"Flexible-Acceptor" General Solubility Equation for beyond Rule of 5 Drugs.

This study describes a novel nonlinear variant of the well-known Yalkowsky general solubility equation (GSE). The modified equation can be trained with small molecules, mostly from the Lipinski Rule of 5 (Ro5) chemical space, to predict the intrinsic aqueous solubility, S0, of large molecules (MW > 800 Da) from beyond the rule of 5 (bRo5) space, to an accuracy almost equal to that of a recently described random forest regression (RFR) machine learning analysis. The new approach replaces the GSE constant factors in the intercept (0.5), the octanol-water log P (-1.0), and melting point, mp (-0.01) terms with simple exponential functions incorporating the sum descriptor, Φ+B (Kier Φ molecular flexibility and Abraham H-bond acceptor potential). The constants in the modified three-variable (log P, mp, Φ+B) equation were determined by partial least-squares (PLS) refinement using a small-molecule log S0 training set (n = 6541) of mostly druglike molecules. In this "flexible-acceptor" GSE(Φ,B) model, the coefficient of log P (normally fixed at -1.0) varies smoothly from -1.1 for rigid nonionizable molecules (Φ+B = 0) to -0.39 for typically flexible (Φ âˆ¼ 20, B ∼ 6) large molecules. The intercept (traditionally fixed at +0.5) varies smoothly from +1.9 for completely inflexible small molecules to -2.2 for typically flexible large molecules. The mp coefficient (-0.007) remains practically constant, near the traditional value (-0.01) for most molecules, which suggests that the small-to-large molecule continuum is mainly solvation responsive, apparently with only minor changes in the crystal lattice contributions. For a test set of 32 large molecules (e.g., cyclosporine A, gramicidin A, leuprolide, nafarelin, oxytocin, vancomycin, and mostly natural-product-derived therapeutics used in infectious/viral diseases, in immunosuppression, and in oncology) the modified equation predicted the intrinsic solubility with a root-mean-square error of 1.10 log unit, compared to 3.0 by the traditional GSE, and 1.07 by RFR.

The Critical Role of Passive Permeability in Designing Successful Drugs.

Passive permeability is a key property in drug disposition and delivery. It is critical for gastrointestinal absorption, brain penetration, renal reabsorption, defining clearance mechanisms and drug-drug interactions. Passive diffusion rate is translatable across tissues and animal species, while the extent of absorption is dependent on drug properties, as well as in vivo physiology/pathophysiology. Design principles have been developed to guide medicinal chemistry to enhance absorption, which combine the balance of aqueous solubility, permeability and the sometimes unfavorable compound characteristic demanded by the target. Permeability assays have been implemented that enable rapid development of structure-permeability relationships for absorption improvement. Future advances in assay development to reduce nonspecific binding and improve mass balance will enable more accurately measurement of passive permeability. Design principles that integrate potency, selectivity, passive permeability and other ADMET properties facilitate rapid advancement of successful drug candidates to patients.

Equilibrium solubility measurement of compounds with low dissolution rate by Higuchi's Facilitated Dissolution Method. A validation study.

Incubation time plays a critical role in the accurate measurement of equilibrium solubility of compounds. Substances which dissolve very slowly generally need long incubation times (days or weeks) to reach equilibrium. However, long times may pose several problems, such as decomposition of solute, molding of buffer, and drifting of pH. Higuchi in 1979 proposed the Facilitated Dissolution Method (FDM) to dramatically reduce incubation time. It employs a small volume of water-immiscible organic solvent to partly solubilize the sample and thereby increase the surface area available for dissolution. The method has been used only rarely. In this study we performed a systematic validation of FDM using progesterone as model compound. The reference solubility value, 7.95±0.21µg/mL (p<0.05, n=5), was determined in Britton-Robinson buffer solution (pH7.4) at 25.0°C by the standardized protocol of Saturation Shake-Flask (SSF) method. Also, the solubility was measured by the FDM approach under varied experimental conditions (e.g., type and volume of organic solvent, time of agitation, and amount of solid excess), and compared to the reference value. It was demonstrated that the small amount of organic solvent used in the FDM does not impact the measured solubility, compared to the reference value. Additionally, four compounds of low dissolution rate (dexamethasone, digoxin, haloperidol and cosalane) were used to demonstrate that FDM can reduce the long equilibration time to the standardized 24h (6h stirring and 18h sedimentation). The time dependence of solubility equilibrium was measured by SSF, and the results were compared with those obtained by FDM. Our study, based on >200 solubility experiments, supports the validity of Higuchi's method. In this study we propose a standardized protocol for the FDM, where 1% v/v of organic solvent is used. Octane (or isooctane) was found to be suitable for highly hydrophobic compounds. Alternatively, octanol or 1,2-dichloroethane can be used for less lipophilic compounds.

