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Through the European Lead Factory model, industry-standard high-throughput screening and hit validation are made available to academia, small and medium-sized enterprises, charity organizations, patient foundations, and participating pharmaceutical companies. The compound collection used for screening is built from a unique diversity of sources. It brings together compounds from companies with different therapeutic area heritages and completely new compounds from library synthesis. This generates structural diversity and combines molecules with complementary physicochemical properties. In 2019, the screening library was updated to enable another 5 years of running innovative drug discovery projects. Here, we investigate the physicochemical and diversity properties of the updated compound collection. We show that it is highly diverse, drug-like, and complementary to commercial screening libraries.

“This is the pre-peer reviewed version of the following article: J. Med. Chem., 2023, 66(1), 716-732, which has been published in final form at https://doi.org/10.1021/acs.jmedchem.2c01646. This article may be used for non-commercial purposes in accordance with ACS Terms and Conditions for Use of Self-Archived Versions."

Recent years have witnessed a global decline in the productivity and advancement of the pharmaceutical industry. A major contributing factor to this is the downturn in drug discovery successes. This can be attributed to the lack of structural (particularly scaffold) diversity and structural complexity exhibited by current small molecule screening collections. Macrocycles have been shown to exhibit a diverse range of biological properties, with over 100 natural product-derived examples currently marketed as FDA-approved drugs. Despite this, synthetic macrocycles are widely considered to be a poorly explored structural class within drug discovery, which can be attributed to their synthetic intractability. Herein we describe a novel complexity-to-diversity strategy for the diversity-oriented synthesis of novel, structurally complex and diverse macrocyclic scaffolds from natural product starting materials. This approach exploits the inherent structural (including functional) and stereochemical complexity of natural products in order to rapidly generate diversity and complexity. Readily-accessible natural product-derived intermediates serve as structural templates which can be divergently functionalized with different building blocks to generate a diverse range of acyclic precursors. Subsequent macrocyclisation then furnishes compounds that are each based around a distinct molecular scaffold. Thus, high levels of library scaffold diversity can be rapidly achieved. In this proof-of-concept study, the natural product quinine was used as the foundation for library synthesis, and six novel structurally diverse, highly complex and functionalized macrocycles were generated.

Large, diverse compound libraries are an essential requisite in target-based drug development. In this work, a robust microwave-assisted synthesis for the diastereoselective generation of 3-saccharinyl-trans-β-lactams is reported. The method is optimised for combinatorial library synthesis in which decoration of the scaffold is varied on both the β-lactam and the saccharine moiety. Within the European Lead Factory (ELF) consortium, a library of 263 compounds was efficiently produced using the developed methodology.

Amphiphilic compounds are used in a variety of applications due to their lyotropic liquid-crystalline phase formation, however only a limited number of compounds, in a potentially limitless field, are currently in use. A library of organic amphiphilic compounds was synthesised consisting of glucose, galactose, lactose, xylose and mannose head groups and double and triple-chain hydrophobic tails. A modular, high-throughput approach was developed, whereby head and tail components were conjugated using the copper-catalysed azide–alkyne cycloaddition (CuAAC) reaction. The tails were synthesised from two core alkyne-tethered intermediates, which were subsequently functionalised with hydrocarbon chains varying in length and degree of unsaturation and branching, while the five sugar head groups were selected with ranging substitution patterns and anomeric linkages. A library of 80 amphiphiles was subsequently produced, using a 24-vial array, with the majority formed in very good to excellent yields. A preliminary assessment of the liquid-crystalline phase behaviour is also presented.

