1539-42-0|Bis(pyridin-2-ylmethyl)amine| Ambeed

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Quality Control of [ 1539-42-0 ] Purity: 97% SDS Specification

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Product Citations

Computational modeling and synthesis of pyridine variants of benzoyl-phenoxy-acetamide with high glioblastoma cytotoxicity and brain tumor penetration

Ingraham, Charles H. IV ; Stalinska, Joanna ; Carson, Sean C. ; Colley, Susan B. ; Rak, Monika ; Lassak, Adam , et al.

DOI: 10.1038/s41598-023-39236-w PubMed ID: 37507404 SCI REP-UK,2023,13(1):12236.

Abstract: Glioblastomas are highly aggressive brain tumors for which therapeutic options are very limited. In a quest for new anti-glioblastoma drugs, we focused on specific structural modifications to the benzoyl-phenoxy-acetamide (BPA) structure present in a common lipid-lowering drug, fenofibrate, and in our first prototype glioblastoma drug, PP1. Here, we propose extensive computational analyses to improve the selection of the most effective glioblastoma drug candidates. Initially, over 100 structural BPA variations were analyzed and their physicochemical properties, such as water solubility (- logS), calculated partition coefficient (ClogP), probability for BBB crossing (BBB_SCORE), probability for CNS penetration (CNS-MPO) and calculated cardiotoxicity (hERG), were evaluated. This integrated approach allowed us to select pyridine variants of BPA that show improved BBB penetration, water solubility, and low cardiotoxicity. Herein the top 24 compounds were synthesized and analyzed in cell culture. Six of them demonstrated glioblastoma toxicity with IC50 ranging from 0.59 to 3.24 µM. Importantly, one of the compounds, HR68, accumulated in the brain tumor tissue at 3.7 ± 0.5 µM, which exceeds its glioblastoma IC50 (1.17 µM) by over threefold.

Purchased from AmBeed: 20173-04-0 ; 1539-42-0 ; 16867-03-1 ; 85622-93-1 ; 13207-66-4 ; 591-54-8 ; 6971-44-4 ; 18364-47-1 ; 45695-03-2 ; 2706-56-1 ; 21035-59-6 ; 90-45-9 ; 40154-75-4 ; 38767-72-5 ; 33630-99-8 ; 3731-52-0 ; 27854-90-6 ; 20173-24-4 ; 3731-53-1 ; 42017-89-0 ; 13010-47-4 ; 154-93-8 ; 3731-51-9 ; 56129-55-6 ; 671-16-9 ; 42017-89-0 ; 90-45-9

Product Details of [ 1539-42-0 ]

CAS No. :	1539-42-0
Formula :	C₁₂H₁₃N₃
M.W :	199.25
SMILES Code :	C(NCC1=NC=CC=C1)C1=NC=CC=C1
MDL No. :	MFCD00129044
InChI Key :	KXZQYLBVMZGIKC-UHFFFAOYSA-N
Pubchem ID :	73759

Safety of [ 1539-42-0 ]

GHS Pictogram:
Signal Word:	Warning
Hazard Statements:	H315-H319-H335
Precautionary Statements:	P261-P305+P351+P338

Computational Chemistry of [ 1539-42-0 ] Show Less

Physicochemical Properties

Num. heavy atoms	15
Num. arom. heavy atoms	12
Fraction Csp3	0.17
Num. rotatable bonds	4
Num. H-bond acceptors	3.0
Num. H-bond donors	1.0
Molar Refractivity	59.09
TPSA ? Topological Polar Surface Area: Calculated from Ertl P. et al. 2000 J. Med. Chem.	37.81 Å²

Lipophilicity

Log P_o/w (iLOGP)? iLOGP: in-house physics-based method implemented from Daina A et al. 2014 J. Chem. Inf. Model.	2.2
Log P_o/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by XLOGP program, version 3.2.2, courtesy of CCBG, Shanghai Institute of Organic Chemistry	0.72
Log P_o/w (WLOGP)? WLOGP: Atomistic method implemented from Wildman SA and Crippen GM. 1999 J. Chem. Inf. Model.	1.46
Log P_o/w (MLOGP)? MLOGP: Topological method implemented from Moriguchi I. et al. 1992 Chem. Pharm. Bull. Moriguchi I. et al. 1994 Chem. Pharm. Bull. Lipinski PA. et al. 2001 Adv. Drug. Deliv. Rev.	0.61
Log P_o/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by FILTER-IT program, version 1.0.2, courtesy of SILICOS-IT, http://www.silicos-it.com	2.35
Consensus Log P_o/w? Consensus Log P_o/w: Average of all five predictions	1.47

