Diversity Synthesis of Complex Pyridines Yields a Probe of a Neurotrophic Signaling Pathway

Recognizing the value of including complex pyridines in small-molecule screening collections, we developed a previously unexplored [2 + 2 + 2]-cycloaddition of silyl-tethered diynes with nitriles. The tether provides high regioselectivity, while the solvent THF allows catalytic CpCo(CO)2 to be used without exogenous irradiation. One of the resulting bicyclic and monocyclic (desilylated) pyridines was identified as an inhibitor of neuregulin-induced neurite outgrowth (EC50 = 0.30 µM) in a screen that probes a pathway likely to be involved in breast cancers and schizophrenia.Chemistry and Chemical Biolog

AAK1 Identified as an Inhibitor of Neuregulin-1/ErbB4-Dependent Neurotrophic Factor Signaling Using Integrative Chemical Genomics and Proteomics

SummaryTarget identification remains challenging for the field of chemical biology. We describe an integrative chemical genomic and proteomic approach combining the use of differentially active analogs of small molecule probes with stable isotope labeling by amino acids in cell culture-mediated affinity enrichment, followed by subsequent testing of candidate targets using RNA interference-mediated gene silencing. We applied this approach to characterizing the natural product K252a and its ability to potentiate neuregulin-1 (Nrg1)/ErbB4 (v-erb-a erythroblastic leukemia viral oncogene homolog 4)-dependent neurotrophic factor signaling and neuritogenesis. We show that AAK1 (adaptor-associated kinase 1) is a relevant target of K252a, and that the loss of AAK1 alters ErbB4 trafficking and expression levels, providing evidence for a previously unrecognized role for AAK1 in Nrg1-mediated neurotrophic factor signaling. Similar strategies should lead to the discovery of novel targets for therapeutic development

Assessment of AI-Based Protein Structure Prediction for the NLRP3 Target

The recent successes of AlphaFold and RoseTTAFold have demonstrated the value of AI methods in highly accurate protein structure prediction. Despite these advances, the role of these methods in the context of small-molecule drug discovery still needs to be thoroughly explored. In this study, we evaluated whether the AI-based models can reliably reproduce the three-dimensional structures of protein–ligand complexes. The structure we chose was NLRP3, a challenging protein target in terms of obtaining a three-dimensional model both experimentally and computationally. The conformation of the binding pockets generated by the AI models was carefully characterized and compared with experimental structures. Further molecular docking results indicated that AI-predicted protein structures combined with molecular dynamics simulations offers a promising approach in small-molecule drug discovery

Highly Selective Novel Heme Oxygenase-1-Targeting Molecules Discovered by DNA-Encoded Library-Machine Learning Model beyond the DEL Chemical Space

DNA-encoded library (DEL) technology has proven to be a powerful method for discovering novel inhibitors for diverse targets. Particularly when combined with machine learning (ML), the DEL-ML workflow expands the chemical space and enhances cost-effectiveness, offering new opportunities to find desired hit molecules. Heme oxygenase-1 (HO-1), primarily a heme-degrading enzyme, has been identified as a potential therapeutic target in diseases such as cancer and neurodegenerative disorders. Despite years of study, the HO-1 inhibitor toolbox remains limited. Here, we report the discovery of five series of novel scaffold HO-1 inhibitors using a DEL-ML workflow that emphasizes the model’s uncertainty quantification and its domain of applicability. The DEL-ML model demonstrated a strong ability to extrapolate to novel chemical spaces by identifying new structures. Approximately 33% of the predicted molecules, validated by biophysical assays, had a binding affinity of K¬D < 15 µM, with the strongest affinity being 141 nM. Fourteen tested molecules showed over 100-fold selectivity towards HO-1 over Heme oxygenase-2 (HO-2). These molecules are also structurally novel compared to the reported HO-1 inhibitors. Further, binding mode simulations via docking provided insights into the possible selectivity rationale of some selective series

DNA-Compatible Cyclization Reaction to Access 1,3,4-Oxadiazoles and 1,2,4-Triazoles

