Discovery of Small‐Molecule Interleukin‐2 Inhibitors from a DNA‐Encoded Chemical Library

Libraries of chemical compounds individually coupled to encoding DNA tags (DNA‐encoded chemical libraries) hold promise to facilitate exceptionally efficient ligand discovery. We constructed a high‐quality DNA‐encoded chemical library comprising 30 000 drug‐like compounds; this was screened in 170 different affinity capture experiments. High‐throughput sequencing allowed the evaluation of 120 million DNA codes for a systematic analysis of selection strategies and statistically robust identification of binding molecules. Selections performed against the tumor‐associated antigen carbonic anhydrase IX (CA IX) and the pro‐inflammatory cytokine interleukin‐2 (IL‐2) yielded potent inhibitors with exquisite target specificity. The binding mode of the revealed pharmacophore against IL‐2 was confirmed by molecular docking. Our findings suggest that DNA‐encoded chemical libraries allow the facile identification of drug‐like ligands principally to any protein of choice, including molecules capable of disrupting high‐affinity protein–protein interactions.     

DNA‐Encoded Dynamic Combinatorial Chemical Libraries

Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA‐encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal‐to‐noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA‐encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high‐affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA‐templated chemical reactions.     

Selection of DNA‐Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery

Dynamic combinatorial libraries (DCLs) is a powerful tool for ligand discovery in biomedical research; however, the application of DCLs has been hampered by their low diversity. Recently, the concept of DNA encoding has been employed in DCLs to create DNA‐encoded dynamic libraries (DEDLs); however, all current DEDLs are limited to fragment identification, and a challenging process of fragment linking is required after selection. We report an anchor‐directed DEDL approach that can identify full ligand structures from large‐scale DEDLs. This method is also able to convert unbiased libraries into focused ones targeting specific protein classes. We demonstrated this method by selecting DEDLs against five proteins, and novel inhibitors were identified for all targets. Notably, several selective BD1/BD2 inhibitors were identified from the selections against bromodomain 4 (BRD4), an important anti‐cancer drug target. This work may provide a broadly applicable method for inhibitor discovery.     

Design,Synthesis and Biological Evaluation of Potent Azadipeptide Nitrile Inhibitors and Activity‐Based Probes as Promising Anti‐Trypanosoma brucei Agents

Trypanosoma cruzi and Trypanosoma brucei are parasites that cause Chagas disease and African sleeping sickness, respectively. There is an urgent need for the development of new drugs against both diseases due to the lack of adequate cures and emerging drug resistance. One promising strategy for the discovery of small‐molecule therapeutics against parasitic diseases has been to target the major cysteine proteases such as cruzain for T. cruzi, and rhodesain/TbCatB for T. brucei. Azadipeptide nitriles belong to a novel class of extremely potent cysteine protease inhibitors against papain‐like proteases. We herein report the design, synthesis, and evaluation of a series of azanitrile‐containing compounds, most of which were shown to potently inhibit both recombinant cruzain and rhodesain at low nanomolar/picomolar ranges. A strong correlation between the potency of rhodesain inhibition (i.e., target‐based screening) and trypanocidal activity (i.e., whole‐organism‐based screening) of the compounds was observed. To facilitate detailed studies of this important class of inhibitors, selected hit compounds from our screenings were chemically converted into activity‐based probes (ABPs), which were subsequently used for in situ proteome profiling and cellular localization studies to further elucidate potential cellular targets (on and off) in both the disease‐relevant bloodstream form (BSF) and the insect‐residing procyclic form (PCF) of Trypanosoma brucei. Overall, the inhibitors presented herein show great promise as a new class of anti‐trypanosome agents, which possess better activities than existing drugs. The activity‐based probes generated from this study could also serve as valuable tools for parasite‐based proteome profiling studies, as well as bioimaging agents for studies of cellular uptake and distribution of these drug candidates. Our studies therefore provide a good starting point for further development of these azanitrile‐containing compounds as potential anti‐parasitic agents.     

Small Targeted Cytotoxics: Current State and Promises from DNA‐Encoded Chemical Libraries

The targeted delivery of potent cytotoxic agents has emerged as a promising strategy for the treatment of cancer and other serious conditions. Traditionally, antibodies against markers of disease have been used as drug‐delivery vehicles. More recently, lower molecular weight ligands have been proposed for the generation of a novel class of targeted cytotoxics with improved properties. Advances in this field crucially rely on efficient methods for the identification and optimization of organic molecules capable of high‐affinity binding and selective recognition of target proteins. The advent of DNA‐encoded chemical libraries allows the construction and screening of compound collections of unprecedented size. In this Review, we survey developments in the field of small ligand‐based targeted cytotoxics and show how innovative library technologies will help develop the drugs of the future.     

