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. 2016 Jul 11;33(11):2604–2616. doi: 10.1007/s11095-016-1983-4

Table III.

Information Around the in-House QSAR Models and Descriptors used to Build the Log%SDiP OPLS Model

QSAR model / Descriptor Details Coefficients with regards to IPRLu QSAR model
FA_rat_v1.logFA_score Output from an inhouse QSAR model that predicts fraction absorbed in the rat, this model was built on a GSK rat oral bioavailability dataset with total clearance values of less than 10 ml/min/kg and therefore minimal first pass effect. +
Perm_chrom_p.perm_score An inhouse PLS-Discriminant analysis model which predicts permeability and oral absorption of compounds. +
MDCK2.Perm_pH74_nm_sec MDCK2.Perm_pH64_nm_sec Inhouse QSAR models which predict passive permeability across a madine darby canine kidney (MDCK) cell monolayer (31) with donor solutions buffered at pH7.4 and pH6.4. +
Pgp_v31.Pgp_Score An inhouse PLS-Discriminant analysis model which predicts the likelihood of a compound being a substrate for the ABC active efflux transporter P-glycoprotein. +
Chrom LogD_v3.value An inhouse OPLS QSAR model that predicts hydrophobicity, the model was built on a GSK dataset of chromatographic hydrophobicity index (CHI) measurements (32) which are converted to a chromLogD value (4). +
neutral_ionised_form % of the molecule in the neutral form at pH7.4. pKa’s calculated using the ACDlabs softwarea ACD_v11. +
logd_pH55_acd Calculated logD value from the ACDlabs software at pH5.5 +
logd_pH65_acd Calculated logD value from the ACDlabs software at pH6.5 +
Bpka1_modified The most basic pka value calculated using ACDlabs software ACD_v11
basic_ionised_form % of the molecule in the acidic form at pH7.4 pKa’s calculated using the ACDlabs software ACD_v11.
abe Andrews Binding energy (33).
cmr Calculated molar refraction
mw Average molecular weight of parent
tpsa Polar surface area calculated by the method of Ertl (34).
hbd Count of the number of hydrogen bond acceptors in a molecule.
pos The count of the number of positively ionisable/charged groups in a molecule.
rb count of the number of rotatable bonds in a molecule.
flex related to the ratio of the number of rotatable bonds to total bonds = int(100*rotatable_bonds/total_bonds) -
alpha An Abraham’s molecular descriptor relating to Hydrogen Bond Acidity (hydrogen bond donors) (30). -
betah An Abraham’s molecular descriptor relating to Hydrogen Bond Basicity (hydrogen bond acceptors) (30). -
pi An Abraham’s molecular descriptor relating to the dipolarity/dipolarizability (30). -
vx An Abraham’s molecular descriptor relating to McGowan characteristic volume (size) (30). -
total_HB Sum of hydrogen bond donors and acceptors (physchem_desc.hba + physchem_desc.hbd) -
total_charge Sum of positive and negative charges (physchem_desc.neg + physchem_desc.pos) -
nonPSA Approximation of total surface area - polar surface area. -

aACDlabs software: Advanced Chemistry Development, Inc. 8 King Street East, Suite 107, Toronto, Ontario, Canada M5C 1B5