Discovery Small-Molecule p300 Inhibitors Derived from a Newly Developed Indazolone-Focused DNA-Encoded Library.

The DNA-encoded library (DEL) is a robust tool for chemical biology and drug discovery. In this study, we developed a DNA-compatible light-promoted reaction that is highly efficient and plate-compatible for DEL construction based on the formation of the indazolone scaffold. Employing this high-efficiency approach, we constructed a DEL featuring an indazolone core, which enabled the identification of a novel series of ligands specifically targeting E1A-binding protein (p300) after DEL selection. Taken together, our findings underscore the feasibility of light-promoted reactions in DEL synthesis and unveil promising avenues for developing p300-targeting inhibitors.

ABPP-CoDEL: Activity-Based Proteome Profiling-Guided Discovery of Tyrosine-Targeting Covalent Inhibitors from DNA-Encoded Libraries.

DNA-encoded chemical library (DEL) has been extensively used for lead compound discovery for decades in academia and industry. Incorporating an electrophile warhead into DNA-encoded compounds recently permitted the discovery of covalent ligands that selectively react with a particular cysteine residue. However, noncysteine residues remain underexplored as modification sites of covalent DELs. Herein, we report the design and utility of tyrosine-targeting DELs of 67 million compounds. Proteome-wide reactivity analysis of tyrosine-reactive sulfonyl fluoride (SF) covalent probes suggested three enzymes (phosphoglycerate mutase 1, glutathione s-transferase 1, and dipeptidyl peptidase 3) as models of tyrosine-targetable proteins. Enrichment with SF-functionalized DELs led to the identification of a series of tyrosine-targeting covalent inhibitors of the model enzymes. In-depth mechanistic investigation revealed their novel modes of action and reactive ligand-accessible hotspots of the enzymes. Our strategy of combining activity-based proteome profiling and covalent DEL enrichment (ABPP-CoDEL), which generated selective covalent binders against a variety of target proteins, illustrates the potential use of this methodology in further covalent drug discovery.

Effect of Organic, Nano, and Inorganic Zinc Sources on Growth Performance, Antioxidant Function, and Intestinal Health of Young Broilers.

The study aimed to determine the effects of different zinc sources on growth performance, antioxidant function, and intestinal health of broilers. In total, 240 Ross 308 male broilers with similar weight were randomly assigned to 4 treatments, including zinc sulfate, methionine zinc (Zn-Met), glycine zinc (Zn-Gly), and nano-zinc oxide (ZnO-NPs), with 80 mg zinc/kg diet supplementation. The experiment lasted for 21 days. Results showed dietary supplemental Zn-Gly and Zn-Met increased average daily gain during 1-14 days (P = 0.011), and Zn-Gly, Zn-Met, and ZnO-NP supplementation decreased the ratio of feed to gain during 1-21 days (P = 0.003) compared to zinc sulfate. ZnO-NPs supplementation tended to increase total SOD activity (P = 0.068) and had higher serum IgA content and lower MDA level than the other three groups (P < 0.05). Compared with zinc sulfate, Zn-Met and ZnO-NP supplementation decreased TNF-α mRNA expression (P = 0.048). However, serum biochemical indices, intestinal morphology, and mRNA expressions of tight junction proteins were not affected by different zinc sources (P > 0.05). A differential trend was observed in the beta diversity of bacterial communities among four groups (P = 0.082). The LEfSe analysis showed that bacterial genera Blautia, Ruminococcaceae, Clostridia, Anaerostipes, Eubacterium_ventriosum, Merdibacter, and Oscillospira were enriched in the ZnSO4 group, and the genera Eubacterium_hallii and Anaerotruncus were enriched in the Zn-Gly group. The genera UCG-009 and UCG010 were enriched in ZnO-NPs and Zn-Met groups, respectively. It should be stated dietary supplemental Zn-Met improved growth performance, ZnO-NPs promoted IgA production and reduced occurrences of oxidative stress and inflammation, and different zinc sources enriched different jejunal bacteria genera.

A Vancomycin-Templated DNA-Encoded Library for Combating Drug-Resistant Bacteria.

It is an urgent need to tackle the global crisis of multidrug-resistant bacterial infections. We report here an innovative strategy for large-scale screening of new antibacterial agents using a whole bacteria-based DNA-encoded library (DEL) of vancomycin derivatives via peripheral modifications. A bacterial binding affinity assay was established to select the modification fragments in high-affinity compounds. The optimal resynthesized derivatives demonstrated excellently enhanced activity against various resistant bacterial strains and provided useful structures for vancomycin derivatization. This work presents the new concept in a natural product-templated DEL and in antibiotic discovery through bacterial affinity screening, which promotes the fight against drug-resistant bacteria.

Enhancing the Predictive Power of Machine Learning Models through a Chemical Space Complementary DEL Screening Strategy.

DNA-encoded library (DEL) technology is an effective method for small molecule drug discovery, enabling high-throughput screening against target proteins. While DEL screening produces extensive data, it can reveal complex patterns not easily recognized by human analysis. Lead compounds from DEL screens often have higher molecular weights, posing challenges for drug development. This study refines traditional DELs by integrating alternative techniques like photocross-linking screening to enhance chemical diversity. Combining these methods improved predictive performance for small molecule identification models. Using this approach, we predicted active small molecules for BRD4 and p300, achieving hit rates of 26.7 and 35.7%. Notably, the identified compounds exhibit smaller molecular weights and better modification potential compared to traditional DEL molecules. This research demonstrates the synergy between DEL and AI technologies, enhancing drug discovery.