Multistep Continuous‐Flow Synthesis in Medicinal Chemistry: Discovery and Preliminary Structure–Activity Relationships of CCR8 Ligands

A three‐step continuous‐flow synthesis system and its application to the assembly of a new series of chemokine receptor ligands directly from commercial building blocks is reported. No scavenger columns or solvent switches are necessary to recover the desired test compounds, which were obtained in overall yields of 49–94 %. The system is modular and flexible, and the individual steps of the sequence can be interchanged with similar outcome, extending the scope of the chemistry. Biological evaluation confirmed activity on the chemokine CCR8 receptor and provided initial structure–activity‐relationship (SAR) information for this new ligand series, with the most potent member displaying full agonist activity with single‐digit nanomolar potency. To the best of our knowledge, this represents the first published example of efficient use of multistep flow synthesis combined with biological testing and SAR studies in medicinal chemistry.     

Selection of DNA‐Encoded Small Molecule Libraries Against Unmodified and Non‐Immobilized Protein Targets

The selection of DNA‐encoded libraries against biological targets has become an important discovery method in chemical biology and drug discovery, but the requirement of modified and immobilized targets remains a significant disadvantage. With a terminal protection strategy and ligand‐induced photo‐crosslinking, we show that iterated selections of DNA‐encoded libraries can be realized with unmodified and non‐immobilized protein targets.     

A DNA‐Encoded Chemical Library Incorporating Elements of Natural Macrocycles

Here we show a seven‐step chemical synthesis of a DNA‐encoded macrocycle library (DEML) on DNA. Inspired by polyketide and mixed peptide‐polyketide natural products, the library was designed to incorporate rich backbone diversity. Achieving this diversity, however, comes at the cost of the custom synthesis of bifunctional building block libraries. This study outlines the importance of careful retrosynthetic design in DNA‐encoded libraries, while revealing areas where new DNA synthetic methods are needed.     

Picolinamides as Effective Ligands for Copper‐Catalysed Aryl Ether Formation: Structure–Activity Relationships,Substrate Scope and Mechanistic Investigations

The use of picolinic acid amide derivatives as an effective family of bidentate ligands for copper‐catalysed aryl ether synthesis is reported. A fluorine‐substituted ligand gave good results in the synthesis of a wide range of aryl ethers. Even bulky phenols, known to be very challenging substrates, were shown to react with aryl iodides with excellent yields using these ligands. At the end of the reaction, the first examples of end‐of‐life Cu species were isolated and identified as Cu^II complexes with several of the anionic ligands tested. A preliminary mechanistic investigation is reported that suggests that the substituents on the ligands might have a crucial role in determining the redox properties of the metal centre and, consequently, its efficacy in the coupling process. An understanding of these effects is important for the development of new efficient and tunable ligands for copper‐based chemistry.     

Structure–Activity Studies of Cysteine‐Rich α‐Conotoxins that Inhibit High‐Voltage‐Activated Calcium Channels via GABAB Receptor Activation Reveal a Minimal Functional Motif

α‐Conotoxins are disulfide‐rich peptides that target nicotinic acetylcholine receptors. Recently we identified several α‐conotoxins that also modulate voltage‐gated calcium channels by acting as G protein‐coupled GABA_B receptor (GABA_BR) agonists. These α‐conotoxins are promising drug leads for the treatment of chronic pain. To elucidate the diversity of α‐conotoxins that act through this mechanism, we synthesized and characterized a set of peptides with homology to α‐conotoxins known to inhibit high voltage‐activated calcium channels via GABA_BR activation. Remarkably, all disulfide isomers of the active α‐conotoxins Pu1.2 and Pn1.2, and the previously studied Vc1.1 showed similar levels of biological activity. Structure determination by NMR spectroscopy helped us identify a simplified biologically active eight residue peptide motif containing a single disulfide bond that is an excellent lead molecule for developing a new generation of analgesic peptide drugs.     

A New Iron‐Based Carbon Monoxide Oxidation Catalyst: Structure–Activity Correlation

A new iron‐based catalyst for carbon monoxide oxidation, as a potential substitute for precious‐metal systems, has been prepared by using a facile impregnation method with iron tris‐acetylacetonate as a precursor on γ‐Al₂O₃. Light‐off and full conversion temperatures as low as 235 and 278 °C can be reached. However, the catalytic activity strongly depends on the loading; lower loadings perform better than higher ones. The different activities can be explained by variations of the structures formed. The structures are thoroughly characterized by a multimethodic approach by using X‐ray diffraction, Brunauer–Emmett–Teller surface areas, and Mössbauer spectroscopy combined with diffuse reflectance UV/Vis and X‐ray absorption spectroscopy. Consequently, isolated tetrahedrally coordinated Fe³⁺ centers and phases of AlFeO₃ are identified as structural requirements for high activity in the oxidation of carbon monoxide.     

