Toolkit/ω-azido-C6-ceramide

ω-azido-C6-ceramide

Construct Pattern·Research·Since 2017

Also known as: ω-azido-functionalized C6-ceramide

Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.

Summary

Determination of the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) demonstrated that short-chain ceramides and a ω-azido-functionalized C6-ceramide were active against Neisseria meningitidis and N. gonorrhoeae.

Usefulness & Problems

Why this is useful

ω-azido-C6-ceramide is a synthetic short-chain ceramide analog reported to kill pathogenic Neisseria and to be rapidly taken up by bacteria. The abstract also describes its membrane localization by fluorescence imaging.; killing pathogenic Neisseria; tracking lipid uptake and localization in bacteria

Source:

ω-azido-C6-ceramide is a synthetic short-chain ceramide analog reported to kill pathogenic Neisseria and to be rapidly taken up by bacteria. The abstract also describes its membrane localization by fluorescence imaging.

Source:

killing pathogenic Neisseria

Source:

tracking lipid uptake and localization in bacteria

Problem solved

It provides a ceramide analog that combines antibacterial activity against pathogenic Neisseria with imaging-compatible localization readouts. This helps connect killing activity with bacterial uptake and membrane distribution.; provides a synthetic short-chain ceramide analog with antibacterial activity against pathogenic Neisseria; enables imaging-based localization of ceramide analogs in bacteria

Source:

It provides a ceramide analog that combines antibacterial activity against pathogenic Neisseria with imaging-compatible localization readouts. This helps connect killing activity with bacterial uptake and membrane distribution.

Source:

provides a synthetic short-chain ceramide analog with antibacterial activity against pathogenic Neisseria

Source:

enables imaging-based localization of ceramide analogs in bacteria

Problem links

enables imaging-based localization of ceramide analogs in bacteria

Literature

It provides a ceramide analog that combines antibacterial activity against pathogenic Neisseria with imaging-compatible localization readouts. This helps connect killing activity with bacterial uptake and membrane distribution.

Source:

It provides a ceramide analog that combines antibacterial activity against pathogenic Neisseria with imaging-compatible localization readouts. This helps connect killing activity with bacterial uptake and membrane distribution.

provides a synthetic short-chain ceramide analog with antibacterial activity against pathogenic Neisseria

Literature

It provides a ceramide analog that combines antibacterial activity against pathogenic Neisseria with imaging-compatible localization readouts. This helps connect killing activity with bacterial uptake and membrane distribution.

Source:

It provides a ceramide analog that combines antibacterial activity against pathogenic Neisseria with imaging-compatible localization readouts. This helps connect killing activity with bacterial uptake and membrane distribution.

Published Workflows

Antibacterial activity of ceramide and ceramide analogs against pathogenic Neisseria

2017

Objective: Evaluate antibacterial activity, host-cell compatibility, and bacterial uptake/localization of sphingolipids and ceramide analogs against pathogenic Neisseria.

Why it works: The workflow combines antibacterial potency assays with kinetic, toxicity, and imaging readouts so that active compounds can be linked to rapid bacterial uptake and membrane localization while checking host-cell compatibility.

rapid bacterial uptakebacterial membrane localizationMIC determinationMBC determinationkinetic killing assayflow cytometryconfocal laser scanning microscopydSTORM

Stages

  1. 1.
    Antibacterial activity profiling by MIC and MBC(broad_screen)

    This stage identifies which sphingolipids and ceramide analogs are active against pathogenic Neisseria and distinguishes them from compounds inactive against comparator bacteria.

    Selection: Compounds showing antibacterial activity against Neisseria meningitidis and N. gonorrhoeae in MIC and MBC assays.

  2. 2.
    Kinetic killing characterization(secondary_characterization)

    This stage characterizes the time scale of bactericidal action for an active compound after initial activity has been established.

    Selection: Measure how quickly an active compound kills N. meningitidis.

