolic process GO:0072593 ↑ INCREASED Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves increased reactive oxygen species metabolic process (GO:0072593). GO:0072593 is a biological process from the Gene Ontology. response to oxidative stress GO:0006979 ↑ INCREASED Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves increased response to oxidative stress (GO:0006979). GO:0006979 is a biological process from the Gene Ontology. cell death GO:0008219 ↑ INCREASED Gene Ontology (GO) Relation: this mechanism module involves this biological process This mechanism module involves increased cell death (GO:0008219). GO:0008219 is a biological process from the Gene Ontology.
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Notes

This is a mechanism module, not a specific disease. Do NOT create a "Xenobiotic Oxidative Phosphorylation Blockade" Disease entry. Disorder entries reference individual nodes via conforms_to, for example "xenobiotic_oxidative_phosphorylation_blockade#Cellular ATP Depletion despite Preserved Oxygen Delivery". Conforming nodes substitute the specific xenobiotic, the respiratory step it blocks, and the tissue in which the bioenergetic failure is expressed. Scope: the agent must act on mitochondrial ATP synthesis itself. A poison that starves tissue of oxygen before it reaches the mitochondrion belongs elsewhere, even though the endpoint looks the same. Carbon monoxide is the instructive case, because it does both: carboxyhemoglobin formation impairs oxygen delivery, which is a separate upstream mechanism, while a distinct and separately measured fraction of its toxicity is direct inhibition of cytochrome c oxidase. Only the latter arm is in scope here, so the carbon monoxide entry conforms at the respiratory-inhibition node and keeps its oxygen-delivery nodes outside this module. The blocked step is deliberately not fixed at the trigger node. Terminal oxidase inhibition, inhibition of an upstream complex, and arrest of mitochondrial protein synthesis are different lesions that converge on the same ATP deficit, and all three are in scope; the node descriptions and the conforming entry carry which one applies. Uncoupling is a fourth recognized route into the same deficit and is named in the general pharmacology cited at the trigger node, but no dismech entry currently models an uncoupler as its primary mechanism, so no conformer exercises that arm yet. The phrase "despite Preserved Oxygen Delivery" in the central effector names the feature that distinguishes this pathway from ischaemic or hypoxaemic energy failure, and it is a statement about the mechanism rather than a promise about any individual patient. A poisoned patient may be simultaneously hypotensive or hypoxaemic from another cause, and in carbon monoxide poisoning impaired delivery genuinely coexists. Read the node as asserting that a block of the respiratory chain is sufficient to produce the ATP deficit without any reduction in oxygen supply. Lactate is placed as an amplifier rather than a bare readout because the acidosis feeds back on the mechanism. The methanol observational series cited there reports formate rising well before lactate and describes the result as a self-enhancing acidotic circle, so the glycolytic shift is modelled as acting on, and not merely reporting, the downstream tissue injury. Known bundling in that same node, recorded rather than fixed: `Anaerobic Glycolytic Shift with Lactic Acidosis` carries a cellular metabolic shift and a systemic acid-base consequence together, and is tagged `ORGANISM` for the latter. Under the single-value scale discipline a node that would naturally take two values is a split signal, and this one would. It is kept whole here because the feedback the amplifier role rests on is a property of the acidosis, so splitting it without also re-pointing that edge would lose the reason the node is an amplifier at all. A later split should separate the cellular shift from the systemic acidosis and land the feedback edge on the acidosis node. Scope leakage to be aware of at the oxidative-stress node, for the same reason the carbon monoxide delivery nodes are excluded above: that entry's `Oxidative stress and free radical generation` node attributes reactive oxygen species both to mitochondrial dysfunction and to nitric oxide displaced from hemoproteins. The second route belongs to the oxygen-delivery arm this module puts outside its boundary, so the conformance carries a little of it in. The bundling predates this module and is not introduced by it; it is named here because the module's own scope paragraph is what makes it visible.
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Used By Disorder Entries

6
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Pathograph

Use the checkboxes to hide or show graph categories. Hover nodes for evidence-backed metadata.
Pathograph: causal mechanism network for Xenobiotic Oxidative Phosphorylation Blockade Module Interactive directed graph showing how this shared module's pathophysiology nodes connect.
