Spatial omics reveals molecular changes in focal cortical dysplasia type II.

Focal cortical dysplasia (FCD) represents a group of diverse localized cortical lesions that are highly epileptogenic and occur due to abnormal brain development caused by genetic mutations, involving the mammalian target of rapamycin (mTOR). These somatic mutations lead to mosaicism in the affected brain, posing challenges to unravel the direct and indirect functional consequences of these mutations. To comprehensively characterize the impact of mTOR mutations on the brain, we employed here a multimodal approach in a preclinical mouse model of FCD type II (Rheb), focusing on spatial omics techniques to define the proteomic and lipidomic changes.

Setup of human liver-chips integrating 3D models, microwells and a standardized microfluidic platform as proof-of-concept study to support drug evaluation.

Human 3D liver microtissues/spheroids are powerful models to study drug-induced liver injury (DILI) but the small number of cells per spheroid limits the models' usefulness to study drug metabolism. In this work, we scale up the number of spheroids on both a plate and a standardized organ-chip platform by factor 100 using a basic method which requires only limited technical expertise. We successfully generated up to 100 spheroids using polymer-coated microwells in a 96-well plate (= liver-plate) or organ-chip (= liver-chip).

Multimodal molecular imaging in drug discovery and development.

In addition to individual imaging techniques, the combination and integration of several imaging techniques, so-called multimodal imaging, can provide large amounts of anatomical, functional, and molecular information accelerating drug discovery and development processes. Imaging technologies aid in understanding the disease mechanism, finding new pharmacological targets, and assessment of new potential drug candidates and treatment response. Here, we describe how different imaging techniques can be used in different phases of drug discovery and development and highlight their strengths, related innovations, and future potential with a focus on the implementation of artificial intelligence (AI) and radiomics for imaging technologies.

Prediction of Chameleonic Efficiency.

Chameleonic properties, i. e., the capacity of a molecule to hide polarity in non-polar environments and expose it in water, help achieving sufficient permeability and solubility for drug molecules with high MW.

Estimating human ADME properties, pharmacokinetic parameters and likely clinical dose in drug discovery.

: Prediction of human absorption, distribution, metabolism, and excretion (ADME) properties, therapeutic dose and exposure has become an integral part of compound optimization in discovery. Incorporation of drug metabolism and pharmacokinetics into discovery projects has largely tempered historical drug failure due to sub-optimal ADME. In the current era, inadequate safety and efficacy are leading culprits for attrition; both of which are dependent upon drug exposure.

Development and Characterization of a Human Hepatocyte Low Intrinsic Clearance Assay for Use in Drug Discovery.

Progression of new chemical entities is a multiparametric process involving a balance of potency; absorption, distribution, metabolism, and excretion; and safety properties. To accurately predict human pharmacokinetics and estimate human efficacious dose, the use of in vitro measures of clearance is often essential. Low metabolic clearance is often targeted to facilitate in vivo exposure and achieve appropriate half-life.

Bioanalysis of Pseudomonas aeruginosa alkyl quinolone signalling molecules in infected mouse tissue using LC-MS/MS; and its application to a pharmacodynamic evaluation of MvfR inhibition.

Alkyl quinolone molecules 2-heptyl-4-quinolone (HHQ) and 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS) are important quorum sensing signals, which play a mediatory role in the pathogenesis of acute and chronic Pseudomonas aeruginosa infection. A targeted approach inhibiting the bacterial 'multiple virulence factor regulon' (MvfR) protein complex, offers the possibility to block the synthesis of MvfR-dependant signal molecules. Here, a high throughput bioanalytical method was developed using LC-MS/MS detection for the selective determination of HHQ and PQS in mouse tissue homogenate, over a sensitive range of 1-5000 and 10-5000pg/mL, respectively.

A new paradigm for navigating compound property related drug attrition.

Improving the efficiency of drug discovery remains a major focus for the pharmaceutical industry. Toxicity accounts for 90% of withdrawals and major early-stage terminations relate to suboptimal efficacy and safety. Traditional oral drug space is well defined with respect to physicochemical properties and ADMET risks but increased focus on ligand-lipophilicity efficiency, maximizing enthalpy contributions and new target classes challenge this paradigm.

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

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.

