Relationship between Passive Permeability and Molecular Polarity Using Block Relevance Analysis.

EPSA is an experimental descriptor of molecular polarity obtained from chromatographic retention in supercritical fluid chromatography (SFC) systems, previously shown by Goetz et al. to correlate with passive permeability of cyclic peptides. The present study focuses on EPSA in relation to passive permeability of small molecules. We applied block relevance (BR) analysis to interpret the relative significance of mechanistic forces prevailing in EPSA. The BR analysis is a computational tool that allows the interpretation of the balance of intermolecular interactions governing systems such as the aforementioned chromatographic retention in EPSA. EPSA and passive permeability determined by Ralph Russ canine kidney cells (RRCK) or low efflux Madin Darby canine kidney cells (MDCK-LE) and human epithelial colorectal adenocarcinoma cells (Caco-2), studied on a data set of commercial drugs, indicated that EPSA is relevant in describing permeability of hydrophilic drugs (CLogP < 1). We then verified, on a data set of 1699 Rule of 5 compliant Pfizer compounds, that when CLogP < 1, a value of EPSA < 100 significantly increases the likelihood of high permeability.

A Fast Chromatographic Method for Estimating Lipophilicity and Ionization in Nonpolar Membrane-Like Environment.

This study describes the design and implementation of a new chromatographic descriptor called log k'80 PLRP-S that provides information about the lipophilicity of drug molecules in the nonpolar environment, both in their neutral and ionized form. The log k'80 PLRP-S obtained on a polymeric column with acetonitrile/water mobile phase is shown to closely relate to log Ptoluene (toluene dielectric constant ε ∼ 2). The main intermolecular interactions governing log k'80 PLRP-S were deconvoluted using the Block Relevance (BR) analysis. The information provided by this descriptor was compared to ElogD and calclog Ptol, and the differences are highlighted. The "charge-flush" concept is introduced to describe the sensitivity of log k'80 PLRP-S to the ionization state of compounds in the pH range 2 to 12. The ability of log k'80 PLRP-S to indicate the propensity of neutral molecules and monoanions to form Intramolecular Hydrogen Bonds (IMHBs) is proven through a number of examples.

Use of 3D properties to characterize beyond rule-of-5 property space for passive permeation.

The application of conformationally dependent measures of size and polarity to characterize beyond rule-of-5 (Ro5) space for passive permeation was investigated. Specifically, radius of gyration, an alternative to molecular weight, and three-dimensional polar surface area and the generalized Born/surface area dehydration free energy, alternatives to hydrogen-bond donor and acceptor counts, were computed on models of the permeating conformations of over 35 000 molecules. The resulting guidelines for size and polarity, described by the 3D properties, should aid the design of Ro5 violators with passive permeability.

Updating the portfolio of physicochemical descriptors related to permeability in the beyond the rule of 5 chemical space.

Beyond rule of 5 (bRo5) molecules are attracting significant interest in modern drug discovery mostly because many novel targets require large and more flexible structures. The main aim of this paper is the identification of ad hoc bRo5 physicochemical descriptors of ionization, lipophilicity, polarity and chameleonicity and their measurement. We used different methods to collect ionization (pKa measures and log k'80 PLRP-S trends), lipophilicity (in octanol/water, in apolar systems and in biomimetic environments), polarity (Δlog Poct-tol, EPSA and Δlog KWIAM) and chameleonicity (ChameLogD) descriptors for 26 bRo5 drugs. A second aim was to check the relationship between physicochemical descriptors and permeability for a subset of compounds for which solid permeability values are reported in the literature. Results showed that the physicochemical profile in the bRo5 chemical space is often experimentally accessible, albeit more tools are required to overcome limitations of individual methods. For the investigated compounds, permeability is governed by Δlog Poct-tol and preliminary data support that chameleonicity could also have an impact.

Permeability prediction for zwitterions via chromatographic indexes and classification into 'certain' and 'uncertain'.