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Pathophysiology

6
Xenobiotic Blockade of Mitochondrial Respiration
trigger
A drug or toxin blocks a step that oxidative phosphorylation requires. The lesion may be inhibition of the terminal oxidase, as with cyanide, carbon monoxide, or the formate generated from methanol and from formaldehyde, all of which act at cytochrome c oxidase; inhibition of an upstream respiratory complex, as with the diglycolic acid generated from diethylene glycol at complex II; or arrest of mitochondrial translation so that short-lived respiratory-chain subunits are not replaced, as with chloramphenicol at the mitochondrial ribosome. These are chemically unrelated lesions at different points of the same pathway, and the module treats them as alternative entry points rather than as separate mechanisms.
electron transport chain GO:0022900 ↓ DECREASED Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves decreased electron transport chain (GO:0022900). GO:0022900 is a biological process from the Gene Ontology.
Show evidence (5 references)
PMID:16863431 SUPPORT DIRECT Other
"Drugs that injure mitochondria usually do so by inhibiting respiratory complexes of the electron chain; inhibiting or uncoupling oxidative phosphorylation; inducing mitochondrial oxidative stress; or inhibiting DNA replication, transcription or translation."
Review of drug-induced mitochondrial toxicity; no primary experimental system. Establishes that chemically distinct agents enter the same bioenergetic pathway at several different steps, which is the claim this trigger node makes in treating terminal-oxidase inhibition, upstream complex inhibition, and translational arrest as alternative entry points.
PMID:17906319 SUPPORT DIRECT In Vitro
"Acute cyanide toxicity is attributed to inhibition of cytochrome c oxidase (CcOX), the oxygen-reducing component of mitochondrial electron transport"
Isolated mitochondria and cell-based measurements of cytochrome c oxidase activity. Documents the terminal-oxidase arm of this node, in which the agent inhibits the oxygen-reducing step of the respiratory chain directly.
PMID:9584335 SUPPORT DIRECT Human Clinical
"cytochrome c oxidase (complex IV) activity showed a 76% inhibition compared to controls during acute poisoning"
Complex IV activity assayed in patients during and after acute poisoning. Shows terminal-oxidase inhibition as a measured finding in poisoned humans, not only in isolated preparations, and quantifies the degree of blockade at this node.
+ 2 more references
Cellular ATP Depletion despite Preserved Oxygen Delivery
central effector
With a required step of the respiratory chain blocked, the cell cannot phosphorylate ADP even though oxygen continues to reach the mitochondrion. This is the rate-limiting, disorder-agnostic step of the module and the key conformance target: every conforming entry funnels through it whichever respiratory step its agent hit. The preserved oxygen supply is what separates this pathway from ischaemic and hypoxaemic energy failure, and it is the reason poisoned tissue can be bioenergetically starved while arterial oxygenation looks adequate.
oxidative phosphorylation GO:0006119 ↓ DECREASED Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves decreased oxidative phosphorylation (GO:0006119). GO:0006119 is a biological process from the Gene Ontology. ATP biosynthetic process GO:0006754 ↓ DECREASED Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves decreased ATP biosynthetic process (GO:0006754). GO:0006754 is a biological process from the Gene Ontology.
Show evidence (5 references)
PMID:25692407 SUPPORT DIRECT Other
"cyanide inhibits cytochrome c oxidase, thus blocking electron transport in the mitochondrial respiratory chain and disrupting oxidative phosphorylation"
Rodent neuroprotection study; the quoted sentence is the mechanistic framing rather than a result of the experiments reported. States the step from a blocked chain to disrupted oxidative phosphorylation, which is the transition this node represents.
PMID:37465777 SUPPORT DIRECT Other
"it blocks the cells from utilizing oxygen by binding to the cytochrome oxidase in the mitochondria"
Clinical toxicology review; no primary experimental system. Supports the defining feature of this node, that the defect is an inability to use oxygen rather than a shortage of it, which is what distinguishes this pathway from ischaemic energy failure.
PMID:21856646 SUPPORT DIRECT In Vitro
"DGA induced necrosis, not apoptosis, as corroborated by severe depletion of cellular adenosine triphosphate levels."
Human proximal tubule cells in culture with direct ATP measurement. Measures the ATP deficit this node asserts and ties it to necrotic rather than apoptotic death, which is the mode of death an acute energy failure produces.