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 drug's biological behavior provide an indirect link back to structure, facilitating the prediction of a biological property as a consequence of a particular molecular manipulation.

Application of in silico, in vitro and preclinical pharmacokinetic data for the effective and efficient prediction of human pharmacokinetics.

In the present age of pharmaceutical research and development, focused delivery of decision making data is more imperative than ever before. Resulting from several years' success, failure and consequential learning, this article also proffers advice and guidance on which in vitro and in vivo experiments to perform to facilitate efficient and cost-effective pursuit of candidate drugs with acceptable human pharmacokinetic profiles. Predictive in silico models are important in directing design toward compounds with the highest probability of having suitable DMPK properties rather than in predicting human pharmacokinetics per se, and the value and utility of such approaches are reviewed with the intention of providing direction to DMPK scientists.

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.

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.

The development, characterization, and application of an OATP1B1 inhibition assay in drug discovery.

The pivotal role of organic anion-transporting polypeptide 1B1 (OATP1B1) in drug disposition has become clear over the last decade. Therefore, an OATP1B1 inhibition assay suitable for use within early drug discovery was developed and characterized. IC(50) estimates for 10 literature compounds using pitavastatin and estradiol-17β-glucuronide as substrates were within 2-fold of each other.

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 compound's 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.

Lipophilicity of acidic compounds: impact of ion pair partitioning on drug design.

In drug discovery projects the ability to show a relationship between a compound's 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.

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 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.

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.

From ATP to AZD6140: the discovery of an orally active reversible P2Y12 receptor antagonist for the prevention of thrombosis.

Starting from adenosine triphosphate (ATP), the identification of a novel series of P2Y(12) receptor antagonists and exploitation of their SAR is described. Modifications of the acidic side chain and the purine core and investigation of hydrophobic substituents led to a series of neutral molecules. The leading compound, 17 (AZD6140), is currently in a large phase III clinical trial for the treatment of acute coronary syndromes and prevention of thromboembolic clinical sequelae.

The thermodynamics of the partitioning of ionizing molecules between aqueous buffers and phospholipid membranes.

Purpose: To study the thermodynamics of partitioning of eight ionising dual D2-recepto beta2-adrenoceptor agonists between vesicles of L-alpha-dimyristoylphosphatidylcholine (DMPC) and aqueous buffers.

Methods: The thermodynamics of partitioning have been studied by isothermal titration calorimetry (ITC).

Results: Compounds which are predominantly cationic at pH 7.

A rapid computational filter for cytochrome P450 1A2 inhibition potential of compound libraries.

QSAR models for a diverse set of compounds for cytochrome P450 1A2 inhibition have been produced using 4 statistical approaches; partial least squares (PLS), multiple linear regression (MLR), classification and regression trees (CART), and bayesian neural networks (BNN). The models complement one another and have identified the following descriptors as important features for CYP1A2 inhibition; lipophilicity, aromaticity, charge, and the HOMO/LUMO energies. Furthermore all models are global and have been used to predict a diverse independent set of compounds.

The binding of drugs to hepatocytes and its relationship to physicochemical properties.

The binding of 17 drugs to rat hepatocytes has been determined using equilibrium dialysis in combination with metabolic inhibitors and a kinetic model for the binding and dialysis processes. Metabolic inhibitors were used to retard the main routes of metabolism such that the half-life for turnover of the drugs was comparable to or greater than the time scale of the equilibrium dialysis process. Further experiments were carried out to determine the kinetics of diffusion of the compounds across the dialysis membrane and the observed extent of binding to hepatocytes.

QSAR and the rational design of long-acting dual D2-receptor/beta 2-adrenoceptor agonists.

This paper describes the development of a QSAR model for the rational control of functional duration of topical long-acting dual D(2)-receptor/beta(2)-adrenoceptor agonists for the treatment of chronic obstructive pulmonary disease. A QSAR model highlighted the importance of lipophilicity and ionization in controlling beta(2) duration. It was found that design rules logD(7.

A comparison of physiochemical property profiles of development and marketed oral drugs.

The process of drug discovery applies rigorous selection pressures. Marketed oral drugs will generally possess favorable physiochemical properties with respect to absorption, metabolism, distribution, and clearance. This paper describes a study in which the distributions of physiochemical properties of oral drugs in different phases of clinical development are compared to those already marketed.