Design of the Global Health chemical diversity library v2 for screening against infectious diseases.

There is a need for novel chemical matter for phenotypic and target-based screens to find starting points for drug discovery programmes in neglected infectious diseases and non-hormonal contraceptives that disproportionately affect Low- and Middle-Income Countries (LMICs). In some disease areas multiple screens of corporate and other libraries have been carried out, giving rise to some valuable starting points and leading to preclinical candidates. Whilst in other disease areas, little screening has been carried out. Much screening against pathogens has been conducted phenotypically as there are few robustly validated protein targets. However, many of the active compound series identified share the same molecular targets. To address the need for new chemical material, in this article we describe the design of a new library, designed for screening in drug discovery programmes for neglected infectious diseases. The compounds have been selected from the Enamine REAL (REadily AccessibLe) library, a virtual library which contains approximately 4.5 billion molecules. The molecules theoretically can be synthesized quickly using commercially available intermediates and building blocks. The vast majority of these have not been prepared before, so this is a source of novel compounds. In this paper we describe the design of a diverse library of 30,000 compounds from this collection (graphical abstract). The new library will be made available to laboratories working in neglected infectious diseases, subject to a review process. The project has been supported by the Bill & Melinda Gates Foundation and the Wellcome Trust (Wellcome).

Identification and development of a series of disubstituted piperazines for the treatment of Chagas disease.

Approximately 6-7 million people around the world are estimated to be infected with Trypanosoma cruzi, the causative agent of Chagas disease. The current treatments are inadequate and therefore new medical interventions are urgently needed. In this paper we describe the identification of a series of disubstituted piperazines which shows good potency against the target parasite but is hampered by poor metabolic stability. We outline the strategies used to mitigate this issue such as lowering logD, bioisosteric replacements of the metabolically labile piperazine ring and use of plate-based arrays for quick diversity scoping. We discuss the success of these strategies within the context of this series and highlight the challenges faced in phenotypic programs when attempting to improve the pharmacokinetic profile of compounds whilst maintaining potency against the desired target.

Design, Synthesis, and Testing of Potent, Selective Hepsin Inhibitors via Application of an Automated Closed-Loop Optimization Platform.

Hepsin is a membrane-anchored serine protease whose role in hepatocyte growth factor (HGF) signaling and epithelial integrity makes it a target of therapeutic interest in carcinogenesis and metastasis. Using an integrated design, synthesis, and screening platform, we were able to rapidly develop potent and selective inhibitors of hepsin. In progressing from the initial hit 7 to compound 53, the IC50 value against hepsin was improved from ∼1 µM to 22 nM, and the selectivity over urokinase-type plasminogen activator (uPA) was increased from 30-fold to >6000-fold. Subsequent in vitro ADMET profiling and cellular studies confirmed that the leading compounds are useful tools for interrogating the role of hepsin in breast tumorigenesis.

Rapid discovery of a novel series of Abl kinase inhibitors by application of an integrated microfluidic synthesis and screening platform.

Drug discovery faces economic and scientific imperatives to deliver lead molecules rapidly and efficiently. Using traditional paradigms the molecular design, synthesis, and screening loops enforce a significant time delay leading to inefficient use of data in the iterative molecular design process. Here, we report the application of a flow technology platform integrating the key elements of structure-activity relationship (SAR) generation to the discovery of novel Abl kinase inhibitors. The platform utilizes flow chemistry for rapid in-line synthesis, automated purification, and analysis coupled with bioassay. The combination of activity prediction using Random-Forest regression with chemical space sampling algorithms allows the construction of an activity model that refines itself after every iteration of synthesis and biological result. Within just 21 compounds, the automated process identified a novel template and hinge binding motif with pIC50 > 8 against Abl kinase--both wild type and clinically relevant mutants. Integrated microfluidic synthesis and screening coupled with machine learning design have the potential to greatly reduce the time and cost of drug discovery within the hit-to-lead and lead optimization phases.

Integrated Synthesis and Testing of Substituted Xanthine Based DPP4 Inhibitors: Application to Drug Discovery.

A novel integrated discovery platform has been used to synthesize and biologically assay a series of xanthine-derived dipeptidyl peptidase 4 (DPP4) antagonists. Design, synthesis, purification, quantitation, dilution, and bioassay have all been fully integrated to allow continuous automated operation. The system has been validated against a set of known DPP4 inhibitors and shown to give excellent correlation between traditional medicinal chemistry generated biological data and platform data. Each iterative loop of synthesis through biological assay took two hours in total, demonstrating rapid iterative structure-activity relationship generation.

Four-component reaction for the preparation of alpha-amino phosphonates from methyleneaziridines.

Alpha-amino phosphonates can be rapidly assembled in moderate to good yields (42-65%) via a "one-pot" process that brings together four components through the construction of three new intermolecular bonds.

