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Example 1

Molecule : Acetaminophen
Canonical SMILES : CC(=O)NC1=CC=C(C=C1)O
Number of Nitrogen atom(s) = 1
Number of Oxygen atom(s) = 2
Ipc index = 2.456
Calculated MDCK permeability coefficient = 483.5 nm/s
Experimental MDCK permeability coefficient = 350 nm/s

 

Example 2

Molecule : Antipyrine
Canonical SMILES : CC1=CC(=O)N(N1C)C2=CC=CC=C2
Number of Nitrogen atom(s) = 2
Number of Oxygen atom(s) = 1
Ipc index = 3.326
Calculated MDCK permeability coefficient = 1018.5 nm/s
Experimental MDCK permeability coefficient = 1500 nm/s

 

Ipc descriptor:

Ipc (information theory polynomial coefficient) is an expression of molecular branching based on two information measures, Wiener number and the largest eigenvalue of the characteristic polynomial. The easiest way to calculate Ipc descriptor is to use ChemDes web server. Alternatively, one may use the ChemoPy source code. The MDCKpred tool accepts Ipc descriptor values calculated by ChemoPy source code or through the interface of ChemDes for ChemoPy.

Users may contact for help in the calculation of Ipc descriptor.

Permeability classification:

Classification Permeability coefficient (nm/s)
Low permeability less than 4
Middle permeability 4 to 70
High permeability above 70

PLEASE CITE:

Patel RD, Kumar SP, Pandya HA and Solanki HA (2018). MDCKpred: A web tool to calculate MDCK permeability coefficient of small molecule using membrane-interaction chemical features. Toxicology Mechanisms and Methods, doi: 10.1080/15376516.2018.1499840. Link to article: https://www.tandfonline.com/doi/abs/10.1080/15376516.2018.1499840

References:

Irvine JD, Takahashi L, Lockhart K, Cheong J, Tolan JW, Selick HE and Grove JR (1999). MDCK (Madin-Darby Canine Kidney) cells: A tool for membrane permeability screening. Journal of Pharmaceutical Sciences, 88, 28-33.
Chen L-L, Yao J, Yang J-B and Yang J (2005).Predicting MDCK cell permeation coefficients of organic molecules using membrane-interaction QSAR analysis. Acta Pharmacologica Sinica, 26, 1322–1333.
Dong J, Cao D-S, Miao H-Y, Liu S, Deng B-C, Yun Y-H, Wang N-N, Lu A-P, Zeng W-B and Chen A (2015). ChemDes: An integrated web-based platform for molecular descriptor and fingerprint computation. Journal of Cheminformatics, 7, 60.
Cao D-S, Xu Q-S, Hu Q-N and Liang Y-Z (2013). ChemoPy: Freely available python package for computational biology and chemoinformatics. Bioinformatics, 29, 1092–1094.