+ 2 more references
Anaerobic Glycolytic Shift with Lactic Acidosis
amplifier
Unable to phosphorylate ADP oxidatively, cells raise glycolytic flux and regenerate NAD+ by reducing pyruvate to lactate. Lactate accumulates and produces a metabolic acidosis with a raised anion gap, which is the laboratory signature of this pathway and a widely used severity marker. The acidosis is modelled as an amplifier rather than as a bare readout because the fall in pH worsens the toxicity that produced it, a feedback described in methanol poisoning as a self-enhancing acidotic circle.
glycolytic process GO:0006096 ↑ INCREASED Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves increased glycolytic process (GO:0006096). GO:0006096 is a biological process from the Gene Ontology.
Show evidence (5 references)
PMID:29923671 SUPPORT DIRECT Human Clinical
"most likely caused by formate inhibition of mitochondrial respiration (type B lactacidosis)"
Observational study of 35 poisoned patients with serial formate, lactate, and blood gas measurements. Attributes the rising lactate to inhibition of mitochondrial respiration rather than to circulatory failure, which is precisely the causal direction this node asserts.
PMID:29923671 SUPPORT DIRECT Human Clinical
"S-lactate and S-formate correlated better with the increased base deficit and anion gap than did S-formate alone."
Same patient series. Ties the accumulating lactate specifically to the raised anion gap, which is the laboratory signature this node is written around, and shows lactate contributes to it beyond the toxic acid itself.
PMID:12352039 SUPPORT DIRECT Human Clinical
"there was a significant correlation between plasma lactate and blood cyanide concentrations"
Clinical series correlating plasma lactate with measured blood toxin concentration. Shows the glycolytic shift scales with the dose of the respiratory inhibitor, supporting lactate as a readout of the blockade rather than an incidental finding.
+ 2 more references
Secondary Mitochondrial Oxidative Stress
amplifier
A blocked respiratory chain with a falling membrane potential leaks reactive oxygen species, so an oxidative insult is superimposed on the energy deficit. This arm explains injury that continues, and in some agents worsens, after the inhibitor itself has been cleared, and it is the step at which lipid peroxidation and the delayed inflammatory component of these poisonings are generated. Two processes are bound here on purpose and they are not redundant: the node's primary claim is that reactive oxygen species are *produced*, which is `GO:0072593`, and the cell's `GO:0006979` response to them is the second, consequent claim. The response term alone would understate the node, and it is also the term the conforming entries carry, so both are kept.
reactive oxygen species metabolic process GO:0072593 ↑ INCREASED Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves increased reactive oxygen species metabolic process (GO:0072593). GO:0072593 is a biological process from the Gene Ontology. response to oxidative stress GO:0006979 ↑ INCREASED Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves increased response to oxidative stress (GO:0006979). GO:0006979 is a biological process from the Gene Ontology.
Show evidence (2 references)
PMID:26386112 SUPPORT DIRECT Other
"The final phase of mitochondrial dysfunction induces loss of mitochondrial membrane potential and an increase in mitochondrial oxidative/nitrative stress, eventually culminating into cell death."
Review of drug-induced mitochondrial cardiotoxicity; no primary experimental system. States the sequence this node represents, from lost membrane potential to mitochondrial oxidative stress to cell death, as a general consequence of chemically impaired mitochondrial function.
PMID:24773392 SUPPORT DIRECT Other
"the oxidative injury induced by reactive oxygen species, free radicals, and neuronal nitric oxide"
Review of oxidative mechanisms in one exemplar poisoning; no primary experimental system. Supports treating reactive oxygen species as a substantive injury arm in its own right rather than as a by-product, which is why this is modelled as an amplifier node and not a readout.
Energy Failure of High Oxidative-Demand Tissue
effector
Tissues differ in how much of their ATP demand they can meet glycolytically, so a uniform systemic block of oxidative phosphorylation produces a strikingly selective injury. The myocardium and the brain, which combine high continuous ATP demand with little anaerobic reserve, fail first; within the brain the deep grey nuclei are the most vulnerable. Conforming entries substitute the organ in which their agent's failure is clinically expressed.
cardiomyocyte CL:0000746 Cell Ontology (CL) Relation: this pathophysiological event involves this cell type This pathophysiological event involves cardiomyocyte, annotated with cardiac muscle cell (CL:0000746). CL:0000746 is a cell type from the Cell Ontology. neuron CL:0000540 Cell Ontology (CL) Relation: this pathophysiological event involves this cell type This pathophysiological event involves neuron (CL:0000540). CL:0000540 is a cell type from the Cell Ontology.