  3. 3.
    Host-cell toxicity check(confirmatory_validation)

    This stage checks whether antibacterial activity is accompanied by significant toxicity to host cells.

    Selection: Assess whether bactericidal concentrations cause significant host-cell toxicity.

  4. 4.
    Bacterial uptake and membrane localization imaging(functional_characterization)

    This stage provides spatial and temporal evidence that ceramide analogs enter bacteria rapidly and distribute in the bacterial membrane.

    Selection: Visualize uptake timing and membrane distribution of ceramide analogs in bacteria.

Steps

  1. 1.
    Measure MIC and MBC of sphingolipids and ceramide analogs against pathogenic Neisseria and comparator bacteriatested antibacterial ceramide analog

    Identify active compounds and assess organism selectivity.

    Initial potency testing is needed before kinetic, toxicity, and localization follow-up can focus on active compounds.

  2. 2.
    Test killing kinetics of ω-azido-C6-ceramide against Neisseria meningitidisactive hit selected for kinetic follow-up

    Determine how rapidly the active compound kills bacteria.

    Kinetic characterization follows initial activity detection to refine understanding of bactericidal performance.

  3. 3.
    Assess host-cell toxicity of ω-azido-C6-ceramide at a bactericidal concentrationactive antibacterial candidate under safety check

    Check whether bactericidal dosing causes significant host-cell toxicity.

    A host-compatibility check is performed after antibacterial activity is established to evaluate whether the active compound remains usable in a host-relevant context.

  4. 4.
    Measure bacterial uptake of ceramide analogs by flow cytometry and CLSMassays used to quantify and visualize uptake

    Determine whether ceramide analogs are rapidly taken up by bacteria.

    After activity and host-compatibility are established, uptake measurements help connect antibacterial behavior to bacterial association.

  5. 5.
    Visualize membrane distribution of ceramide analogs by CLSM and dSTORMimaging assays used for localization

    Determine spatial distribution of ceramide analogs in the bacterial membrane.

    Localization imaging follows uptake detection to provide higher-resolution spatial evidence about where the compounds accumulate.

Taxonomy & Function

Primary hierarchy

Mechanism Branch

Architecture: A reusable architecture pattern for arranging parts into an engineered system.

Target processes

localization

Implementation Constraints

cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: sensor

Its antibacterial activity was assessed by MIC, MBC, and kinetic killing assays. Uptake and localization required flow cytometry, confocal laser scanning microscopy, and dSTORM imaging.; activity and imaging evidence in the abstract are limited to pathogenic Neisseria-focused assays; requires flow cytometry and microscopy methods for localization readout

The abstract indicates it was inactive against E. coli and S. aureus, so it does not appear to be a broad-spectrum antibacterial agent. The abstract also does not establish a detailed killing mechanism.; inactive against Escherichia coli and Staphylococcus aureus

Validation

Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication

Supporting Sources

Ranked Claims

Claim 1activitysupports2017Source 1needs review

Short-chain ceramides and ω-azido-C6-ceramide are active against Neisseria meningitidis and Neisseria gonorrhoeae.

Determination of the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) demonstrated that short-chain ceramides and a ω-azido-functionalized C6-ceramide were active against Neisseria meningitidis and N. gonorrhoeae
Claim 2host compatibilitysupports2017Source 1needs review

At a bactericidal concentration, ω-azido-C6-ceramide had no significant toxic effect on host cells.

Of note, at a bactericidal concentration, ω-azido-C6-ceramide had no significant toxic effect on host cells.
Claim 3kineticssupports2017Source 1needs review

ω-azido-C6-ceramide killed Neisseria meningitidis within 2 hours at 1× MIC.

Kinetic assays showed that killing of N. meningitidis occurred within 2 h with ω-azido-C6-ceramide at 1 X the MIC.
killing time 2 h
Claim 4localizationsupports2017Source 1needs review

CLSM and dSTORM showed homogeneous distribution of ceramide analogs in the bacterial membrane.

