Benzoxazole piperidines as selective and potent somatostatin receptor subtype 5 antagonists.

SAR studies of a recently described SST5R selective benzoxazole piperidine lead series are described with particular focus on the substitution pattern on the benzyl and benzoxazole side-chains. Introduction of a second meta substituent at the benzyl unit significantly lowers residual hH1 activity and insertion of substituents onto the benzoxazole periphery entirely removes remaining h5-HT2B activity. Compounds with single digit nM activity, functional antagonism and favorable physicochemical properties endowed with a good pharmacokinetic profile in rats are described which should become valuable tools for exploring the pharmacological role of the SST5 receptor in vivo.

Safety screening in early drug discovery: An optimized assay panel.

BACKGROUND: Several factors contribute to the development failure of novel pharmaceuticals, one of the most important being adverse effects in pre-clinical and clinical studies. Early identification of off-target compound activity can reduce safety-related attrition in development. In vitro profiling of drug candidates against a broad range of targets is an important part of the compound selection process. Many compounds are synthesized during early drug discovery, making it necessary to assess poly-pharmacology at a limited number of targets. This paper describes how a rational, statistical-ranking approach was used to generate a cost-effective, optimized panel of assays that allows selectivity focused structure-activity relationships to be explored for many molecules. This panel of 50 targets has been used to routinely screen Roche small molecules generated across a diverse range of therapeutic targets. Target hit rates from the Bioprint® database and internal Roche compounds are discussed. We further describe an example of how this panel was used within an anti-infective project to reduce in vivo testing. METHOD: To select the optimized panel of targets, IC50 values of compounds in the BioPrint® database were used to identify assay "hits" i.e. IC50 ≤ 1 µM in 123 different in vitro pharmacological assays. If groups of compounds hit the same targets, the target with the higher hit rate was selected, while others were considered redundant. Using a step-wise analysis, an assay panel was identified to maximize diversity and minimize redundancy. Over a five-year period, this panel of 50 off-targets was used to screen ≈1200 compounds synthesized for Roche drug discovery programs. Compounds were initially tested at 10 µM and hit rates generated are reported. Within one project, the number of hits was used to refine the choice of compounds being assessed in vivo. RESULTS: 95% of compounds from the BioPrint® panel were identified within the top 47-ranked assays. Based on this analytical approach and the addition of three targets with established safety concerns, a Roche panel was created for external screening. hERG is screened internally and not included in this analysis. Screening at 10 µM in the Roche panel identified that adenosine A3 and 5HT2B receptors had the highest hit rates (~30%), with 50% of the targets having a hit rate of ≤4%. An anti-infective program identified that a high number of hits in the Roche panel was associated with mortality in 19 mouse tolerability studies. To reduce the severity and number of such studies, future compound selections integrated the panel hit score into the selection process for in vivo studies. It was identified that compounds which hit less targets in the panel and had free plasma exposures of ~2 µM were generally better tolerated. DISCUSSION: This paper describes how an optimized panel of 50 assays was selected on the basis of hit similarity at 123 targets. This reduced panel, provides a cost-effective screening panel for assessing compound promiscuity, whilst also including many safety-relevant targets. Frequent use of the panel in early drug discovery has provided promiscuity and safety-relevant information to inform pre-clinical drug development at Roche.

Benzodioxoles: novel cannabinoid-1 receptor inverse agonists for the treatment of obesity.

The application of the evolutionary fragment-based de novo design tool TOPology Assigning System (TOPAS), starting from a known CB1R (CB-1 receptor) ligand, followed by further refinement principles, including pharmacophore compliance, chemical tractability, and drug likeness, allowed the identification of benzodioxoles as a novel CB1R inverse agonist series. Extensive multidimensional optimization was rewarded by the identification of promising lead compounds, showing in vivo activity. These compounds reversed the CP-55940-induced hypothermia in Naval Medical Research Institute (NMRI) mice and reduced body-weight gain, as well as fat mass, in diet-induced obese Sprague-Dawley rats. Herein, we disclose the tools and strategies that were employed for rapid hit identification, synthesis and generation of structure-activity relationships, ultimately leading to the identification of (+)-[( R)-2-(2,4-dichloride-phenyl)-6-fluoro-2-(4-fluoro-phenyl)-benzo[1,3]dioxol-5-yl]-morpholin-4-yl-methanone ( R)-14g . Biochemical, pharmacokinetic, and pharmacodynamic characteristics of ( R)-14g are discussed.