DNA-encoded chemical library (DECL) technology is a commonly employed screening platform in both the pharmaceutical industry and academia. To expand the chemical space of DECLs, new and robust DNA-compatible reactions are sought after. In particular, DNA-compatible cyclization reactions are highly valued, as these reactions tend to be atom economical and thus may provide lead- and drug-like molecules. Herein, we report two new methodologies employing DNA-conjugated thiosemicarbazides as a common precursor, yielding highly substituted 1,3,4-oxadiazoles and 1,2,4-triazoles. These two novel DNA-compatible reactions feature a high conversion efficiency and broad substrate scope under mild conditions that do not observably degrade DNA

Structure-Aided Identification of an Inhibitor Targets Mps1 for the Management of Plant-Pathogenic Fungi

ABSTRACT Blast disease caused by Magnaporthe oryzae threatens rice production worldwide, and chemical control is one of the main methods of its management. The high mutation rate of the M. oryzae genome results in drug resistance, which calls for novel fungicide targets. Fungal proteins that function during the infection process might be potential candidates, and Mps1 (M. oryzae mitogen-activated protein kinase 1) is such a protein that plays a critical role in appressorium penetration of the plant cell wall. Here, we report the structure-aided identification of a small-molecule inhibitor of Mps1. High-throughput screening was performed with Mps1 against a DNA-encoded compound library, and one compound, named A378-0, with the best performance was selected for further verification. A378-0 exhibits a higher binding affinity than the kinase cosubstrate ATP and can inhibit the enzyme activity of Mps1. Cocrystallization of A378-0 with Mps1 revealed that A378-0 binds to the catalytic pocket of Mps1, while the three ring-type substructures of A378-0 constitute a triangle that squeezes into the pocket. In planta assays showed that A378-0 could inhibit both the appressorium penetration and invasive growth but not the appressorium development of M. oryzae, which is consistent with the biological function of Mps1. Furthermore, A378-0 exhibits binding and activity inhibition abilities against Mpk1, the Mps1 ortholog of the soilborne fungal pathogen Fusarium oxysporum. Collectively, these results show that Mps1 as well as its orthologs can be regarded as fungicide targets, and A378-0 might be used as a hit compound for the development of a broad-spectrum fungicide. IMPORTANCE M. oryzae is the causal agent of rice blast, one of the most devastating diseases of cultivated rice. Chemical control is still the main strategy for its management, and the identification of novel fungicide targets is indispensable for overcoming existing problems such as drug resistance and food safety. With a combination of structural, biochemical, and in planta assays, our research shows that Mps1 may serve as a fungicide target and confirms that compound A378-0 binds to Mps1 and possesses bioactivity in inhibiting M. oryzae virulence. As fungal orthologs of Mps1 are conserved, A378-0 may serve as a hit for broad-spectrum fungicide development, as evidenced with Mpk1, the Mps1 ortholog of F. oxysporum. Additionally, A378-0 contains a novel chemical scaffold that has not been reported in approved kinase inhibitors, suggesting its potential to be considered the basis for the development of other kinase inhibitors

<i>In vivo</i> half-life extension of BMP1/TLL metalloproteinase inhibitors using small-molecule human serum albumin binders

Reducing the required frequence of drug dosing can improve the adherence of patients to chronic treatments. Hence, drugs with longer half-lives are highly desirable. One of the most promising approaches to extend the half-life of drugs is conjugation to human serum albumin (HSA). In this work, we describe the use of , a small-molecule noncovalent HSA binder, to extend the half-life and pharmacology of small-molecule BMP1/TLL inhibitors in humanized mice (HSA KI/KI). A series of conjugates of with BMP1/TLL inhibitors were prepared. In particular, showed good solubility and a half-life extension of &gt;20-fold versus the parent molecule in the HSA KI/KI mice, reaching half-lives of &gt;48 h with maintained maximal inhibition of plasma BMP1/TLL. The same conjugate showed a half-life of only 3 h in the wild-type mice, suggesting that the half-life extension was principally due to specific interactions with HSA. It is envisioned that conjugation to should be applicable to a wide range of small molecule or peptide drugs with short half-lives. In this context, AlbuBinders represent a viable alternative to existing half-life extension technologies