In-Bead Screening of Hydroxamic Acids for the Identification of HDAC Inhibitors

Hydrogel-Encapsulated Beads Enable Proximity-Driven Encoded Library Synthesis and Screening

Encoded combinatorial library technologies have dramatically expanded the chemical space for screening but are usually only analyzed by affinity selection binding. It would be highly advantageous to reformat selection outputs to "one-bead-one-compound" solid-phase libraries, unlocking activity-based and cellular screening capabilities. Here, we describe hydrogel-encapsulated magnetic beads that enable such a transformation. Bulk emulsion polymerization of polyacrylamide hydrogel shells around magnetic microbeads yielded uniform particles (7 ± 2 μm diameter) that are compatible with diverse in-gel functionalization (amine, alkyne, oligonucleotides) and transformations associated with DNA-encoded library synthesis (acylation, enzymatic DNA ligation). In a case study of reformatting mRNA display libraries, transcription from DNA-templated magnetic beads encapsulated in gel particles colocalized both RNA synthesis via hybridization with copolymerized complementary DNA and translation via puromycin labeling. Two control epitope templates (V5, HA) were successfully enriched (50- and 99-fold, respectively) from an NNK5 library bead screen via FACS. Proximity-driven library synthesis in concert with magnetic sample manipulation provides a plausible means for reformatting encoded combinatorial libraries at scale.

Convergent Total Synthesis of Exochelin 772SM

A convergent total synthesis of the natural mycobacterial iron chelator desferri-exochelin 772SM (D-EXO) is described. The synthetic procedure proceeds in 11 steps in the longest linear sequence, with an overall yield of 8.6%. The described procedure uses cheap starting materials and requires a limited number of chromatographic purifications. The concise strategy divides the exochelin into five key building blocks, allowing easy alternation of each single building block. Herein, the presented synthetic strategy is well suited to facilitate the synthesis of analogues and medicinal chemistry development efforts in a time- and resource-efficient manner.

Highly Potent, Selective, Biostable, and Cell-Permeable Cyclic d-Peptide for Dual-Targeting Therapy of Lung Cancer

The application of peptide drugs in cancer therapy is impeded by their poor biostability and weak cell permeability. Therefore, it is imperative to find biostable and cell-permeable peptide drugs for cancer treatment. Here, we identified a potent, selective, biostable, and cell-permeable cyclic d-peptide, NKTP-3, that targets NRP1 and KRAS^G12D using structure-based virtual screening. NKTP-3 exhibited strong biostability and cellular uptake ability. Importantly, it significantly inhibited the growth of A427 cells with the KRAS^G12D mutation. Moreover, NKTP-3 showed strong antitumor activity against A427 cell-derived xenograft and KRAS^G12D-driven primary lung cancer models without obvious toxicity. This study demonstrates that the dual NRP1/KRAS^G12D-targeting cyclic d-peptide NKTP-3 may be used as a potential chemotherapeutic agent for KRAS^G12D-driven lung cancer treatment.

Approaches for the synthesis of o-nitrobenzyl and coumarin linkers for use in photocleavable biomaterials and bioconjugates and their biomedical applications

Photocleavable biomaterials and bioconjugates are particularly interesting because light sources are easy to obtain and the responsiveness of materials is convenient to control. In recent years, various photocleavable biomaterials and bioconjugates have been synthesized for the control of payload release, regulation of biomolecule activity, 3D cell culture, and investigation of molecular mechanisms. Photocleavable linkers are crucial components of photocleavable biomaterials, which significantly influence the photoresponsive capabilities of materials. Photosensitive molecules, such as o-nitrobenzyls and coumarins, have been extensively developed as photocleavable linkers. In the present review, we provide comprehensive knowledge regarding the synthetic strategies of o-nitrobenzyl and coumarin derived linkers with various functional groups and their applications for the construction of photocleavable biomaterials and bioconjugates. Finally, the biomedical applications of o-nitrobenzyl and coumarin-based photocleavable biomaterials and bioconjugates will be summarized and discussed.

An overview of DNA-encoded libraries: A versatile tool for drug discovery

DNA-encoded libraries (DELs) are collections of small molecules covalently attached to amplifiable DNA tags carrying unique information about the structure of each library member. A combinatorial approach is used to construct the libraries with iterative DNA encoding steps, facilitating tracking of the synthetic history of the attached compounds by DNA sequencing. Various screening protocols have been developed which allow protein target binders to be selected out of pools containing up to billions of different small molecules. The versatile methodology has allowed identification of numerous biologically active compounds and is now increasingly being adopted as a tool for lead discovery campaigns and identification of chemical probes. A great focus in recent years has been on developing DNA compatible chemistries that expand the structural diversity of the small molecule library members in DELs. This chapter provides an overview of the challenges and accomplishments in DEL technology, reviewing the technological aspects of producing and screening DELs with a perspective on opportunities, limitations, and future directions.

