5.1.2.4 Pharmacokinetic predictors

Several secondary filters that are built upon published combinations of simpler properties are included. These include Lipinski [1], Veber(GSK) [9], Martin (Abbott)[8] and Pharmacopia (Egan)[10]. The Lipinski filter allows one to specify the number of allowed violations (the published work allows compounds to pass with a single violation but not multiple violations). All other filters in this category simply allow a boolean flag of whether the filter should be applied.

All of these properties are used for filtering in the default filters.

The Veber, Lipinski, Martin, and Egan (pharmacopia) filters are turned on by inclusion of one of the following lines in a filter file:

psa

Peter Ertl's Topological Polar surface area (Phosphorus and Sulfur area is optional)

PSA_USE_SandP   false    "Count S and P as polar atoms"
MIN_2D_PSA      0.0      "Minimum 2-Dimensional (SMILES) Polar Surface Area"
MAX_2D_PSA      150.0    "Maximum 2-Dimensional (SMILES) Polar Surface Area"

GSK/Veber

Veber's measure of bioavailability (PSA > 140 or Rotatable bonds >10) [9]

GSK_VEBER      true      "PSA>140 or >10 rot bonds"

Lipinski Violations

Number of Lipinski violations. A single Lipinski violation is considered acceptable[1]

MAX_LIPINSKI   1         "Maximum number of Lipinski violations"

Abbott/Martin

Yvonne Martin's Abbott Bioavailability Score. This is reported as a probability that F>10% in rats. (ABS)[8]

MIN_ABS 0.5              "Minimum probability F>10% in rats"

Pharmacopia/Egan

``Egan egg'' measure of bioavailability (LogP >5.88 or PSA > 131.6)[10]

PHARMACOPIA    true      "LogP > 5.88 or PSA > 131.6"

				FILTER Database preparation Property calculation

				FILTER Database preparation Property calculation