GNF-5837

Protein target name:

TRKA, TRKB, TRKC

Mechanism of action:

Inhibitor

Recommended Concentration for use in cells:

~~up to 100 nM~~

Reviewer suggested Concentration for use in cells:

50-500 nM

Probe Availability

TOCRIS

MedChemExpress

Selleck Chemicals

Probe Information

Target and Probe Information

Target Details

Target class:

Protein kinase

Subclass:

HUGO ID:

HGNC:8031 HGNC:8032 HGNC:8033

Entrez gene ID:

4914 4915 4916

UNIPROT ID:

P04629 Q16620 Q16288

Target alias:

MTC; TRK; TRK1; TRKA; Trk-A; p140-TrkA; OBHD; TRKB; DEE58; trk-B; EIEE58; GP145-TrkB; TRKC; GP145-TrkC; gp145(trkC)

Probe Details

Chemical Probes Portal ID:

CPP1236

Probe alias:

GNF 5837, GNF5837, compound 22

PubChem CID:

59397065

ChEMBL ID:

CHEMBL2037226

SMILES string:

CC1=C(C=C(C=C1)NC(=O)NC2=C(C=CC(=C2)C(F)(F)F)F)NC3=CC4=C(C=C3)/C(=C/C5=CC=CN5)/C(=O)N4

InChi Key:

YYDUWLSETXNJJT-MTJSOVHGSA-N

PAINs evaluation:

PAINS-Free

Physico-chemical properties

NMR:

1H NMR (400 MHz, DMSO-d6) δ 13.16 (s, 1 H), 10.72 (s, 1 H), 9.08 (s, 1 H), 8.78 (d, J = 2.8 Hz, 1 H), 8.58 (dd, J = 2.0, 7.2 Hz, 1 H), 7.62 (s, 1 H), 7.52 - 7.40 (m, 3 H), 7.38 - 7.32 (m, 2 H), 7.27 - 7.23 (m, 1 H), 7.13 (d, J = 8.4 Hz, 1 H), 7.04 (dd, J = 2.4, 8.4 Hz, 1 H), 6.71 - 6.68 (m, 1 H), 6.57 (dd, J = 2.0, 8.4 Hz, 1 H), 6.47 (d, J = 1.6 Hz, 1 H), 6.31 - 6.27 (m, 1 H), 2.15 (s, 3 H).

13C NMR (100 Hz, DMSO-d6) δ 169.8, 153.3 (d, J = 246.4 Hz), 151.9, 144.8, 141.3, 140.2, 137.4, 131.1, 129.7, 128.9 (d, J = 10.8 Hz), 123.8 (q, J = 275.3 Hz), 125.3 (dd, J = 31.7, 6.7 Hz), 124.1, 123.7, 122.5, 119.4, 119.0, 118.3, 117.8, 116.3, 116.1, 115.9 (d, J = 22.9 Hz), 112.2, 110.8, 110.2, 109.3, 97.6, 17.3.

Validation in Cells and Model Organisms

In vitro validation

On target activity

Potency:

IC50

8 (A), 12 (B) nM

Potency assay:

HTRF Assay

PDB ID for probe-target interaction (3D structure):

3V5Q

Structure-activity relationship:

yes

Off target activity

Probe Selectivity in Vitro:

Highly selective in a Biochemical Kinase Panel (Invitrogen).

In cell validation

On target activity in cells

Potency in cells:

IC50

11 nM TRKA, 9 nM TRKB, 7 nM TRKC

Potency assay (cells):

cellular Ba/F3 assays, anti-proliferation assay,

Off target activity in cells

Potency assay, off target (cells):

Ba/F3 Cellular assay

Probe Selectivity in Cell:

In Ba/F3 Cellular Kinase Panel of 25 Kinases fused with Tel dimerisation partner showed IC50 >3 uM except for c-KIT 910 nM and PDGFRβ 870 nM

In vivo validation

Organism:

male Balb/c mice (M)Sprague–Dawley rats (R)

Dose:

50-100 mg/Kg

Route of delivery:

OralIntravenous

Plasma half life:

4.4, 4.5 (M) h 7.5, 7.1 (R) h

Systemic clearance:

8.2 (M), 9 (R) mL/min/kg

Fraction of probe bound to plasma protein:

18 (M) %19 (R) %

Cmax:

16360 (IV) 1173 (PO) nM (M)5196 (IV) 449 (PO) nM (R)

Primary Reference

Reference (doi):

10.1021/ml200261d 10.1530/ERC-17-0201

Reference (PMID):

24900443 29563190

Endorsed probe

The Chemical Probes Portal endorses this compound as chemical probe for use in cells and in model organisms.

SAB Rating

Rating for use in Cells

3 review(s)

Rating for use in Model Organisms

3 review(s)

SAB Members

SAB Comments

There are more well-characterized tools, in particular Laratrectinib which is both approved for human use and better profiled for selectivity against more kinases (link)or perhaps clinical compounds AZD7451.

Cell Concentration notes: Fig1 of the 2nd reference shows a plateau of activity from 50-500 nM in GOT1 cell.

Ref1 demonstrates sufficient IV and PO exposure for human tumor xenograft studies plus demonstrated efficacy. However, given the ~86% similarity between human and rat/mouse TRKA, I would recommend confirming rat or mouse potency comparable to humans before using rats or mice as an efficacy model in a non-human xenograft study

Aug 4 2021 - 9:23pm

Together the two reference documents provide acceptable evidence that cell-based and organism-based anticancer activity may be due to pan TRK inhibition, and the E-R Cancer study shows evidence of target inhibition in cells. However, like many kinase inhibitor studies, more evidence may be required to be certain that in vivo efficacy reflects target engagement and further, also like many kinase inhibitor studies, in the absence of an entirely comprehensive kinase profile and other profiling (including tubulin for example), some caution is still advised in assuming that all cell-based activity arises from pan Trk inhibition since the kinase inhibitor field continues to surprise. Finally, it would be useful to identify a negative control – perhaps an N-methylated analogue or better, one with the CF3 moved to the para position (if all Trk activity is lost), and to use this in all studies.

Aug 26 2021 - 9:13am

GNF-5837

Probe Availability

Probe Information

Target Details

MTC; TRK; TRK1; TRKA; Trk-A; p140-TrkA; OBHD; TRKB; DEE58; trk-B; EIEE58; GP145-TrkB; TRKC; GP145-TrkC; gp145(trkC)

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

In vivo validation

Primary Reference

Supporting Organizations

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Search form

GNF-5837

Probe Availability

Probe Information

Target Details

MTC; TRK; TRK1; TRKA; Trk-A; p140-TrkA; OBHD; TRKB; DEE58; trk-B; EIEE58; GP145-TrkB; TRKC; GP145-TrkC; gp145(trkC)

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

In vivo validation

Primary Reference

Supporting Organizations

Interested in supporting the portal?