Physico-chemical properties were calculated using the Pipeline Pilot Chemistry Collection (version 8.0.1.500) from Accelrys (San Diego, CA, USA). The properties calculated were Molecular Weight (MW), octanol-water partition coefficient (ALOGP) (using the atom-based method by Ghose and Crippen24 ), number of hydrogen bond donors (HBD), number of hydrogen bond acceptors (HBA), molecular polar surface area (PSA), number of rotatable bonds (ROTB) and the number of aromatic rings (AROM)25 (link), 26 (link). Finally, a substructure search was performed against each drug using a curated reference set of 94 functional moieties that are potentially mutagenic, reactive or have unfavourable pharmacokinetic properties27 (link). The number of matches for each compound was captured (ALERTS). We chose to omit the acid dissociation constant (pKa) as the available high-throughput computational approaches do not provide sufficient accuracy48 (link).
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Computational Analysis of Compound Properties
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Other organizations : University of Dundee, AstraZeneca (Sweden)
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Variable analysis
independent variables
- Molecular Weight (MW)
- Octanol-water partition coefficient (ALOGP)
- Number of hydrogen bond donors (HBD)
- Number of hydrogen bond acceptors (HBA)
- Molecular polar surface area (PSA)
- Number of rotatable bonds (ROTB)
- Number of aromatic rings (AROM)
- Number of matches for each compound against a curated reference set of 94 functional moieties (ALERTS)
- Physico-chemical properties
- Curated reference set of 94 functional moieties
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