In silico prediction of brain and CSF permeation of small molecules using PLS regression models.

Computational partial least square (PLS) regression models were developed, which can be applied to predict central nervous system (CNS) penetration of drug-like organic molecules. For modeling, a dataset of 77 structurally diverse compounds was used with reported steady-state rat brain to plasma ratios (BPR). Information on steady-state cerebrospinal fluid distribution (CSF to plasma ratio or CSFPR) was available for 37 of these compounds. The molecules were from different chemical series and included bases, acids, zwitterions and neutral molecules. They were CNS active and were therefore assumed to penetrate the blood-brain barrier and/or the blood-liquor barrier. Using these PLS models, the dataset could be described accurately (r(2)=0.78, StErrorEst=0.30 and r(2)=0.75, StErrorEst=0.28 for BPR and CSFPR, respectively). Molecular descriptors used for the prediction of passive membrane transport were lipophilicity, polar and hydrophobic surface areas as well as structural parameters and net charge at physiological pH. There was no apparent correlation between experimental brain and CSF exposure. Consequently, different PLS models and guiding rules were developed and discussed for the prediction of BPR or CSFPR. The present models provide a cost-effective and efficient strategy to guide synthetic efforts in medicinal chemistry at an early stage of the drug discovery and development process.

Absorption-excipient-pH classification gradient maps: sparingly soluble drugs and the pH partition hypothesis.

This study of sparingly soluble model drugs assesses (a) how pH and the aqueous boundary layer factors may affect in vitro and in vivo absorption, (b) to what extent single excipients (sodium taurocholate, hydroxypropyl-beta-cyclodextrin, KCl, propylene glycol, methylpyrrolidone, and polyethylene glycol 400) can mitigate adverse absorption effects, and (c) how a novel rank-order visualization tool can be applied in high-throughput screening to identify promising single-excipient effects on the absorption potential of test compounds. The products of accurately measured solubility and artificial-membrane permeability (PAMPA) values at pH 5.0, 6.2, and 7.4, fully taking into account factors such as aqueous boundary layer resistance, membrane retention, and the formation of drug dimers and trimers, were used to define a flux function. A "self-organized" data visualization tool based on the flux function was mined for the promising excipient-drug combinations. In excipient-free solutions, most of the compounds studied formed aggregates. The presence of an excipient predominantly lowered permeability, but most often not by the same amount as solubility was elevated. The compounds with absorption potential most helped by excipients were: clotrimazole>griseofulvin>progesterone>dipyridamole>glibenclamide>mefenamic acid>butacaine>astemizole. The HP-beta-CD effect observed for albendazole and glibenclamide appeared to follow Cmax trends in published pharmacokinetics studies. A surprising outcome of the in vitro measurements was that the classical pH Partition Hypothesis can be "inverted" in its monotonicity by sparingly soluble compounds.

Discovery of Risdiplam, a Selective Survival of Motor Neuron-2 ( SMN2) Gene Splicing Modifier for the Treatment of Spinal Muscular Atrophy (SMA).

SMA is an inherited disease that leads to loss of motor function and ambulation and a reduced life expectancy. We have been working to develop orally administrated, systemically distributed small molecules to increase levels of functional SMN protein. Compound 2 was the first SMN2 splicing modifier tested in clinical trials in healthy volunteers and SMA patients. It was safe and well tolerated and increased SMN protein levels up to 2-fold in patients. Nevertheless, its development was stopped as a precautionary measure because retinal toxicity was observed in cynomolgus monkeys after chronic daily oral dosing (39 weeks) at exposures in excess of those investigated in patients. Herein, we describe the discovery of 1 (risdiplam, RG7916, RO7034067) that focused on thorough pharmacology, DMPK and safety characterization and optimization. This compound is undergoing pivotal clinical trials and is a promising medicine for the treatment of patients in all ages and stages with SMA.

