ADME descriptors

From a methodological viewpoint, our results suggest that range and sensitivity are useful descriptors of property spaces and can parameterize the capacity of a given molecule to span broad conformational and property spaces. In other words, range and sensitivity appear as promising descriptors of the dynamic behavior of a molecule. Their application to other dynamic QSAR studies [in particular, absorphon, distribution, metabolism and excretion (ADME) behavior] is under investigahon. 

Hou, T. J., Xu, X. J. ADME evaluation in drug discovery. 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. /. Chem. Inf. Model. 2003, 43, 2137-2152. 

Prediction of ADME properties should be simple, since the number of descriptors underlying the properties is relatively small, compared to the number associated with effective drug-receptor binding space. In fact, prediction of ADME is difficult The current ADME experimental data reflect a multiplicity of mechanisms, making prediction uncertain. Screening systems for biological activity are typically single mechanisms, where computational models are easier to develop [1],... 

In the following section, the calculation of the VolSurf parameters from GRID interaction energies will be explained and the physico-chemical relevance of these novel descriptors demonstrated by correlation with measured absorption/ distribution/metabolism/elimination (ADME) properties. The applications will be shown by correlating 3D molecular structures with Caco-2 cell permeabilities, thermodynamic solubilities and metabolic stabilities. Special emphasis will be placed on interpretation of the models by multivariate statistics, because a rational design to improve molecular properties is critically dependent on an understanding of how molecular features influence physico-chemical and ADME properties. 

One of the simplest and most common ways to evaluate a molecule for ADME properties is a qualitative examination of its basic descriptor values such as molecular weight (MW), ClogP for lipophilicity, polar surface area (PSA), counts of hydrogen bond donors and acceptors (HBD, HBA), and count of rotatable bonds (RB). This type of approach popularized by Lipinski s famous Rule of 5 was published a decade ago [6]. Lipinski et al. established cutoffs for MW (500), ClogP (5), HBA (10), and HBD (5). These cutoffs were based on the 90th percentile of distributions of molecules in the World Drug Index having USAN or INN names. The Rule of 5 considers a violation of any two of these cutoffs to be an alert for poor absorption or permeability. 

Use of Broad Biological Profiling as a Relevant Descriptor to Describe and Differentiate Compounds Structure-/ Vitro (Pharmacology-ADME)-/n Vivo (Safety) Relationships... 

Hou TJ, Xu XJ (2003) ADME Evaluation in Drug Discovery. 3. Modeling Blood-Brain Barrier Partitioning Using Simple Molecular Descriptors. Erratum in J Chem Inf Comput Sci. 2004 Mar-Apr 44(2) 766-70. J Chem Inf Comput Sci 43 2137-2152. 

More recently, another linear discriminant analysis (LDA) model was constructed for a set of 157 compounds for which Pcaco-2 was measured [43]. This model, which applied DRAGON descriptors, achieved an accuracy of classification at 91 % for the training set and 84% for the test set. When this model was applied to predict a set of 241 drugs for which HIA data were available, good correlation (>81%) was achieved between the two ADME-Tox properties. 

Key Words 3D-QSAR hydrophobicity lipophilicity 3D-LogP conformation-dependent lipophilicity alignment-independent 3D descriptor molecular lipophilicity potential (MLP) ADME-related descriptor. 

Breneman, C., Bennett, Bi, J., Song, M., and Embrechts, M. (2002) New electron density-derived descriptors and machine learning techniques for computational ADME and molecular design. MidAtlantic Computational Chemistry Meeting, Princeton University, Princeton, NJ. 

PreADME Computer Aided Molecular Design Research Centre camd.ssu.ac.kr/adme (free, on-line calculations) Constitutional, topological, physicochemical, and geometrical descriptors. 

---