Discovery and Optimization of WDR5 Inhibitors via Cascade Deoxyribonucleic Acid-Encoded Library Selection Approach.

The DNA-encoded library (DEL) is a powerful hit generation tool for chemical biology and drug discovery; however, the optimization of DEL hits remained a daunting challenge for the medicinal chemistry community. In this study, hit compounds targeting the WIN binding domain of WDR5 were discovered by the initial three-cycle linear DEL selection, and their potency was further enhanced by a cascade DEL selection from the focused DEL designed based on the original first run DEL hits. As expected, these new compounds from the second run of focused DEL were more potent WDR5 inhibitors in the protein binding assay confirmed by the off-DNA synthesis. Interestingly, selected inhibitors exhibited good antiproliferative activity in two human acute leukemia cell lines. Taken together, this new cascade DEL selection strategy may have tremendous potential for finding high-affinity leads against WDR5 and provide opportunities to explore and optimize inhibitors for other targets.

Discovery, SAR Study of GST Inhibitors from a Novel Quinazolin-4(1H)-one Focused DNA-Encoded Library.

The DNA-encoded library (DEL) is a powerful hit-generation tool in drug discovery. This study describes a new DEL with a privileged scaffold quinazolin-4(3H)-one developed by a robust DNA-compatible multicomponent reaction and a series of novel glutathione S-transferase (GST) inhibitors that were identified through affinity-mediated DEL selection. A novel inhibitor 16 was subsequently verified with an inhibitory potency value of 1.55 ± 0.02 µM against SjGST and 2.02 ± 0.20 µM against hGSTM2. Further optimization was carried out via various structure-activity relationship studies. And especially, the co-crystal structure of the compound 16 with the SjGST was unveiled, which clearly demonstrated its binding mode was quite different from the known GSH-like compounds. This new type of probe is likely to play a different role compared with the GSH, which may provide new opportunities to discover more potent GST inhibitors.

Ruthenium-Mediated [2 + 2 + 2] Cyclization: A Route to Forge Indane and Isoindoline Core and Its Application in DNA-Encoded Library Technology.

Indane and isoindoline are attractive bicyclic systems in biologically active compounds but are rarely reported in DNA-encoded libraries. In this paper, we reported an efficient and versatile approach for assembling indane and isoindoline scaffolds via a ruthenium-catalyzed [2 + 2 + 2] cyclotrimerization reaction. This method exhibits a broad substrate scope and has been successfully applied to construct a 53K-membered DNA-encoded library (DEL). In order to test its application, we carried out a preliminary selection of this DEL against Aurora A protein and identified a hit compound with 9.3 µM inhibition activity.

Triazine-Based Covalent DNA-Encoded Libraries for Discovery of Covalent Inhibitors of Target Proteins.

Since ibrutinib was approved by the FDA as an effective monotherapy for chronic lymphocytic leukemia (CLL) and multilymphoma, more and more FDA-approved covalent drugs are coming back into the market. On this occasion, the resurgence of interest in covalent drugs calls for more hit discovery techniques. However, the limited numbers of covalent libraries prevent the development of this area. Herein, we report the design of covalent DNA-encoded library (DEL) and its selection method for the discovery of covalent inhibitors for target proteins. These triazine-based covalent DELs yielded potent compounds after covalent selection against target proteins, including Bruton's Tyrosine Kinase (BTK), Janus kinase 3 (JAK3), and peptidyl-prolyl cis/trans isomerase NIMA-interacting-1 (Pin1).

Streamlined construction of peptide macrocycles via palladium-catalyzed intramolecular S-arylation in solution and on DNA.

A highly efficient and versatile method for construction of peptide macrocycles via palladium-catalyzed intramolecular S-arylation of alkyl and aryl thiols with aryl iodides under mild conditions is developed. The method exhibits a broad substrate scope for thiols, aryl iodides and amino acid units. Peptide macrocycles of a wide range of size and composition can be readily assembled in high yield from various easily accessible building blocks. This method has been successfully employed to prepare an 8-million-membered tetrameric cyclic peptide DNA-encoded library (DEL). Preliminary screening of the DEL library against protein p300 identified compounds with single digit micromolar inhibition activity.

Diversified strategy for the synthesis of DNA-encoded oxindole libraries.

DNA-encoded library technology (DELT) employs DNA as a barcode to track the sequence of chemical reactions and enables the design and synthesis of libraries with billions of small molecules through combinatorial expansion. This powerful technology platform has been successfully demonstrated for hit identification and target validation for many types of diseases. As a highly integrated technology platform, DEL is capable of accelerating the translation of synthetic chemistry by using on-DNA compatible reactions or off-DNA scaffold synthesis. Herein, we report the development of a series of novel on-DNA transformations based on oxindole scaffolds for the design and synthesis of diversity-oriented DNA-encoded libraries for screening. Specifically, we have developed 1,3-dipolar cyclizations, cyclopropanations, ring-opening of reactions of aziridines and Claisen-Schmidt condensations to construct diverse oxindole derivatives. The majority of these transformations enable a diversity-oriented synthesis of DNA-encoded oxindole libraries which have been used in the successful hit identification for three protein targets. We have demonstrated that a diversified strategy for DEL synthesis could accelerate the application of synthetic chemistry for drug discovery.