Multiplex Automated Genome Engineering (MAGE) allows simultaneous mutagenesis of multiple target sites in bacterial genomes using short oligonucleotides. However, large-scale mutagenesis requires hundreds to thousands of unique oligos, which are costly to synthesize and impossible to scale-up by traditional phosphoramidite column-based approaches. Here, we describe a novel method to amplify oligos from microarray chips for direct use in MAGE to perturb thousands of genomic sites simultaneously. We demonstrated the feasibility of large-scale mutagenesis by inserting T7 promoters upstream of 2585 operons in E. coli using this method, which we call Microarray-Oligonucleotide (MO)-MAGE. The resulting mutant library was characterized by high-throughput sequencing to show that all attempted insertions were estimated to have occurred at an average frequency of 0.02% per locus with 0.4 average insertions per cell. MO-MAGE enables cost-effective large-scale targeted genome engineering that should be useful for a variety of applications in synthetic biology and metabolic engineering.

With the developments in high performance chromatography and mass spectrometry, the analysis of complex mixtures of closely related triacylglycerols has come within reach. Currently, however, the availability of chemically pure triacylglycerols is limited, mainly due to the lack of efficient synthetic methods that allow their synthesis. Here, we report an efficient and operationally simple three-step synthesis of enantiopure triacylglycerols with yields ranging from 79 to 92%, that tolerates a broad range of saturated and unsaturated fatty acids. Furthermore, we developed an automated protocol, which might greatly facilitate the synthesis of triacylglycerol libraries. Practical applications: The analysis of the composition of milk fat and as analytical standards in lipidomics. An efficient three-step synthesis of enantiopure triacylglycerols with yields ranging from 79 to 92% is reported. This is accompanied by an automated protocol for triacylglycerol synthesis.

A series of substituted diaryltriazoles was prepared by a solid-phase-synthesis protocol using a modified Wang resin. The copper(I)- or ruthenium(II)-catalyzed 1,3-cycloaddition on the polymer bead allowed a rapid synthesis of the target compounds in a parallel fashion with in many cases good to excellent yields. Substituted diaryltriazoles resemble a molecular structure similar to established terphenyl-alpha-helix peptide mimics and have therefore the potential to act as selective inhibitors for protein–protein interactions.

We prepared a series of peptide-like 14-membered macrocycles containing an imidazole-4,5-dicarboxylic acid scaffold by using known coupling reagents and protecting group strategies. Yields of the purified macrocycles were poor on average, yet seemingly independent of amino acid substitution or stereochemistry. The macrocycles retain some level of conformational variability as observed by both molecular modeling and X-ray crystallography. These macrocycles represent a new class of structures for further development and for future application in high-throughput screening against a variety of biological targets.

Flow chemistry has gained considerable recognition as a simple, efficient, and safe technology for the synthesis of many types of organic and inorganic molecules ranging in scope from large complex natural products to silicon nanoparticles. In this paper we describe a method that adapts flow chemistry to the synthesis of libraries of compounds using a fluorous immiscible solvent as a spacer between reactions. The methodology was validated in the synthesis of two small heterocycle containing libraries. The reactions were performed on a 0.2 mmol scale, enabling tens of milligrams of material to be generated in a single 200 mL reaction plug. The methodology allowed library synthesis in half the time of conventional microwave synthesis while maintaining similar yields. The ability to perform multiple, potentially unrelated reactions in a single run is ideal for making small quantities of many different compounds quickly and efficiently.