CLSM and super-resolution fluorescence imaging by direct stochastic optical reconstruction microscopy demonstrated homogeneous distribution of ceramide analogs in the bacterial membrane.
Claim 5specificitysupports2017Source 1needs review

Short-chain ceramides and ω-azido-C6-ceramide were inactive against Escherichia coli and Staphylococcus aureus.

whereas they were inactive against Escherichia coli and Staphylococcus aureus
Claim 6uptake localizationsupports2017Source 1needs review

Ceramide analogs were rapidly taken up by bacteria within 5 minutes.

Lipid uptake and localization was studied by flow cytometry and confocal laser scanning microscopy (CLSM) and revealed a rapid uptake by bacteria within 5 min.
uptake time 5 min

Approval Evidence

1 source5 linked approval claimsfirst-pass slug azido-c6-ceramide
Determination of the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) demonstrated that short-chain ceramides and a ω-azido-functionalized C6-ceramide were active against Neisseria meningitidis and N. gonorrhoeae.

Source:

activitysupports

Short-chain ceramides and ω-azido-C6-ceramide are active against Neisseria meningitidis and Neisseria gonorrhoeae.

Determination of the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) demonstrated that short-chain ceramides and a ω-azido-functionalized C6-ceramide were active against Neisseria meningitidis and N. gonorrhoeae

Source:

host compatibilitysupports

At a bactericidal concentration, ω-azido-C6-ceramide had no significant toxic effect on host cells.

Of note, at a bactericidal concentration, ω-azido-C6-ceramide had no significant toxic effect on host cells.

Source:

kineticssupports

ω-azido-C6-ceramide killed Neisseria meningitidis within 2 hours at 1× MIC.

Kinetic assays showed that killing of N. meningitidis occurred within 2 h with ω-azido-C6-ceramide at 1 X the MIC.

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specificitysupports

Short-chain ceramides and ω-azido-C6-ceramide were inactive against Escherichia coli and Staphylococcus aureus.

whereas they were inactive against Escherichia coli and Staphylococcus aureus

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uptake localizationsupports

Ceramide analogs were rapidly taken up by bacteria within 5 minutes.

Lipid uptake and localization was studied by flow cytometry and confocal laser scanning microscopy (CLSM) and revealed a rapid uptake by bacteria within 5 min.

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Comparisons

Source-stated alternatives

The paper contrasts ω-azido-C6-ceramide with other sphingolipids including sphingosine, short-chain C6-ceramides, and long-chain C16-ceramides.

Source:

The paper contrasts ω-azido-C6-ceramide with other sphingolipids including sphingosine, short-chain C6-ceramides, and long-chain C16-ceramides.

Source-backed strengths

active against Neisseria meningitidis and N. gonorrhoeae; kills N. meningitidis within 2 h at 1× MIC; shows rapid bacterial uptake within 5 min; had no significant toxic effect on host cells at a bactericidal concentration

Source:

active against Neisseria meningitidis and N. gonorrhoeae

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kills N. meningitidis within 2 h at 1× MIC

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shows rapid bacterial uptake within 5 min

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had no significant toxic effect on host cells at a bactericidal concentration

Compared with eNpHR

ω-azido-C6-ceramide and eNpHR address a similar problem space because they share localization.

Shared frame: same top-level item type; shared target processes: localization

Strengths here: looks easier to implement in practice; may avoid an exogenous cofactor requirement.

Compared with GPCR agonist integrator sensor

ω-azido-C6-ceramide and GPCR agonist integrator sensor address a similar problem space because they share localization.

Shared frame: same top-level item type; shared target processes: localization

Compared with kinase translocation reporters

ω-azido-C6-ceramide and kinase translocation reporters address a similar problem space because they share localization.

Shared frame: same top-level item type; shared target processes: localization

Ranked Citations

  1. 1.
    StructuralSource 1Scientific Reports2017Claim 1Claim 2Claim 3

    Extracted from this source document.