Stabilization of protein–protein interactions (PPIs) holds great potential for therapeutic agents, as illustrated by the successful drugs rapamycin and lenalidomide. However, how such interface-binding molecules can be created in a rational, bottom-up manner is a largely unanswered question. We report here how a fragment-based approach can be used to identify chemical starting points for the development of small-molecule stabilizers that differentiate between two different PPI interfaces of the adapter protein 14-3-3. The fragments discriminately bind to the interface of 14-3-3 with the recognition motif of either the tumor suppressor protein p53 or the oncogenic transcription factor TAZ. This X-ray crystallography driven study shows that the rim of the interface of individual 14-3-3 complexes can be targeted in a differential manner with fragments that represent promising starting points for the development of specific 14-3-3 PPI stabilizers.

The front cover picture shows the process of photocrosslinking a small molecule functionalized with a diaziridino group to its putative target upon UV irradiation, a critical step in photoaffinity chemical proteomics and target deconvolution. Though not intended to reflect the mode of binding, this depiction shows the photocrosslinking between a 1,2,3-thiadiazole-5-carboxamide (TDZ) series with SERCA2, one of the binding partners identified after enrichment and mass spectrometry analysis. Cellular effects observed with the TDZ series are consistent with mitochondrial dysfunction and SERCA engagement and modulation being mechanisms of actions. Front cover art created by Matias Casás-Selves and Julie Grouleff. More information can be found in the Full Paper by Andrew X. Zhang, et al. on page 917 in Issue 12, 2017 (DOI: 10.1002/cmdc.201700028).

Wnt signaling is critical for development, cell proliferation and differentiation, and mutations in this pathway resulting in constitutive signaling have been implicated in various cancers. A pathway screen using a Wnt-dependent reporter identified a chemical series based on a 1,2,3-thiadiazole-5-carboxamide (TDZ) core with sub-micromolar potency. Herein we report a comprehensive mechanism-of-action deconvolution study toward identifying the efficacy target(s) and biological implication of this chemical series involving bottom-up quantitative chemoproteomics, cell biology, and biochemical methods. Through observing the effects of our probes on metabolism and performing confirmatory cellular and biochemical assays, we found that this chemical series inhibits ATP synthesis by uncoupling the mitochondrial potential. Affinity chemoproteomics experiments identified sarco(endo)plasmic reticulum Ca2+ -dependent ATPase (SERCA2) as a binding partner of the TDZ series, and subsequent validation studies suggest that the TDZ series can act as ionophores through SERCA2 toward Wnt pathway inhibition.

Guest Editors Robert Goodnow and Christopher Davie recap the first Boston Symposium of Encoded Library Platforms and introduce the <italic>MedChemComm</italic> web collection on ‘DNA Encoded Libraries’.

Key Points DNA-encoded chemical library technologies are increasingly being adopted in drug discovery for hit and lead generation. DNA-encoded chemistry enables the exploration of chemical spaces four to five orders of magnitude more deeply than is achievable by traditional high-throughput screening methods. DNA-encoded chemical library technology involves the creation of large mixtures of small molecules that are encoded with sequences or single-stranded or double-stranded DNA. High-affinity hits from such mixtures are identifiable by sequencing the DNA tags associated with each compound. DNA-encoded library technology began with a publication by Brenner and Lerner in 1992. The technology has subsequently evolved to be practised by several large pharmaceutical and biotechnology companies. DNA-directed synthesis is a related approach. In this method, the specificity of DNA base pairing serves for both encoding and synthesis. DNA-encoded library synthesis as it is currently practised is based on reactions that are tolerant to water. The creation of hundreds of millions of DNA-encoded library compounds is less expensive and more feasible than assembling a library of single compounds on milligram scale.

The tertiary amino effect reaction was explored and developed for application to DNA-encoded library synthesis.

Modest success rates in fragment-based lead generation (FBLG) projects at AstraZeneca (AZ) prompted operational changes to improve performance. In this review, we summarize these changes, emphasizing the construction and composition of the AZ fragment library, screening practices and working model. We describe the profiles of the screening method for specific fragment subsets and statistically assess our ability to follow up on fragment hits through near-neighbor selection. Performance analysis of our second-generation fragment library (FL2) in screening campaigns illustrates the complementary nature of flat and 3D fragments in exploring protein-binding pockets and highlights our ability to deliver fragment hits using multiple screening techniques for various target classes. The new model has had profound impact on the successful delivery of lead series to drug discovery projects.

Complex mixtures of DNA encoded small molecules may be readily interrogated via high-throughput sequencing. These DNA encoded libraries (DELs) are commonly used to discover molecules that interact with pharmaceutically relevant proteins. The chemical diversity displayed by the library is key to successful discovery of potent, novel, and drug-like chemical matter. The small molecule moieties of DELs are generally synthesized though a multistep process, and each chemical step is accomplished while it is simultaneously attached to an encoding DNA oligomer. Hence, library chemical diversity is often limited to DNA compatible synthetic reactions. Herein, protocols for 24 reactions are provided that have been optimized for high-throughput production of DELs. These protocols detail the multistep synthesis of benzimidazoles, imidazolidinones, quinazolinones, isoindolinones, thiazoles, and imidazopyridines. Additionally, protocols are provided for a diverse range of useful chemical reactions including BOC deprotection (under pH neutral conditions), carbamylation, and Sonogashira coupling. Last, step-by-step protocols for synthesizing functionalized DELs from trichloronitropyrimidine and trichloropyrimidine scaffolds are detailed.

