Patrick Barton

A rapid computational filter for predicting the rate of human renal clearance.

In silico models that predict the rate of human renal clearance for a diverse set of drugs, that exhibit both active secretion and net re-absorption, have been produced using three statistical approaches. Partial Least Squares (PLS) and Random Forests (RF) have been used to produce continuous models whereas Classification And Regression Trees (CART) has only been used for a classification model. The best models generated from either PLS or RF produce significant models that can predict acids/zwitterions, bases and neutrals with approximate average fold errors of 3, 3 and 4, respectively, for an independent test set that covers oral drug-like property space. These models contain additional information on top of any influence arising from plasma protein binding on the rate of renal clearance. Classification And Regression Trees (CART) has been used to generate a classification tree leading to a simple set of Renal Clearance Rules (RCR) that can be applied to man. The rules are influenced by lipophilicity and ion class and can correctly predict 60% of an independent test set. These percentages increase to 71% and 79% for drugs with renal clearances of < 0.1 ml/min/kg and > 1 ml/min/kg, respectively. As far as the authors are aware these are the first set of models to appear in the literature that predict the rate of human renal clearance and can be used to manipulate molecular properties leading to new drugs that are less likely to fail due to renal clearance.

A Method for Measuring the Lipophilicity of Compounds in Mixtures of 10

Lipophilicity is an important parameter for any potential drug candidate. Accurate and efficient lipophilicity measurements facilitate the development of high-quality predictive in silico models that support the design of future drugs. Lipophilicity estimates derived from the traditional 1-octanol/water shake flask techniques have been the most widely employed and are therefore the best understood. This technique can be considered to give a good measure of a compound’s lipophilicity, albeit slower and more labor intensive to run compared with some other methodologies. Herein is described and validated an efficient 1-octanol/water shake flask technique that has sufficient capacity to be run as a primary screen within the drug discovery process. This is achieved by the simultaneous measurement of the distribution coefficients of mixtures of up to 10 compounds using high-performance liquid chromatography and tandem mass spectrometry. Concerns regarding ion pair partitioning that could result in erroneous results due to interactions between compounds within a mixture are discussed.

In silico physicochemical parameter predictions.

Drug discovery is a complex process with the aim of discovering efficacious molecules where their potency and selectivity are balanced against ADMET properties to set the appropriate dose and dosing interval. The link between physicochemical properties and molecular structure are well established. The subsequent connections between physicochemical properties and a drugs biological behavior provide an indirect link back to structure, facilitating the prediction of a biological property as a consequence of a particular molecular manipulation. Due to this understanding, during early drug discovery in vitro physicochemical property assays are commonly performed to eliminate compounds with properties commensurate with high attrition risks. However, the goal is to accurately predict physicochemical properties to prevent the synthesis of high risk compounds and hence minimize wasted drug discovery efforts. This paper will review the relevance to ADMET behaviors of key physicochemical properties, such as ionization, aqueous solubility, hydrogen bonding strength and hydrophobicity, and the in silico methodology for predicting them.

A Highly Automated Assay for Determining the Aqueous Equilibrium Solubility of Drug Discovery Compounds

Aqueous solubility is an important physicochemical parameter for any potential drug candidate, and high-throughput kinetic assays are frequently used in drug discovery to give an estimate of a compounds aqueous solubility. However, the aqueous solubility data from an equilibrium (thermodynamic) shake-flask technique is considered more relevant, but is slower and more labor intensive to generate. A highly automated aqueous equilibrium solubility shake-flask technique is described and validated on a set of 15 marketed drugs, whose aqueous solubilities cover four orders of magnitude. The assay uses a Tecan Freedom Evo 200 liquid handling robot (Tecan Group Ltd., Männerdorf, Switzerland) with integrated appliances for the transportation, decapping and recapping, and centrifugation of sample tubes. These bespoke automation solutions help overcome the labor intensive steps associated with performing conventional, gold standard, aqueous equilibrium solubility shake-flask measurements, enabling the assay to be used as a primary-wave drug discovery screen.

Scaffold-hopping with zwitterionic CCR3 antagonists: identification and optimisation of a series with good potency and pharmacokinetics leading to the discovery of AZ12436092.

The discovery and optimisation of a series of zwitterionic CCR3 antagonists is described. Optimisation of the structure led to AZ12436092, a compound with excellent selectivity over activity at hERG and outstanding pharmacokinetics in preclinical species.