Photolabile Linkers for Solid-Phase Synthesis

Photolabile linkers are the subjects of intense research because they allow the release of the target molecule simply by irradiation. Photochemical release of synthesis products is often facilitated without additional reagents under mild reaction conditions, which may even be environmentally friendly and appealing in the context of greener chemistry. The mild conditions also allow for applications of released material in subsequent biological screening experiments, where contamination with cleavage reagents would be detrimental. This Review pays attention to the increasing number of photolabile linkers developed for solid-phase synthesis and release and covers: (i) o-nitrobenzyloxy linkers, (ii) o-nitrobenzylamino linkers, (iii) α-substituted o-nitrobenzyl linkers, (iv) o-nitroveratryl linkers, (v) phenacyl linkers, (vi) p-alkoxyphenacyl linkers, (vii) benzoin linkers, (viii) pivaloyl linkers, and (ix) other photolabile linkers.

Bead-based screening in chemical biology and drug discovery

High-throughput screening is an important component of the drug discovery process. The screening of libraries containing hundreds of thousands of compounds requires assays amenable to miniaturisation and automization. Combinatorial chemistry holds a unique promise to deliver structurally diverse libraries for early drug discovery. Among the various library forms, the one-bead-one-compound (OBOC) library, where each bead carries many copies of a single compound, holds the greatest potential for the rapid identification of novel hits against emerging drug targets. However, this potential has not yet been fully realized due to a number of technical obstacles. In this feature article, we review the progress that has been made in bead-based library screening and its application to the discovery of bioactive compounds. We identify the key challenges of this approach and highlight key steps needed for making a greater impact in the field.

Palladium-Catalyzed External-CO-Free Carbonylation of Aryl Bromides Using 2,4,6-Trichlorophenyl Formate

A practical Pd-catalyzed carbonylation of (hetero)aryl bromides using a crystalline carbon monoxide (CO) surrogate, 2,4,6-trichlorophenyl formate (TCPF), was developed. This reaction proceeds without the slow addition technique that was previously required and with a low catalyst loading (1 mol%). The utility of this Pd-catalyzed external-CO-free carbonylation using TCPF was demonstrated in the synthesis of a histone deacetylase inhibitor.

A Highly Sensitive and Label-Free Microbead-Based ‘Turn-On’ Colorimetric Sensor for the Detection of Mercury(II) in Urine Using a Peroxidase-Like Split G-Quadruplex–Hemin DNAzyme

A highly sensitive and label-free microbead-based ‘turn-on’ assay was developed for the detection of Hg2+ in urine based on the Hg2+-mediated formation of intermolecular split G-quadruplex–hemin DNAzymes. In the presence of Hg2+, T–T mismatches between the two partial cDNA strands were stabilized by a T–Hg2+–T base pair, and can cause the G-rich sequences of the two oligonucleotides to associate to form a split G-quadruplex which is able to bind hemin to form the catalytically active G-quadruplex–hemin DNAzyme. This microbead-based ‘turn-on’ process allows the detection of Hg2+ in urine samples at concentrations as low as 0.5 pM. The relative standard deviation and recovery are 1.2–3.9 and 98.7–103.2%, respectively. The remarkable sensitivity for Hg2+ is mainly attributed to the enhanced mass transport ability that is inherent in homogeneous microbead-based assays. Compared with previous developments of intermolecular split G-quardruplex–hemin DNAzymes for the homogeneous detection of Hg2+ (the limit of detection was 19nM), a signal enhancement of ~1000 times is obtained when such an assay is performed on the surface of microbeads.

A Linker for the Solid-Phase Synthesis of Hydroxamic Acids and Identification of HDAC6 Inhibitors

We herein present broadly useful, readily available and nonintegral hydroxylamine linkers for the routine solid-phase synthesis of hydroxamic acids. The developed protocols enable the efficient synthesis and release of a wide range of hydroxamic acids from various resins, relying on high control and flexibility with respect to reagents and synthetic processes. A trityl-based hydroxylamine linker was used to synthesize a library of peptide hydroxamic acids. The inhibitory effects of the compounds were examined for seven HDAC enzyme subtypes using a chemiluminescence-based assay.

An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening

DNA-encoded synthesis is rekindling interest in combinatorial compound libraries for drug discovery and in technology for automated and quantitative library screening. Here, we disclose a microfluidic circuit that enables functional screens of DNA-encoded compound beads. The device carries out library bead distribution into picoliter-scale assay reagent droplets, photochemical cleavage of compound from the bead, assay incubation, laser-induced fluorescence-based assay detection, and fluorescence-activated droplet sorting to isolate hits. DNA-encoded compound beads (10-μm diameter) displaying a photocleavable positive control inhibitor pepstatin A were mixed (1920 beads, 729 encoding sequences) with negative control beads (58 000 beads, 1728 encoding sequences) and screened for cathepsin D inhibition using a biochemical enzyme activity assay. The circuit sorted 1518 hit droplets for collection following 18 min incubation over a 240 min analysis. Visual inspection of a subset of droplets (1188 droplets) yielded a 24% false discovery rate (1166 pepstatin A beads; 366 negative control beads). Using template barcoding strategies, it was possible to count hit collection beads (1863) using next-generation sequencing data. Bead-specific barcodes enabled replicate counting, and the false discovery rate was reduced to 2.6% by only considering hit-encoding sequences that were observed on >2 beads. This work represents a complete distributable small molecule discovery platform, from microfluidic miniaturized automation to ultrahigh-throughput hit deconvolution by sequencing.