PAMPA--critical factors for better predictions of absorption.

PAMPA, log P(OCT), and Caco-2 are useful tools in drug discovery for the prediction of oral absorption, brain penetration and for the development of structure-permeability relationships. Each approach has its advantages and limitations. Selection criteria for methods are based on many different factors: predictability, throughput, cost and personal preferences (people factor). The PAMPA concerns raised by Galinis-Luciani et al. (Galinis-Luciani et al., 2007, J Pharm Sci, this issue) are answered by experienced PAMPA practitioners, inventors and developers from diverse research organizations. Guidelines on how to use PAMPA are discussed. PAMPA and PAMPA-BBB have much better predictivity for oral absorption and brain penetration than log P(OCT) for real-world drug discovery compounds. PAMPA and Caco-2 have similar predictivity for passive oral absorption. However, it is not advisable to use PAMPA to predict absorption involving transporter-mediated processes, such as active uptake or efflux. Measurement of PAMPA is much more rapid and cost effective than Caco-2 and log P(OCT). PAMPA assay conditions are critical in order to generate high quality and relevant data, including permeation time, assay pH, stirring, use of cosolvents and selection of detection techniques. The success of using PAMPA in drug discovery depends on careful data interpretation, use of optimal assay conditions, implementation and integration strategies, and education of users.

Novel Triazolopyrimidine-Derived Cannabinoid Receptor 2 Agonists as Potential Treatment for Inflammatory Kidney Diseases.

The cannabinoid receptor 2 (CB2) system is described to modulate various pathological conditions, including inflammation and fibrosis. A series of new heterocyclic small-molecule CB2 receptor agonists were identified from a high-throughput screen. Lead optimization gave access to novel, highly potent, and selective (over CB1) triazolopyrimidine derivatives. A preliminary structure-activity relationship was established, and physicochemical properties in this compound class were significantly improved toward better solubility, lipophilicity, and microsomal stability. An optimized triazolopyrimidine derivative, (3S)-1-[5-tert-butyl-3-[(1-cyclopropyltetrazol-5-yl)methyl]triazolo[4,5-d]pyrimidin-7-yl]pyrrolidin-3-ol (39), was tested in a kidney ischemia-reperfusion model, in which it showed efficacy at a dose of 10 mg kg(-1) (p.o.). A significant depletion of the three measured kidney markers indicated a protective role of CB2 receptor activation toward inflammatory kidney damage. Compound 39 was also protective in a model of renal fibrosis. Oral treatment with 39 at 3 mg kg(-1) per day significantly decreased the amount of fibrosis by ∼ 40% which was induced by unilateral ureter obstruction.

Can we discover pharmacological promiscuity early in the drug discovery process?

The term 'pharmacological promiscuity' describes the activity of a single compound against multiple targets. When undesired, promiscuity is a major safety concern that needs to be detected as early as possible in the drug discovery process. The analysis of large datasets reveals that the majority of promiscuous compounds are characterized by recognizable molecular properties and structural motifs, the most important one being a basic center with a pK(a)(B)>6. These compounds interact with a small set of targets such as aminergic GPCRs; some of these targets attract surprisingly high hit rates. In this review, we discuss current trends in the assessment of pharmacological promiscuity and propose strategies to enable early detection and mitigation.

Extending pKa prediction accuracy: high-throughput pKa measurements to understand pKa modulation of new chemical series.

