---
title: Tricky compounds & inhibitors
disqus: hackmd
---
:::success
> Documentation [name=MrDr.Staffan]
###### tags: `compounds` `inhibitors` `lists`

### Table of Contents
[TOC]
:::
[Top](#Table-of-Contents)

[Also See sheet compounds](https://docs.google.com/spreadsheets/d/10e16IkGVGYTxh0exVJsc9q6Zaggp0YUaV1iSiHhVyAA/edit#gid=1677083374)

# Carnitine related compounds

# DRB - reversibly inhibit transcription
5,6-dichlorobenzimidazole 1-β-d-ribofuranoside (DRB)

https://docs.google.com/presentation/d/14CaYS1_arK7MZh09CnVHSebq9kEgbrtQc1kzyIN0qDo/edit#slide=id.ge53b2acb73_1_31
[Fuchs et al 2014](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-5-r69)
4sUDRB-seq

DRB inhibits 4sU reverse?

Bbox1 increase
[Interpretion?: HOW can transcripts be up if transcription is inhibited?]

# 2-BromoPalmitate inhibiting lipid processing
An inhibitor of S-palmitoylation by DHHC is 2-Bromopalmitate (2-BP). 2-BP is a nonspecific inhibitor that also halts many other lipid-processing enzymes

# Sulfinpyrazone - inhibiting Na channels
[Top](#Table-of-Contents)

anion transport inhibitor sulfinpyrazone

Used by SIUSHANSIAN & WILSON (1995) to look at intracellular ascorbate uptake - if it is dependent on extracellular Na+.

Concentration: **(1 mM)**

# Tetrodotoxin (TTX) - Inhibiting vNa channels
[Top](#Table-of-Contents)

From puffer fish.

Selective blocking of the sodium channel, was shown definitively in 1964 by Toshio Narahashi and John W. Moore.

It inhibits the firing of action potentials in neurons by binding to the voltage-gated sodium

Suggested by John to see what happens if Neurons cant fire.

**Concentration:** Tetrodotoxin inhibits TTX-s Na+ channels at concentrations of around 1-10 nM

# Dexamethasonev(DXM) - Synchronize CLOCK genes in culture
[Top](#Table-of-Contents)

**Generation of Mouse Primary Hypothalamic Neuronal Cultures for Circadian Bioluminescence Assays** https://bio-protocol.org/e3944

n. On day 9 in vitro (DIV9), synchronize the cells for 2 h with 100 nM dexamethasone. Therefore, pipette 25 µl pre-warmed feeding medium containing 900 nM dexamethasone into the wells containing 200 µl medium and incubate for 2 h at 37 °C and 5% CO2

n2. After incubation aspirate medium and change to pre-warmed feeding medium

Concentration: 100nM

https://www.sciencedirect.com/science/article/pii/S0160412019321865

# Valproic acid - Deplete carnitine
[Top](#Table-of-Contents)

valproate

Valproic acid (VPA) is a broad-spectrum antiepileptic drug

ref. needed

# Sodium salicylate - nonselective NF-κB inhibitor
[Top](#Table-of-Contents)

Sodium salicylate

# BODIPY™ 581/591 C11 (Lipid Peroxidation Sensor)
https://www.thermofisher.com/order/catalog/product/D3861#/D3861
Description
BODIPY® 581/591 undecanoic acid can be used to detect reactive oxygen species (ROS) in cells and membranes. Oxidation of the polyunsaturated butadienyl portion of the dye results in a shift of the fluorescence emission peak from ~590 nm to ~510 nm.

Reference: https://www.sciencedirect.com/science/article/pii/S0092867419303873#fig1
We first assessed whether lipids undergo peroxidation following NMDA treatment using the BODIPY 581/591 C11 (BD-C11) ratiometric lipid peroxidation sensor

# Lactate kit
L-lactate Assay kit (Abcam, #ab65331)
Is this an indirect assay?
"lactate is oxidized by lactate dehydrogenase to generate a product which interacts with a probe to produce a color".
[# The kit converts lactate to pyruvate - which interacts with a probe]

Lactate assay protocol summary:
- add samples and standards to wells
- add reaction mix and incubate for 30 min at room temp
- analyze with microplate reader

- **L-Lactate assay kit ab65331** is our most popular L-Lactate assay kit (colorimetric 450nm, range 0.02 mM - 10 mM). Alternative L-Lactate assay kits offer different readout modes/wavelengths and sensitivity/range:
- **L-Lactate assay ab65330**: colorimetric 570 nm, fluorometric Ex/Em 535/587 nm, range 0.001 mM - 10 mM
- **L-Lactate assay ab169557**: fluorometric Ex/Em 535/587 nm, range 0.2 µM - 50 µM

Reference
[Timper et al.,](https://www.sciencedirect.com/science/article/pii/S1550413120302400?via%3Dihub)

# Floxuridine 5FDU
Inhibits DNA synthesis therefore prevents rapidly dividing cells.

Also has "minor effects on RNA synthesis."