Background: The development of zwitterions to a drug is likely to be more challenging than compounds of other charge types. Results: Two chromatographic indexes (log k'80 PLRP-S and log KWIAM) can be successfully used as permeability classifiers of ampholytes. Moreover, a pragmatic classification into ordinary ampholytes; zwitterions 'certain' (i.e., the zwitterionic species is dominant in the physiological pH range); and zwitterions 'uncertain' (multiple species are present in the physiological pH range) enables to study the permeability of ampholytic compounds in relation to species distribution. Methodology: Potentiometry (pKa), reversed-phase (RP)-chromatography, tri-layer parallel artificial membrane permeability assays, quantitative structure-property relationships (QSPR) and block relevance (BR) analysis, receiver operating characteristic (ROC) curves. Conclusion: Structures considered as poorly permeable like zwitterions can be integrated in drug discovery programs by applying ad hoc experimental and computational tools.

Prediction of human volume of distribution values for neutral and basic drugs. 2. Extended data set and leave-class-out statistics.

We present an extension and confirmation of our previously published method (J. Med. Chem. 2002, 45, 2867-2876) for the prediction of volume of distribution (VD) in humans for neutral and basic compounds. It is based on two experimentally determined physicochemical parameters, ElogD(7.4) and f(i(7.4)), the latter being the fraction of compound ionized at pH 7.4, and on the fraction of free drug in plasma (fu). By regressing the fraction unbound in tissues, fut, vs the above parameters, we demonstrate the ruggedness of the method in predicting VD through the Oie-Tozer equation, via the use of several testing approaches. A comparison is also presented between several methods based on animal pharmacokinetic data, using the same set of proprietary compounds, and it lends further support for the use of this method, as opposed to methods that require the gathering of pharmacokinetic data in laboratory animals. The reduction in the use of animals and the overall faster and cheaper accessibility of the parameters used make this method highly attractive for prospectively predicting the VD of new chemical entities in humans.

Prediction of volume of distribution values in humans for neutral and basic drugs using physicochemical measurements and plasma protein binding data.

We present a method for the prediction of volume of distribution in humans, for neutral and basic compounds. It is based on two experimentally determined physicochemical parameters, ElogD(7.4) and f(i(7.4)), the latter being the fraction of compound ionized at pH 7.4 and on the fraction of free drug in plasma (f(u)). The fraction unbound in tissues (f(ut)), determined via a regression analysis from 64 compounds using the parameters described, is then used to predict VD(ss) via the Oie-Tozer equation. Accuracy of this method was determined using a test set of 14 compounds, and it was demonstrated that human VD(ss) values could be predicted, on average, within or very close to 2-fold of the actual value. The present method is as accurate as reported methods based on animal pharmacokinetic data, using a similar set of compounds, and ranges between 1.62 and 2.20 as mean-fold error. This method has the advantage of being amenable to automation, and therefore fast throughput, it is compound and resources sparing, and it offers a rationale for the reduction of the use of animals in pharmacokinetic studies. A discussion of the potential errors that may be encountered, including errors in the determination of f(u), is offered, and the caveats about the use of computed vs experimentally determined logD and pK(a) values are addressed.

In silico ADME prediction: data, models, facts and myths.

A critical review of a very recent work in the field of in silico ADME prediction is presented with emphasis on the work published during the period 2000-2002, and several other review articles are mentioned in order to offer a broader view of the field. We find that not much progress has been made in developing robust and predictive models, and that the lack of accurate data, together with the use of questionable modeling end-points, has greatly hindered the real progress in defining generally applicable models. Due to the largely empirical nature of QSAR/QSPR approaches, general and truly predictive models for complex phenomena, such as absorption and clearance, may still be chimeric. The development of local models for use within focused chemical series may be the most appropriate way of utilizing in silico ADME predictions, once experience and data have been gained on a given project and/or structural class.

The effect of disorder on the chemical reactivity of an organic solid, tetraglycine methyl ester: change of the reaction mechanism.

Many drugs undergo chemical changes in the solid state, and understanding chemical reactivity of organic crystals is a critical factor in the drug development process. In this report, the impact of milling on the thermal chemical reactivity of an organic solid, tetraglycine methyl ester, was studied using DSC, isothermal calorimetry, chemical analysis (HPLC and insoluble residue determination), and powder X-ray diffraction. Significant changes in both X-ray diffraction patterns and DSC curves were detected after very brief milling (5 s). The changes were interpreted as the formation of a disordered phase. The disordered phase was tentatively identified as a crystal mesophase that combines properties of both crystalline (i.e., long-range order) and amorphous (i.e., glass transition) states. In the disordered material, the reaction mechanism changed from the methyl transfer reaction, which was observed in the intact crystal, to a polycondensation reaction when the reaction was performed at 165 degrees C. Such changes in the reaction mechanism occurred in materials milled for > 30 s.

