Topological descriptors polar surface area

Of the physicochemical descriptors, lipophilicity (as described by clogP and Topological Polar Surface Area (TPSA) gave the strongest overall correlation to incidence of adverse in vivo outcomes, whether analyzed in terms of free or total drug threshold concentrations. In the case of free drug threshold analysis, a Random Forest statistical method indicated that there was a higher chance of a compound with TPSA <70... 

We can also look at other literature datasets to gain an idea of how similar our compounds are to compounds for which QMPRPlus gives very good predictions. We have looked at four simple descriptors molecular weight, topological polar surface area [40], chemical complexity [41], and rotatable bond count, using John Bradshaw s... 

Most of the commercial molecular modeling systems also provide some property calculations, which range from simply calculating the polar surface area of a structure to a full range of topological and physicochemical descriptors. These may be based on fragment additivity, like most of the programs mentioned above, or they may involve correlations with quantum mechanical or even molecular dynamics-based calculations. 

Fig. 9.1-7 Example of principle component analysis comparison of synthetic drugs and natural products. A set of 20 synthetic drugs, including the top 10 best-sellers in 2004, and 20 natural products was analyzed for nine molecular descriptors molecular weight, hydrophobicity (X log P or C log P), hydrogen-bond donors, hydrogen-bond acceptors, rotatable bonds, topological polar surface area [43], stereogenic centers, nitrogen atoms, oxygen atoms. PCA was used to reduce the nine-dimensional vectors to two-dimensional vectors, which were then replotted as shown. The first principal component accounts for 55.1% of the original information and the first two...

The descriptor uses readily calculable physicochemical properties from the topological structure. The descriptors used in this study were atomic weight, hydropho-bicity, molecular refractivity, atomic charge, polar surface area, hydrogen bond acceptors, and hydrogen bond donors. The authors note that Martin et al. [32] applied a similar approach for the design of diverse combinatorial libraries. 

MOE Chemical Computing Group Calculates over 600 molecular descriptors including topological indices, structural keys. E-state indices, physical properties (such as LogP, molecular weight and molar refractivity), topological polar surface area (TPSA) and CCG s VSA descriptors http //www.chem-comp.com/software-chem.htm... 

Among the several CODESSA descriptors, implemented in the homonymous software CODESSA (Comprehensive DEscriptors for Structural and Statistical Analysis) [Katritzky and Gordeeva, 1993 CODESSA- Katritzky, Lobanov et al., 1996 Katritzky, Lobanov et al, 1996], are molecular weight, molecular volume, —> count descriptors, —> topological indices, charge descriptors, shadow indices, charged partial surface area descriptors, quantum-chemical descriptors, and —> electric polarization descriptors. 

For each molecule in these struetures, 131 molecular descriptors were calculated. These included simple atom, bond and group eounts, hydrogen bond donor and acceptor counts, topological indices, a variety of partitioned and charge weighted surface areas and deseriptors of molecular size, shape, polarity... 

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