We have recently developed a tool, MoKa, to predict the pK(a) of organic compounds using a large dataset of over 26,500 literature pK(a) values as a training set. However, predicting accurately pK(a) (<0.5 pH units) remains challenging for novel series, and this can be a drawback in the optimization of activity and ADME properties of lead compounds. To address this issue it is important to expand our knowledge of pK(a) determinants, therefore we have conducted high-throughput pK(a) measurements by using Spectral Gradient Analysis (SGA) on novel series of compounds selected from vendor databases. Here we report our findings on the effect of specific chemical groups and steric constraints on the pK(a) of common functionalities in medicinal chemistry, such as amines, sulfonamides, and amides. Furthermore, we report the pK(a) of ionizable groups that were not well represented in the database of literature pK(a) of MoKalpha, such as hydrazide derivatives. These findings helped us to enhance MoKalpha, which is here benchmarked on a set of experimental pK(a) values from the Roche in-house library (N = 5581; RMSE = 1.09; R2 = 0.82). The accuracy of the predictions was greatly improved (RMSE = 0.49, R2 = 0.96) after training the software by using the automated tool Kibitzer with 6226 pK(a) values taken from a different set of Roche compounds appropriately selected, and this demonstrates the value of using high-throughput pK(a) measurements to expand the training set of pK(a) values used by the software MoKalpha.

Coexistence of passive and carrier-mediated processes in drug transport.

The permeability of biological membranes is one of the most important determinants of the pharmacokinetic processes of a drug. Although it is often accepted that many drug substances are transported across biological membranes by passive transcellular diffusion, a recent hypothesis speculated that carrier-mediated mechanisms might account for the majority of membrane drug transport processes in biological systems. Based on evidence of the physicochemical characteristics and of in vitro and in vivo findings for marketed drugs, as well as results from real-life discovery and development projects, we present the view that both passive transcellular processes and carrier-mediated processes coexist and contribute to drug transport activities across biological membranes.

Solubility-excipient classification gradient maps.

This study assessed the effect of excipients (sodium taurocholate, 2-hydroxypropyl-f-cyclodextrin, potassium chloride, propylene glycol, 1-methyl-2-pyrrolidone, and polyethylene glycol 400) on the apparent intrinsic solubility properties of eight sparingly soluble drugs (four bases, two neutrals, and two acids): astemizole, butacaine, clotrimazole, dipyridamole, griseofulvin, progesterone, glibenclamide, and mefenemic acid. Over 1,200 UV-based solubility measurements (pH 3-10) were made with a high-throughput instrument. New equations, based on the "shift-in-pKa" method, were derived to interpret the complicated solubility-pH dependence observed, and poorly predicted by the Henderson-Hasselbalch equation. An intrinsic solubility-excipient classification gradient map visualization tool was developed to rank order the compounds and the excipients. In excipient-free solutions, all of the ionizable compounds formed either uncharged or mixed-charge aggregates. Mefenamic acid formed anionic dimers and trimers. Glibenclamide displayed a tendency to form monoanionic dimers. Dipyridamole and butacaine tended to form uncharged aggregates. With strong excipients, the tendency to form aggregates diminished, except in the case of glibenclamide. We conclude that a low-cost, compound-sparing, and reasonably accurate high-throughput assay which can be used in early screening to prioritize candidate molecules by their eventual developability via the excipient route is possible with the aid of the "self-organized" intrinsic solubility-excipient classification gradient maps.

Predicting and tuning physicochemical properties in lead optimization: amine basicities.

This review describes simple and useful concepts for predicting and tuning the pK(a) values of basic amine centers, a crucial step in the optimization of physical and ADME properties of many lead structures in drug-discovery research. The article starts with a case study of tricyclic thrombin inhibitors featuring a tertiary amine center with pK(a) values that can be tuned over a wide range, from the usual value of around 10 to below 2 by (remote) neighboring functionalities commonly encountered in medicinal chemistry. Next, the changes in pK(a) of acyclic and cyclic amines upon substitution by fluorine, oxygen, nitrogen, and sulfur functionalities, as well as carbonyl and carboxyl derivatives are systematically analyzed, leading to the derivation of simple rules for pK(a) prediction. Electronic and stereoelectronic effects in cyclic amines are discussed, and the emerging computational methods for pK(a) predictions are briefly surveyed. The rules for tuning amine basicities should not only be of interest in drug-discovery research, but also to the development of new crop-protection agents, new amine ligands for organometallic complexes, and in particular, to the growing field of amine-based organocatalysis.