High throughput method for the indirect detection of intramolecular hydrogen bonding.

A supercritical fluid chromatography method was developed for the detection of intramolecular hydrogen bonds in pharmaceutically relevant molecules. The identification of compounds likely to form intramolecular hydrogen bonds is an important drug design consideration given the correlation of intramolecular hydrogen bonding with increased membrane permeability. The technique described here correlates chromatographic retention with the exposed polarity of a molecule. Molecules that can form an intramolecular hydrogen bond can hide their polarity and therefore exhibit lower retention than similar compounds that cannot. By use of a pairwise analysis strategy, intramolecular hydrogen bonds are identified within a test set of compounds with diverse topologies. The chromatographic results are confirmed by NMR chemical shift and temperature coefficient studies.

Integrating intramolecular hydrogen bonding (IMHB) considerations in drug discovery using ΔlogP as a tool.

This study demonstrates that ΔlogP(oct-tol) (difference between logP(octanol) and logP(toluene)) describes compounds propensity to form intramolecular hydrogen bonds (IMHB) and may be considered a privileged molecular descriptor for use in drug discovery and for prediction of IMHB in drug candidates. We identified experimental protocols for acquiring reliable ΔlogP(oct-tol) values on a set of compounds representing IMHB motifs most prevalent in medicinal chemistry, mainly molecules capable of forming 6-, 7-member IMHB rings. Furthermore, computational ΔlogP(oct-tol) values obtained with COSMO-RS software provided a good estimate of experimental results and can be used prospectively to assess IMHB. The proposed interpretation method based on ΔlogP(oct-tol) data allowed categorization of the compounds into 2 groups: with high propensity to form IMHB and poor propensity or poor relevance of IMHB. The relative (1)H NMR chemical shift of an exchangeable proton was used to verify presence of IMHB and to validate the IMHB interpretation scheme.

Measurement of dissociation constants (pKa values) of organic compounds by multiplexed capillary electrophoresis using aqueous and cosolvent buffers.

Evaluation of a multiplexed capillary electrophoresis (CE) method for pK(a) measurements of organic compounds, including low solubility compounds, is presented. The method is validated on a set of 105 diverse compounds, mostly drugs, and results are compared to literature values obtained from multiple references. Two versions of the instrument in two different labs were used to collect data over a period of 3 years and inter-laboratory and inter-instrument variations are discussed. Twenty-four point aqueous and mixed cosolvent buffer systems were employed to improve the accuracy of pK(a) measurements. It has been demonstrated that the method allows direct pK(a) measurements in aqueous buffers for many compounds of low solubility, often unattainable by other methods. The pK(a) measurements of compounds with extremely low solubility using multiplexed CE with methanol/water cosolvent buffers are presented.

In silico prediction of ionization constants of drugs.

Most pharmacologically active molecules contain one or more ionizing groups, and it is well-known that knowledge of the ionization state of a drug, indicated by the pKa value, is critical for understanding many properties important to the drug discovery and development process. The ionization state of a compound directly influences such important pharmaceutical characteristics as aqueous solubility, permeability, crystal structure, etc. Tremendous advances have been made in the field of experimental determination of pKa, in terms of both quantity/speed and quality/accuracy. However, there still remains a need for accurate in silico predictions of pKa both to estimate this parameter for virtual compounds and to focus screening efforts of real compounds. The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) was used to predict the ionization state of a drug. This program has been developed based on the solid physical chemistry of reactivity models and applied to successfully predict numerous physical properties as well as chemical reactivity parameters. SPARC predicts both macroscopic and microscopic pKa values strictly from molecular structure. In this paper, we describe the details of the SPARC reactivity computational methods and its performance on predicting the pKa values of known drugs as well as Pfizer internal discovery/development compounds. A high correlation (r2=0.92) between experimental and the SPARC calculated pKa values was obtained with root-mean-square error (RMSE) of 0.78 log unit for a set of 123 compounds including many known drugs. For a set of 537 compounds from the Pfizer internal dataset, correlation coefficient r2=0.80 and RMSE=1.05 were obtained.