Show evidence (2 references)
PMID:27753502 SUPPORT DIRECT Other
"cellular mitochondrial respiration, cellular energy utilization, inflammation, and free radical generation, especially in the brain and heart"
Review of the poisoning's pathogenesis; no primary experimental system. Names the two organs this node selects and attributes their involvement to impaired mitochondrial respiration and energy utilization, which is the organ-selection claim the node makes.
PMID:26386112 SUPPORT DIRECT Other
"deterioration in mitochondrial function eventually leads to cardiomyocyte and endothelial cell death and consequent cardiovascular dysfunction"
Review of drug-induced mitochondrial cardiotoxicity; no primary experimental system. Supports the myocardial arm of this node, from impaired mitochondrial function to cardiomyocyte death to circulatory failure.
Selective Deep Grey Matter and Myocardial Necrosis
consequence
The outcome of the module: necrosis concentrated in the deep grey nuclei of the brain and in the myocardium, with the remainder of the organ relatively spared. In survivors the pallidal and putaminal lesions underlie the delayed movement disorders and neuropsychiatric sequelae that follow these poisonings by days to weeks, while myocardial involvement presents acutely as circulatory failure. The anatomical pattern is the fingerprint of this mechanism, and it is shared across chemically unrelated agents, which is the strongest single argument that they are one pathway.
cell death GO:0008219 ↑ INCREASED Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves increased cell death (GO:0008219). GO:0008219 is a biological process from the Gene Ontology.
Show evidence (4 references)
PMID:12223384 SUPPORT DIRECT Human Clinical
"The toxicity of cyanide causes damage, primarily to the basal ganglia"
Serial MR imaging after a documented human poisoning. Establishes the anatomical selectivity this node asserts for a terminal-oxidase inhibitor.
PMID:36377024 SUPPORT DIRECT Human Clinical
"Haemorrhagic necrosis of bilateral basal ganglia, particularly of the putamen, is one of the distinctive features of this entity."
Human imaging report. Shows the same deep grey matter necrosis after a chemically unrelated agent whose inhibitor is a generated metabolite, which is the cross-agent convergence that justifies this shared node.
PMID:26563790 SUPPORT DIRECT Other
"abnormalities in the globus pallidus are most commonly seen on MRI following CO exposure"
Clinical review of imaging findings; no primary experimental system. Adds a third unrelated agent with the same deep grey matter target, and names the specific nucleus most often affected.
+ 1 more reference
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Treatments

1
Antidotal Scavenging of the Respiratory-Chain Inhibitor (Hydroxocobalamin)
Pharmacotherapy NCIT:C15986 NCI Thesaurus (NCIT) Relation: this treatment is this clinical intervention This treatment is Pharmacotherapy (NCIT:C15986). NCIT:C15986 is a clinical intervention from the NCI Thesaurus.
Agent: hydroxocobalamin CHEBI:27786 Chemical Entities of Biological Interest (CHEBI) Relation: this treatment uses this therapeutic agent This treatment uses hydroxocobalamin (CHEBI:27786). CHEBI:27786 is a therapeutic agent from Chemical Entities of Biological Interest.
Platform: Small molecule
Hydroxocobalamin binds cyanide directly, forming cyanocobalamin, and so lowers the concentration of free inhibitor available to cytochrome c oxidase. It is included here because it is the clearest worked example of this module's drug-target design pattern: an effective antidote acts on the trigger node, removing or displacing the inhibitor, rather than on any downstream consequence. Treating the acidosis or supporting the circulation addresses a consequence and does not restore oxidative phosphorylation. Conforming entries substitute their own agent at the same point in the chain, for example high-concentration oxygen displacing carbon monoxide from cytochrome c oxidase, or fomepizole preventing generation of the inhibitory metabolite in the first place.
Mechanism target:
INHIBITS Xenobiotic Blockade of Mitochondrial Respiration — Scavenging free inhibitor relieves the blockade at its source, which is the only point in this chain at which oxidative phosphorylation can be restored rather than compensated. Evidence: 1
Evidence: 1