PAMPA - excipient classification gradient map.

The effect of excipients on the artificial membrane permeability (Double-Sink PAMPA) properties of eight sparingly soluble drugs was studied. Quantities of excipient were selected to match the concentrations expected in the gastrointestinal fluid under clinically relevant conditions. Over 1,200 measurements were performed. To correct for the effects of the aqueous boundary layer and determine the intrinsic permeability, precisely measured ionization constants were used. The intrinsic permeability of weak acids was enhanced (up to 100 fold) but that of weak bases depressed (up to 270 fold) by the excipients: mefenamic acid > glybenclamide > progesterone > griseofulvin > clotrimazole > astemizole > dipyridamole > butacaine. Excipient enhancement ranked: 3 mM NaTC > 0.24% PEG400 > 0.2 M KCl > 0.24% NMP > 5% PEG400 > 0.24% PG > 1% PEG400 > 0.1M KCl > 1% PG > 1% NMP > 5% PG > 0.24% HP-beta-CD > 1% HP-beta-CD > 15 mM NaTC. The study clearly indicates that the method is suitable for use in preclinical development to assess the effect of excipients on the permeability of sparingly soluble drug candidates. The method is quick, cost-effective, and reasonably accurate. The self-rank-ordered PAMPA-Mapping may be a helpful visualization tool for delivery screening.

Comparison of a 3D-model of the classical alpha-scorpion toxin V from Leiurus quinquestriatus quinquestriatus with other scorpion toxins.

In the present paper, a study of classical and insect alpha-scorpion toxins is described. A homology model of the classical alpha-toxin LqqV from Leiurus quinquestriatus quinquestriatus was developed. The model was compared to stable and energetically favourable conformations of AaHII from Androctonus australis Hector and LqhalphaIT from Leiurus quinquestriatus hebraeus, which are the most active alpha-toxins in mammals and insects. The conformations were retrieved from molecular dynamics simulations of known structures. The model of LqqV shows a C-terminal conformation similar to LqhalphaIT. This is mainly caused by electrostatic interactions between Lys10 /Lys60 and Glu59, which are comparable to the cation-pi interactions of Tyr10 and Arg64 in LqhalphaIT. During the simulations the structures of AaHII and LqqV were stabilised through electrostatic interactions between Glu32 and Lys50 and especially the loop adjacent to the alpha-helix is affected, which is in contrast to LqhalphaIT. When the molecular electrostatic potentials of the toxins were studied, a possibly important difference between the classical alpha-toxins and the insect alpha-toxin LqhalphaIT was found in the area around Lys30 and Arg56 of AaHII, where a positive potential is missing in LqhalphaIT. A large negative potential caused by Asp3, Glu15 and Asp19 in LqhalphaIT is also unique for this toxin. It is proposed that Arg18, which is important for activity of LqhalphaIT, restricts the negative potential in this area and is not essential for toxins where negatively charged residues in comparable positions are not present.

Fluorine in medicinal chemistry.

Fluorinated compounds are synthesized in pharmaceutical research on a routine basis and many marketed compounds contain fluorine. The present review summarizes some of the most frequently employed strategies for using fluorine substituents in medicinal chemistry. Quite often, fluorine is introduced to improve the metabolic stability by blocking metabolically labile sites. However, fluorine can also be used to modulate the physicochemical properties, such as lipophilicity or basicity. It may exert a substantial effect on the conformation of a molecule. Increasingly, fluorine is used to enhance the binding affinity to the target protein. Recent 3D-structure determinations of protein complexes with bound fluorinated ligands have led to an improved understanding of the nonbonding protein-ligand interactions that involve fluorine.