Water Solubility

Log S (ESOL):? ESOL: Topological method implemented from Delaney JS. 2004 J. Chem. Inf. Model.	-1.86
Solubility	2.77 mg/ml ; 0.0139 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Very soluble
Log S (Ali)? Ali: Topological method implemented from Ali J. et al. 2012 J. Chem. Inf. Model.	-1.09
Solubility	16.1 mg/ml ; 0.0808 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Very soluble
Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by FILTER-IT program, version 1.0.2, courtesy of SILICOS-IT, http://www.silicos-it.com	-5.04
Solubility	0.00184 mg/ml ; 0.00000923 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Moderately soluble

Pharmacokinetics

GI absorption? Gatrointestinal absorption: according to the white of the BOILED-Egg	High
BBB permeant? BBB permeation: according to the yolk of the BOILED-Egg	Yes
P-gp substrate? P-glycoprotein substrate: SVM model built on 1033 molecules (training set) and tested on 415 molecules (test set) 10-fold CV: ACC=0.72 / AUC=0.77 External: ACC=0.88 / AUC=0.94	No
CYP1A2 inhibitor? Cytochrome P450 1A2 inhibitor: SVM model built on 9145 molecules (training set) and tested on 3000 molecules (test set) 10-fold CV: ACC=0.83 / AUC=0.90 External: ACC=0.84 / AUC=0.91	Yes
CYP2C19 inhibitor? Cytochrome P450 2C19 inhibitor: SVM model built on 9272 molecules (training set) and tested on 3000 molecules (test set) 10-fold CV: ACC=0.80 / AUC=0.86 External: ACC=0.80 / AUC=0.87	No
CYP2C9 inhibitor? Cytochrome P450 2C9 inhibitor: SVM model built on 5940 molecules (training set) and tested on 2075 molecules (test set) 10-fold CV: ACC=0.78 / AUC=0.85 External: ACC=0.71 / AUC=0.81	No
CYP2D6 inhibitor? Cytochrome P450 2D6 inhibitor: SVM model built on 3664 molecules (training set) and tested on 1068 molecules (test set) 10-fold CV: ACC=0.79 / AUC=0.85 External: ACC=0.81 / AUC=0.87	No
CYP3A4 inhibitor? Cytochrome P450 3A4 inhibitor: SVM model built on 7518 molecules (training set) and tested on 2579 molecules (test set) 10-fold CV: ACC=0.77 / AUC=0.85 External: ACC=0.78 / AUC=0.86	Yes
Log Kp (skin permeation)? Skin permeation: QSPR model implemented from Potts RO and Guy RH. 1992 Pharm. Res.	-7.0 cm/s

Druglikeness

Lipinski? Lipinski (Pfizer) filter: implemented from Lipinski CA. et al. 2001 Adv. Drug Deliv. Rev. MW ≤ 500 MLOGP ≤ 4.15 N or O ≤ 10 NH or OH ≤ 5	0.0
Ghose? Ghose filter: implemented from Ghose AK. et al. 1999 J. Comb. Chem. 160 ≤ MW ≤ 480 -0.4 ≤ WLOGP ≤ 5.6 40 ≤ MR ≤ 130 20 ≤ atoms ≤ 70	None
Veber? Veber (GSK) filter: implemented from Veber DF. et al. 2002 J. Med. Chem. Rotatable bonds ≤ 10 TPSA ≤ 140	0.0
Egan? Egan (Pharmacia) filter: implemented from Egan WJ. et al. 2000 J. Med. Chem. WLOGP ≤ 5.88 TPSA ≤ 131.6	0.0
Muegge? Muegge (Bayer) filter: implemented from Muegge I. et al. 2001 J. Med. Chem. 200 ≤ MW ≤ 600 -2 ≤ XLOGP ≤ 5 TPSA ≤ 150 Num. rings ≤ 7 Num. carbon > 4 Num. heteroatoms > 1 Num. rotatable bonds ≤ 15 H-bond acc. ≤ 10 H-bond don. ≤ 5	1.0
Bioavailability Score? Abbott Bioavailability Score: Probability of F > 10% in rat implemented from Martin YC. 2005 J. Med. Chem.	0.55

Medicinal Chemistry

PAINS? Pan Assay Interference Structures: implemented from Baell JB. & Holloway GA. 2010 J. Med. Chem.	0.0 alert
Brenk? Structural Alert: implemented from Brenk R. et al. 2008 ChemMedChem	0.0 alert: heavy_metal
Leadlikeness? Leadlikeness: implemented from Teague SJ. 1999 Angew. Chem. Int. Ed. 250 ≤ MW ≤ 350 XLOGP ≤ 3.5 Num. rotatable bonds ≤ 7	No; 1 violation:MW<1.0
Synthetic accessibility? Synthetic accessibility score: from 1 (very easy) to 10 (very difficult) based on 1024 fragmental contributions (FP2) modulated by size and complexity penaties, trained on 12'782'590 molecules and tested on 40 external molecules (r² = 0.94)	1.58

Application In Synthesis of [ 1539-42-0 ]

* All experimental methods are cited from the reference, please refer to the original source for details. We do not guarantee the accuracy of the content in the reference.