With the constant need for the development of new therapeutics, library synthesis has become a staple of modern drug discovery. This technique allows for the synthesis of multiple compounds in parallel to gain insight to activity relationships associated with biological targets. Within this body of work is the development of structure-activity relationships (SAR) at two biologically relevant targets, DPP-IV and NS1. DPP-IV has been shown to play a critical role in the regulation of incretin hormones responsible for stimulating insulin production. Two known inhibitors of DPPIV (Vildagliptin and Saxagliptin) fall into the class of compounds known as cyanopyrrolidines and display large hydrophobic substituents at either the N-terminus or the α-carbon. Previous SAR studies have examined substitution patterns at the N-terminus, with little attention given to substitution at both the α-carbon and the N-terminus. A 42-compound library was designed to systematically examine steric restrictions within the DPP-IV binding pocket. Additionally, three compounds were synthesized to be used in the development of a functioning assay. Initial work suggested that the substrate Nle-Pro-AMC was participating in substrate inhibition with DPP-IV at concentrations above 50μM. Once this model of analysis was identified, a protocol was developed to screen compounds for biological activity. The Influenza virus non-structural protein 1 (NS1) is a multifunctional protein which plays a critical role in viral replication. Recent research has identified NS1 as a viable target to treat influenza based on the highly conserved structure across different strains of influenza A and the important cellular interactions which are involved with viral replication. Following a large scale screen, an SAR was developed to design and synthesize novel inhibitors of NS1. Initial studies identified key interactions with the left hand side of the molecule which may play a role in antiviral activity. The resulting compounds were highly potent while exhibiting little cytotoxicity. When amino acids were used as building blocks, antiviral activity was observed for multiple influenza A virus strains. With this result, a 96-compound library was designed and synthesized using 48 different carboxylic acids, amino acids, or dipeptides to further probe essential structural features required for antiviral activity.

Ziel dieser Dissertation war die Entwicklung einer flexiblen Synthesestrategie, die mittels einer einstufigen Robinson-Anellierung unter Einsatz eines breiten Spektrums an Ausgangstoffen zu einer Dekalin-Bibliothek führt, die zusammen mit weiteren Naturstoffprojekten der Arbeitsgruppe Information z.B. zur Enzym-Inhibierung liefern sollte. Dabei sollte die Strategie so ausgearbeitet werden, dass sowohl die Vorteile der Lösungs- als auch der Festphasensynthese genutzt werden. Im Rahmen dieser Arbeit ist es gelungen, zuerst eine einstufige Lösungssynthese für den Aufbau von Dekalinen mittels Robinson-Anellierung aus Methylvinylketonanaloga und Cyclohexanonderivaten zu entwickeln. Dabei wurde das Cyclohexanonderivat als Enamin aktiviert wobei verschiedene Amine bzw. auch Prolin getestet wurden.Um ein breite Variabilität an Substituentenmustern der Dekaline erhalten zu können, wurden zum einen Synthesestrategien zur Darstellung von unterschiedlich substituierten Analoga von Methylvinylketon entwickelt. Zum anderen gelang in der Robinson-Anellierung auch der Einsatz eines breiten Spektrums an Cyclohexanonderivaten sowie heterozyklischer Analoga. Mit der Synthese von ca. 150 Grundgerüsten ist die Entwicklung eines flexiblen Eintopfvefahrens zur Darstellung von Dekalinen und heterozyklischer Analoga gelungen.Basierend auf diesen Dekalingerüsten wurde einige Derivatisierungen in Lösung durchgeführt. Neben der Entschützung sämtlicher Schutzgruppen wurden z.B. Substitutionen durchgeführt, um weitere funktionelle Gruppen in die Moleküle einführen zu können.Für die Übertragung der Reaktion an die feste Phase war die Anbindung der Methylvinylketonanaloga an den polymeren Träger ein bedeutender Schritt. Im Rahmen dieser Versuche ist es gelungen, substituierte Analoga auch am polymeren Träger darzustellen. Basierend auf diesen festphasengebundenen Ausgangsstoffen ist es erstmal gelungen, die Robinson-Anellierung auch am polymeren Träger (Polystyrolharz) durchzuführen, wobei wiederum verschiedene Cyclohexanonanaloga zum Einsatz kamen.Im letzten Abschnitt der Arbeit wurde eine für einen Großteil der Moleküle anwendbarer Anker zur Anbindung an einen polymeren Träger entwickelt. In Beispielreaktionen wurden diese Derivate an die feste Phase gebunden und z.B. mittels Aldolreaktionen weiter derivatisiert. So konnten neben der Lösungssynthese durch die Derivatisierung in Lösung und an der festen Phase weitere 50 Derivate dargestellt werden.Es wurde bereits mit der biologischen Evaluierung begonnen, diese wird jedoch in den nächsten Monaten noch fortgesetzt.