Lipophilicity of acidic compounds: Impact of ion pair partitioning on drug design

In drug discovery projects the ability to show a relationship between a compounds molecular structure and its pharmacokinetic, in vivo efficacy, or toxicity profile is paramount for the design of better analogues. To aid this understanding the measurement of distribution coefficients at some physiologically relevant pH, for example, log D(7.4), is common practice as they are used as a key descriptor in mathematical models for predicting various biological parameters. Evidence is presented that under typical experimental conditions ion pair partitioning can contribute greatly to log D(7.4) results for acidic compounds; if this is ignored it may compromise data analysis within drug discovery projects where the modulation of lipophilicity is a primary design strategy. The work herein focuses on acidic compounds and reflects the experience of AstraZeneca R&D Charnwood (AZ) where ion pair partitioning contributions can be minimized by the routine measurement of log D(5.5) data. The magnitude of ion pair partitioning contributions to the log D(7.4) measurements of 24 acidic drugs are investigated, and the risks to drug discovery projects that ignore such contributions are discussed. The superiority of measured lipophilicity data over calculated data for a set of AZ proprietary acidic compounds is also presented.

Application of an in vitro OAT assay in drug design and optimization of renal clearance

Abstract 1. Optimization of renal clearance is a complex balance between passive and active processes mediated by renal transporters. This work aimed to characterize the interaction of a series of compounds with rat and human organic anion transporters (OATs) and develop quantitative structure–activity relationships (QSARs) to optimize renal clearance. 2. In vitro inhibition assays were established for human OAT1 and rat Oat3 and rat in vivo renal clearance was obtained. Statistically significant quantitative relationships were explored between the compounds’ physical properties, their affinity for OAT1 and oat3 and the inter-relationship with unbound renal clearance (URC) in rat. 3. Many of the compounds were actively secreted and in vitro analysis demonstrated that these were ligands for rat and human OAT transporters (IC50 values ranging from <1 to >100 µM). Application of resultant QSAR models reduced renal clearance in the rat from 24 to <0.1 ml/min/kg. Data analysis indicated that the properties associated with increasing affinity at OATs are the same as those associated with reducing URC but orthogonal in nature. 4. This study has demonstrated that OAT inhibition data and QSAR models can be successfully used to optimize rat renal clearance in vivo and provide confidence of translation to humans.

The discovery of CCR3/H1 dual antagonists with reduced hERG risk

A series of dual CCR3/H(1) antagonists based on a bispiperidine scaffold were discovered. Introduction of an acidic group overcame hERG liability. Bioavailability was optimised by modulation of physico-chemical properties and physical form to deliver a compound suitable for clinical evaluation.

A kinetic method for the determination of plasma protein binding of compounds unstable in plasma: Specific application to enalapril

Traditional methods for the determination of plasma protein binding (PPB), such as equilibrium dialysis and ultrafiltration, normally operate on a timescale ranging from tens of minutes to several hours and are not suitable for measuring compounds that have significant chemical degradation on this timescale. One such compound is enalapril. Although stable in human plasma enalapril is subject to rapid esterase-catalyzed hydrolysis in rat plasma. A method has been developed which allows the extent of rat PPB of enalapril to be determined from initial rates kinetics of the adsorption of the unstable compound to dextran coated charcoal (DCC). The method has been applied to stable compounds, and the results are consistent with those from traditional equilibrium dialysis experiments. The experimental method is simple to run, requires no specialized equipment, and can potentially be applied to other compounds that show instability in plasma where traditional experimental techniques are unsuitable.

In Vitro Models for Plasma Binding and Tissue Storage

Measurement of the extent of plasma protein binding (PPB) and tissue disposition together with an understanding of the molecular properties that control binding is of fundamental importance in the drug discovery process. The extent of plasma protein binding of a candidate drug molecule has an influence on a number of critical areas such as the determination of safety margins in toxicology studies, the efficacy of a drug candidate, and its metabolism and pharmacokinetics. The measurement of tissue storage and a molecular understanding of tissue affinity has, historically, not been studied to the same extent as plasma protein binding. However, the now widespread use of physiologically-based pharmokinetics (PBPK) modeling has necessitated a greater understanding of tissue disposition and the properties controlling it.