Downstream synthetic route of [ 1539-42-0 ]

[ 1539-42-0 ] Synthesis Path-Downstream 1~33

1
[ 1539-42-0 ]
[ 99970-84-0 ]
4,4'-bis[(2,2'-dipicolylamino)methyl]-2,2'-bipyridine [ No CAS ]

References: [1]Chemical Communications,2004,p. 420 - 421.
[2]Organic and Biomolecular Chemistry,2008,vol. 6,p. 493 - 499.

2
[ 81998-05-2 ]
[ 1539-42-0 ]
[ 344367-69-7 ]

References: [1]Organic and Biomolecular Chemistry,2008,vol. 6,p. 493 - 499.

3
[ 23602-63-3 ]
[ 1539-42-0 ]
[ 1105704-31-1 ]

References: [1]New Journal of Chemistry,2008,vol. 32,p. 2279 - 2291.

4
[ 904886-25-5 ]
[ 1539-42-0 ]
[ 1252796-44-3 ]

References: [1]Chemical Communications,2010,vol. 46,p. 6554 - 6556.

5
[ 3314-30-5 ]
[ 1539-42-0 ]
[ 345349-15-7 ]

References: [1]Journal of the American Chemical Society,2010,vol. 132,p. 14570 - 14576.

6
[ 55589-47-4 ]
[ 1517-69-7 ]
[ 54010-75-2 ]
[ 1539-42-0 ]
[ 75-05-8 ]
C₂₉H₃₁N₅OZn⁽²⁺⁾ [ No CAS ]

References: [1]Chemical Science,2016,vol. 7,p. 4085 - 4090.
[2]Journal of the American Chemical Society,2016,vol. 138,p. 8045 - 8047.

7
[ 55589-47-4 ]
[ 52019-78-0 ]
[ 54010-75-2 ]
[ 1539-42-0 ]
[ 75-05-8 ]
C₂₇H₃₅N₅OZn⁽²⁺⁾ [ No CAS ]

References: [1]Chemical Science,2016,vol. 7,p. 4085 - 4090.
[2]Journal of the American Chemical Society,2016,vol. 138,p. 8045 - 8047.

8
[ 55589-47-4 ]
[ 37982-27-7 ]
[ 54010-75-2 ]
[ 1539-42-0 ]
[ 75-05-8 ]
C₃₃H₃₇N₅OZn⁽²⁺⁾ [ No CAS ]

References: [1]Chemical Science,2016,vol. 7,p. 4085 - 4090.

9
[ 55589-47-4 ]
[ 1517-66-4 ]
[ 54010-75-2 ]
[ 1539-42-0 ]
[ 75-05-8 ]
C₂₆H₃₃N₅OZn⁽²⁺⁾ [ No CAS ]

References: [1]Chemical Science,2016,vol. 7,p. 4085 - 4090.
[2]Journal of the American Chemical Society,2016,vol. 138,p. 8045 - 8047.

10
[ 55589-47-4 ]
[ 31087-44-2 ]
[ 54010-75-2 ]
[ 1539-42-0 ]
[ 75-05-8 ]
C₂₆H₃₃N₅OZn⁽²⁺⁾ [ No CAS ]

References: [1]Chemical Science,2016,vol. 7,p. 4085 - 4090.
[2]Journal of the American Chemical Society,2016,vol. 138,p. 8045 - 8047.

11
[ 55589-47-4 ]
[ 16404-54-9 ]
[ 54010-75-2 ]
[ 1539-42-0 ]
[ 75-05-8 ]
C₂₇H₃₅N₅OZn⁽²⁺⁾ [ No CAS ]

References: [1]Chemical Science,2016,vol. 7,p. 4085 - 4090.
[2]Journal of the American Chemical Society,2016,vol. 138,p. 8045 - 8047.

12
[ 54221-96-4 ]
[ 1517-69-7 ]
[ 54010-75-2 ]
[ 1539-42-0 ]
[ 75-05-8 ]
C₂₉H₃₁N₅O₂Zn⁽²⁺⁾ [ No CAS ]