MolProp TK
The MolProp TK provides a customizable framework for molecular property calculation geared towards enabling rapid database filtering. Filtering attempts to eliminate inappropriate or undesirable compounds from a large set before beginning to use them in modelling studies. The goal is to remove all of the compounds that should not be suggested to a medicinal chemist as a potential hit. This exercise is obviously case dependent, depending on ease of the assay, intended target, personal bias of the modeller & medicinal chemist, strengths of the company, etc. which makes this problem one that is highly amenable to a toolkit solution.
The criteria for passing or failing a given molecule fall into three categories:
Physical properties
- Molecular weight
- Topological polar surface area (TPSA)
- logP
- Bioavailability
Atomic and functional group content
- Absolute and relative content of heteroatoms
- Limits on a very wide variety of functional groups
Molecular graph topology
- Number and size of ring systems
- Flexibility of the molecule
- Size and shape of non-ring chains
Beyond the standard molecular properties available from OEChem TK such as molecular weight and atom type counts, MolProp TK calculates XlogP [1], XlogS, and PSA [2]. There are also a variety of ADME filter available such as Lipinski [3], Egan [4], Veber [5] and Martin [6]. In addition to calculating properties and filtering on those properties, MolProp TK provides a variety of preprocessing tools for metal and salt removal, pKa normalization, normalization, reagent selection and type checking.
References
- Wang, R., Ying, F., Lai, L.J., Chem. Info. Comput. Sci., 1997, 37, 615.
- Ertl, P., Rohde, B., Selzer, P., J. Med. Chem., 2000, 37, 3714.
- Lipinski, C., et. al., Adv. Drug. Deliv. Rev., 1997, 23, 3.
- Egan, W.J., Merz, K.M., Baldwin, J.J., J. Med. Chem., 2000, 43, 3867.
- Veber, D.F., Johnson, S.R., Cheng, H.Y., Smith, B.R., Ward, K.W., Kipple, K.D., J. Med. Chem., 2002, 45, 2615.
- Martin, Y.C., J. Med. Chem., 2005, 48, 3164.