Synthesis and Structure–Activity Relationship of Vicenistatin,a Cytotoxic 20‐Membered Macrolactam Glycoside

We have developed two syntheses of vicenistatin and its analogues. Our first‐generation strategy included the rapid and sequential assembly of the macrocyclic lactam by using an intermolecular Horner–Wadsworth–Emmons reaction between the C3–C13 fragment and the C1–C2, C14–C19 fragment, followed by an intramolecular Stille coupling reaction. The second‐generation strategy utilized a ring‐closing metathesis of a hexaene intermediate to generate the desired 20‐membered macrolactam. This second‐generation strategy made it possible to prepare synthetic analogues of vicenistatin, including the C20‐ and/or C23‐demethyl analogues. Evaluation of the cytotoxic effect of these analogues indicated the importance of the fixed conformation of aglycon for determining the biological activity of the vicenistatins.     

Structure–Activity Relationship of Palladium Phosphanesulfonates: Toward Highly Active Palladium‐Based Polymerization Catalysts

Palladium phosphanesulfonate [R₂P(C₆H₄‐o‐SO₃)PdMeL] catalysts permit the copolymerization of an exceptional large number of functional olefins with ethylene. However, these catalysts usually have reduced activity. We here have conducted a systematic study on the influence of the phosphane substituent, R, on activity and molecular weight. Phosphanes with strong σ‐donating character are shown to lead to the most active catalysts. Thus, the catalyst based on phosphane bis‐tert‐butyl‐phosphanyl‐benzenesulfonic acid (R=tBu) exhibits unprecedented high activity, rapidly polymerizing ethylene at room temperature to yield a linear polymer of high molecular weight (M_w=116 000 g mol^?1). The influence of the R group on the catalyst ability to incorporate methyl acrylate is also investigated.     

Evaluation of the Structure–Activity Relationship of Rifabutin and Analogs: A Drug–Membrane Study

This work focuses on the influence of rifabutin and two novel analogs, namely, N′‐acetyl‐rifabutin and N′‐butanoyl‐rifabutin, on the biophysical properties of lipid membranes. Monolayers and multilamellar vesicles composed of egg L ‐α‐phosphatidylcholine:cholesterol in a molar ratio of 4:1 are chosen to mimic biological membranes. Several accurate biophysical techniques are used to establish a putative relationship between the chemical structure of the antimycobacterial compounds and their activity on the membranes. A combination of in situ experimental techniques, such as Langmuir isotherms, Brewster angle microscopy, polarization‐modulated infrared reflection–absorption spectroscopy, and small‐angle X‐ray scattering, is used to assess the drug–membrane interaction. A relationship between the effect of a drug on the organization of the membranes and their chemical structure is found and may be useful in the development of new drugs with higher efficacy and fewer toxic effects.     

Selective Inhibition of the Immunoproteasome by Structure‐Based Targeting of a Non‐catalytic Cysteine

Clinically applied proteasome inhibitors induce cell death by concomitant blockage of constitutive and immunoproteasomes. In contrast, selective immunoproteasome inhibition is less cytotoxic and has the potential to modulate chronic inflammation and autoimmune diseases. In this study, we rationally designed decarboxylated peptides that covalently target a non‐catalytic cysteine of the immunoproteasome subunit β5i with α‐chloroacetamide‐containing sidechains. The enhanced isoform specificity decreased cytotoxic effects and the compound suppressed the production of inflammatory cytokines. Structure‐based optimization led to over 150‐fold selectivity for subunit β5i over β5c. This new compound class provides a promising starting point for the development of selective immunoproteasome inhibitors as potential anti‐inflammatory agents.     

Synthesis of Self‐Threading Bithiophenes and their Structure–Property Relationships Regarding Cyclic Side‐Chains with Atomic Precision

We have recently reported a self‐threading polythiophene as a new family of insulated molecular wires. Herein, we focused on the structure–property relationships of the unique three‐dimensional architecture of the monomer. We have synthesized nine self‐threading bithiophene monomers that have cyclic side‐chains of different size and flexibility: i.e., 21‐, 22‐, 23‐, 24‐, 26‐, and 30‐membered rings composed of paraffinic, olefinic, or alkynic chains. To investigate their structure–property relationships, ¹H NMR spectroscopy, UV absorption, and fluorescence spectroscopy measurements were conducted. We found that cyclic side‐chains define the movable range of the dihedral angle of the bithiophene backbone, thereby affecting its photophysical properties. Therefore, the ability to design a structure with atomic precision as described herein would lead to the fine‐tuning of the electronic properties of insulated molecular wires.