Starting from screening hit, (4S,7R)-1,7,8,8-tetramethyl-2-phenyl-1,2,4,5,6,7-hexahydro-4,7-methano-indazol-3-one (7), we optimized the potency and pharmacokinetic properties. This led to the identification of compounds with good in vivo activity in a mouse pharmacodynamic model of inhibition of 11βHSD1.

We designed and synthesized a novel series of phenylamino- and phenoxy-substituted pyrazolo[3,4-d]pyrimidine derivatives as GPR119 agonists. SAR studies indicated that electron-withdrawing substituents on the phenyl ring are important for potency and full efficacy. Compound 26 combined good potency with a promising pharmacokinetic profile in mice, and lowered the glucose excursion in mice in an oral glucose-tolerance test.

To date, the majority of applications for DNA-Encoded Library (DEL) have supported the identification of high-affinity ligands for exploring chemical/biological target space. The continuing need for new ligands with drug-like properties drive the use of DELs as a tool in drug discovery. The potentially huge diversity in DELs provides models of how large molecules such as siRNA may tap into receptor-mediated cell surface binding as well as differential subcellular compartmental internalization. The reagents needed to produce a DEL of 800 million compounds cost approximately US$150,000. Given the DEL method of synthesis, the chemistry is likely to be readily amenable to high-throughput chemistry procedures, and therefore, follow-up synthesis of individual hits should be routine. DEL technology has become a compelling, complementary approach in identifying molecules that create a positive impact in drug discovery and other chemistry-related sciences.

Small-molecule combinatorial chemistry has been the focus of much research and innovation during the last 20 years. With respect to the application of combinatorial chemistry to small-molecule drug discovery, an initial great excitement gave way to more conservative applications as well as outright skepticism. The application of combinatorial methods for the development of new catalysis and the exploration and development of process methods and in materials research has continued steadily. It is from this background of vigorous innovation and problem solving that DNA-encoded chemistry methods have emerged. High-yielding synthetic conditions have been developed for peptide and oligonucleotide synthesis, but there are only a few reactions that have been studied and refined to accommodate a broad chemical reaction diversity. In many cases, combinatorial chemistry required too much effort for the development of the necessary chemistry, at the expense of delivering useful compounds in a timely rate.

The synthesis of methyl 2-amino-6-methoxynicotinate, a valuable building block for the preparation of fused 2-pyridones, is reported. The optimized synthesis includes sequential microwave-induced regioselective 6-methoxylation, esterification, followed by microwave-induced reaction with p-methoxybenzylamine, and final deprotection under flow reaction hydrogenation conditions. Two key steps in the reported synthesis are a microwave-induced methoxylation and a microfluidic hydrogenation that afford improved regioselectivity and purity profile of the reaction products.

Methyl trimethylsilyl sulfide is used for the first time as methylthiolation reagent for the nucleophilic displacement of aromatic nitro groups.

The inhibition of LTB(4) binding to and activation of G-protein-coupled receptors BLT1 and BLT2 is the premise of a treatment for several inflammatory diseases. In a lead optimization effort starting with the leukotriene B(4) (LTB(4)) receptor antagonist (2), members of a series of 3,5-diarylphenyl ethers were found to be highly potent inhibitors of LTB(4) binding to BLT1 and BLT2 receptors, with varying levels of selectivity depending on the substitution. In addition, compounds 33 and 38 from this series have good in vitro ADME properties, good oral bioavailability, and efficacy after oral delivery in guinea pig LTB(4) and nonhuman primate allergen challenge models. Further profiling in a rat non-GLP toxicity experiment provided the rationale for differentiation and selection of one compound (33) for clinical development.

Asthma, chronic obstructive pulmonary disease (COPD) and acute lung injury/acute respiratory distress syndrome (ALI/ARDS) are characterized by neutrophilic inflammation and elevated levels of leukotriene B4 (LTB4). However, the exact role of LTB4 pathways in mediating pulmonary neutrophilia and the potential therapeutic application of LTB4 receptor antagonists in these diseases remains controversial. Here we show that a novel dual BLT1 and BLT2 receptor antagonist, RO5101576, potently inhibited LTB4-evoked calcium mobilization in HL-60 cells and chemotaxis of human neutrophils. RO5101576 significantly attenuated LTB4-evoked pulmonary eosinophilia in guinea pigs. In non-human primates, RO5101576 inhibited allergen and ozone-evoked pulmonary neutrophilia, with comparable efficacy to budesonide (allergic responses). RO5101576 had no effects on LPS-evoked neutrophilia in guinea pigs and cigarette smoke-evoked neutrophilia in mice and rats. In toxicology studies RO5101576 was well-tolerated. Theses studies show differential effects of LTB4 receptor antagonism on neutrophil responses in vivo and suggest RO5101576 may represent a potential new treatment for pulmonary neutrophilia in asthma.

The synthesis of various aryl methyl sulfides has been achieved by treatment of nitroarenes with a combination of (methylthio)trimethylsilane and cesium carbonate in dimethylsulfoxide. This reaction gives access to aryl methyl sulfide derivatives in high yields.