Leakiness and size exclusion of paracellular channels in cultured epithelial cell monolayers-interlaboratory comparison.

PURPOSE: To determine and compare the paracellular characteristics of permeability (Papp) of Caco (-2), MDCK, and 2/4/A1 cell lines. METHODS: The Papp data from 14 studies were analyzed by weighted nonlinear regression in terms of the paracellular parameters: porosity-pathlength (epsilon/delta), pore radius (R), and electrostatic potential drop (deltaphi). Aqueous diffusivities, Daq, for the analysis, were empirically determined. The required hydrodynamic radii, rHYD, were estimated without knowledge of compound density. Mannitol iso-paracellular profiles allowed comparisons of "leakiness" across labs. RESULTS: Daq (37 degreeC) was predicted as 9.9x10(-5) MW(-0.453); rHYD=(0.92+21.8 MW(-1))xrSE, where rSE is the Stokes-Einstein radius. Values of pore radius ranged from 4.0(+/-0.1) to 18(+/-3) A, with the 2/4/A1 indicating the largest pores. The epsilon/delta capacity factor ranged from 0.2 (+/-0.1) to 69 (+/-5) cm(-1), with most values <1.5 cm(-1). The average potential drop for Caco-2 models was deltaphi(wt avg) Caco(-2)=(-43)+/-20 mV. The paracellular model predicted measured log Papp values with pooled r2=0.93 and s=0.17 (n=108). CONCLUSION: R and epsilon/delta are negatively correlated to a large extent. Papp can be rate-limited by either factor, with a wide range of possible combinations still indicating nearly constant leakiness for a given marker.

Classification analysis of P-glycoprotein substrate specificity.

Prediction of P-glycoprotein substrate specificity (S(PGP)) can be viewed as a constituent part of a compound's "pharmaceutical profiling" in drug design. This task is difficult to achieve due to several factors that raised many contradictory opinions: (i) the disparity between the S(PGP) values obtained in different assays, (ii) the confusion between Pgp substrates and inhibitors, (iii) the confusion between lipophilicity and amphiphilicity of Pgp substrates, and (iv) the dilemma of describing class-specific relationships when Pgp has no binding sites of high ligand specificity. In this work, we compiled S(PGP) data for 1000 compounds. All data were represented in a binary format, assigning S(PGP) = 1 for substrates and S(PGP) = 0 for non-substrates. Each value was ranked according to the reliability of experimental assay. Two data sets were considered. Set 1 included 220 compounds with S(PGP) from polarized transport across MDR1 transfected cell monolayers. Set 2 included the entire list of 1000 compounds, with S(PGP) values of generally lower reliability. Both sets were analysed using a stepwise classification structure-activity relationship (C-SAR) method, leading to derivation of simple rules for crude estimation of S(PGP) values. The obtained rules are based on the following factors: (i) compound's size expressed through molar weight or volume, (ii) H-accepting given by the Abraham's beta (that can be crudely approximated by the sum of O and N atoms), and (iii) ionization given by the acid and base pKa values. Very roughly, S(PGP) can be estimated by the "rule of fours". Compounds with (N + O) > or = 8, MW > 400 and acid pKa > 4 are likely to be Pgp substrates, whereas compounds with (N + O) < or = 4, MW < 400 and base pKa < 8 are likely to be non-substrates. The obtained results support the view that Pgp functioning can be compared to a complex "mini-pharmacokinetic" system with fuzzy specificity. This system can be described by a probabilistic version of Abraham's solvation equation, suggesting a certain similarity between Pgp transport and chromatographic retention. The chromatographic model does not work in the case of "marginal" compounds with properties close to the "global" physicochemical cut-offs. In the latter case various class-specific rules must be considered. These can be associated with the "amphiphilicity" and "biological similarity" of compounds. The definition of class-specific effects entails construction of the knowledge base that can be very useful in ADME profiling of new drugs.