Cyclodextrin-derived host molecules as reversal agents for the neuromuscular blocker rocuronium bromide: synthesis and structure-activity relationships.

A series of mono- and per-6-substituted cyclodextrin derivatives were synthesized as synthetic receptors (or host molecules) of rocuronium bromide, the most widely used neuromuscular blocker in anaesthesia. By forming host-guest complexes with rocuronium, these cyclodextrin derivatives reverse the muscle relaxation induced by rocuronium in vitro and in vivo and therefore can be used as reversal agents of the neuromuscular blocker to assist rapid recovery of patients after surgery. Because this supramolecular mechanism of action does not involve direct interaction with the cholinergic system, the reversal by these compounds, e.g., compound 14 (Org 25969), is not accompanied by cardiovascular side effects usually attendant with acetylcholinesterase inhibitors such as neostigmine. The structure-activity relationships are consistent with this supramolecular mechanism of action and are discussed herein. These include the effects of binding cavity size and hydrophobic and electrostatic interaction on the reversal activities of these compounds.

2-O-substituted cyclodextrins as reversal agents for the neuromuscular blocker rocuronium bromide.

A series of secondary face modified cyclodextrins (CDs) were synthesised with the aim of constructing host molecules capable of forming host-guest complexes with neuromuscular blockers, especially with rocuronium bromide. Perfacial 2-O-substitution of gamma-CD with 4-carboxybenzyl resulted in a CD host molecule 1 that forms a 1:1 binary complex with rocuronium bromide (K(a) 6.2 x 10(5) M(-1)). The biological activities of this compound and other derivatives as reversal agents of rocuronium bromide were examined in vitro (mouse hemi-diaphragm) and in vivo (anaesthetized guinea pigs). The host molecule 1 was found to exert potent reversal activity (ED(50) 0.21 micromol/kg, iv) against rocuronium-induced neuromuscular block, and thus proved the viability of using host molecules as antidotes of a biologically active compound.

Oxyaniliniums as acetylcholinesterase inhibitors for the reversal of neuromuscular block.

A series of oxyanilinium-based AChE inhibitors have been synthesised and tested for the reversal of vecuronium-induced neuromuscular block. Several compounds, for example 2-hydroxy- and 2-methoxy-N,N-dimethyl-N-allylanilinium bromide (3 and 6) showed comparable reversal potencies to edrophonium and clean in vivo cardiovascular profiles.

Metal- and Ligand-Accelerated Catalysis of the Baylis-Hillman Reaction.

The Baylis-Hillman reaction, the coupling of an unsaturated carbonyl compound/nitrile with aldehydes, is a valuable reaction but is limited in its practicality by poor reaction rates. We have endeavored to accelerate the reaction using Lewis acids and found that while conventional Lewis acids gave reduced rates group III, and lanthanide triflates (5 mol %) gave increased rates. The optimum metal salts were La(OTf)(3) and Sm(OTf)(3), which gave rate accelerations (k(rel)) of approximately 4.7 and 4.9, respectively, in reactions between tert-butyl acrylate and benzaldehyde when using stoichiometric amounts of DABCO. At low loadings of DABCO (up to 10 mol %), no reaction occurred due to association of DABCO with the metal. Use of additional ligands to displace the DABCO from the metal was studied, and the rate of reaction was found to increase further in most cases. Of the ligands tested, at 5 mol %, (+)-binol gave one of the largest rate accelerations (3.4-fold) and was studied in more detail. It was found that reactions occurred even at low DABCO concentration so that here the Lewis base and Lewis acid were able to promote the reaction without interference from each other. While the (+)-binol (and other chiral ligands) failed to provide any significant asymmetric induction, a substantial nonlinear effect was observed with binol. Thus, use of racemic binol gave no effect on the rate. In seeking to maximize the rate attainable, more soluble (liquid) ligands were studied. Diethyl tartrate and triethanolamine gave rate enhancements of 5.2x and 3.5x at 50 mol %, respectively, versus 1.5x and 2.3x at 5 mol %. The best protocol was to use 100 mol % DABCO, 50 mol % triethanolamine, and 5 mol % La(OTf)(3). This gave overall rate accelerations of between 23-fold and 40-fold depending on the acrylate and approximately 5-fold for acrylonitrile. A simple acid wash removed the reagents, leaving the product in the organic phase. While triethanolamine accelerated the reaction without the lanthanum triflate (18-22-fold at 80 mol %), the reaction in the presence of the metal salt was faster. The system was tested synthetically on various substrates and found to give good rate accelerations with both activated (benzaldehyde and p-nitrobenzaldehyde) and less activated aldehydes (anisaldehyde and cyclohexanecarboxaldehyde) with acrylates. The limited amount of dimerized acrylate in the latter reactions is noteworthy and should extend the range of substrates that can be made by the Baylis-Hillman reaction using our optimum conditions.