# GLP-1R agonist liraglutide (liraglutide594)
Fluorescent GLP-1R agonist

Reference
[Timper et al.,](https://www.sciencedirect.com/science/article/pii/S1550413120302400?via%3Dihub)

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Nonspecific cell damage was observed for triacsin C (≥120 nM), etomoxir (≥400 μM), and fumonisin B1 (≥200 μM). Paumen 1997.

# Triacsin C
Triacsin C inhibits ACSL:s
(1-hydroxy-3-(E,E,E-2',4',7'-undecatrienylidine) triazene)

After their passage across the blood-brain barrier, LCFAs are esterified to LCFA-CoAs within neurons and glial cells. This reaction is catalyzed by the enzyme long-chain acyl-CoA synthetase (ACSLs).

Tony K T Lam, Alessandro Pocai, Roger Gutierrez-Juarez, Silvana Obici, Joseph Bryan, Lydia Aguilar-Bryan, Gary J Schwartz & Luciano Rossetti
https://www.nature.com/articles/nm1201

(Paumen 1997.) 150 nM

# Fumonisin B1
Stock dissolved in water 10mM (Paumen 1997.)
50 μM

Fumonisin B1 is the most prevalent member of a family of toxins, known as fumonisins, produced by several species of Fusarium molds, such as Fusarium verticillioides,[1] which occur mainly in maize (corn), wheat and other cereals.

# Cpt1 inhibitors

**perhexiline**
Perhexiline (Pexsig) is a prophylactic antianginal agent used primarily in Australia and New Zealand. Perhexiline is thought to act by inhibiting mitochondrial carnitine palmitoyltransferase-1. This shifts myocardial metabolism from fatty acid to glucose utilisation which results in increased ATP production for the same O2 consumption

**Teglicar** // ST1326 Inhibitor (reversible)

**ST1340** Inhibitor-inactive-stereo

TDGA Inhibitor (irreversible)
2-tetradecylglydate

# Etomoxir, Cpt1 inhibitor, (inhibitor of B-oxidation)
Stock dissolved in water 10mM (Paumen 1997.)

irreversible inhibitor of carnitine palmitoyltransferase-1 (CPT-1) on the inner face of the outer mitochondrial membrane

Ref. in culture

## [Timper](https://www.sciencedirect.com/science/article/pii/S1550413120302400?via%3Dihub#bib82)
40 μM etomoxir (#E1905, Sigma, preincubation 15 min)

## [Ioannou](https://www.cell.com/cell/fulltext/S0092-8674(19)30387-3)
"Lipid droplet assay" 300 nM etoxomir
unless otherwise indicated, for 4 h at 37°C.

## [Paumen](https://www.jbc.org/article/S0021-9258(19)78383-5/fulltext)
200 μM

## Ref. "applied to mitochondria"
Fatty acid and pyruvate oxidation was assessed using whole-muscle homogenates or isolated skeletal muscle mitochondria as in the study by Hulver et al. (46); etomoxir was used at a final concentration of 100 μM
https://www.pnas.org/content/112/25/E3300.long

Original report:
https://doi.org/10.1016%2F0006-2952%2887%2990458-8

# Mildronate inhibitor of Carnitine synthesis. (mimetic)

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## glibenclamide (GLI) K~ATP~ blocker
"glyburide"
used to treat diabetes mellitus type 2
It is not as good as either metformin or insulin in those who have gestational diabetes.

works by binding to and inhibiting the ATP-sensitive potassium channels (KATP) inhibitory regulatory subunit sulfonylurea receptor 1 (SUR1) in pancreatic beta cells

This inhibition causes cell membrane depolarization, opening voltage-dependent calcium channels. This results in an increase in intracellular calcium in the pancreatic beta cell and subsequent stimulation of insulin release.

https://doi.org/10.1128%2FAAC.00617-06

# Glucocorticoid Receptor inhibitor RU-486
1 µM RU 486 inhibits Glucocorticoid Receptor Activity.
https://nyaspubs.onlinelibrary.wiley.com/doi/abs/10.1196/annals.1320.014?sid=nlm%3Apubmed

# ouabain NaCl dependency

# Activation of PKC
phorbol 12-myristate-13-acetate
phorbol-ester

# Inhibitor of putrescine synthesis.
DFMO, α-difluoromethylornithine, an irreversible inhibitor of ODC


# 4Br-Crotonic acid - b-oxidation
4Br-Crotonic acid]
See talk about myelin use for energy reserves

Optic nerve ex vivo + Glucose starvation model.

Also looked at autophagosomes to see if myelin is degraded