Unexpected Cyclization Product Discovery from the Photoinduced Bioconjugation Chemistry between Tetrazole and Amine

DNA-Compatible N-Formylation of Amines by Using TMSCF2Br

DNA-encoded libraries (DELs) have emerged as powerful tools in drug discovery. Protected amino acids serve as essential building blocks in the construction of DELs, resulting in the widespread presence of amino groups within these libraries. N-formylation of free amines not only enhances the activity of lead compounds but also functions as an effective amino-protecting strategy. In this study, we introduce trimethyl(bromodifluoromethyl)silane (TMSCF2Br) as a novel N-formylation reagent for DEL synthesis. This approach demonstrates robustness in DEL-compatible synthesis and enables library diversification through functional group transformation (FGT). Additionally, we achieved efficient removal of formyl groups, enabling the formyl group to be strategically used for on-DNA amino protection orthogonal to Fmoc and Boc groups.

Flexibility-tuning of dual-display DNA-encoded chemical libraries facilitates cyclic peptide ligand discovery

Cyclic peptides constitute an important drug modality since they offer significant advantages over small molecules and macromolecules. However, access to diverse chemical sets of cyclic peptides is difficult on a large library scale. DNA-encoded Chemical Libraries (DELs) provide a suitable tool to obtain large chemical diversity, but cyclic DELs made by standard DEL implementation cannot efficiently explore their conformational diversity. On the other hand, dual-display Encoded Self-Assembling Chemical (ESAC) Libraries can be used for modulating macrocycle flexibility since the two displayed peptides can be connected in an incremental fashion. In this work, we construct a 56 million dual-display ESAC library using a two-step cyclization strategy. We show that varying the level of conformational restraint is essential for the discovery of specific ligands for the three protein targets thrombin, human alkaline phosphatase and streptavidin.

Light-induced chemistry for protein functionalisation

Derivatising biomolecules like monoclonal antibodies with drugs or imaging agents, whilst preserving their bioactivity, is a challenging task. Protein functionalisation ideally requires methods that operate under mild conditions, are rapid, efficient (high yielding), chemoselective or site-specific, and importantly, non-denaturing. A broad collection of thermally mediated reagents for direct labelling using protein-based reactivity, or bioorthogonal strategies, has been developed, but arguably the most exciting opportunities lie in the application of photochemistry to create new covalent bioconjugate bonds. With current chemical methods for auxochromic tuning of the spectral features of photoactive groups, and with cheap, high-powered light-emitting diodes with precise emission properties, it has never been easier to explore the use of light-induced chemistry for making protein-based bioactive molecules. In biomedicine, the nature of the covalent bond to the protein can have a dramatic impact on the physicochemical properties and performance of the protein-conjugate. Photochemical methods provide access to new types of covalent linkages on protein with the potential to fine-tune biological interactions, leading to improvements in target uptake, binding specificity, metabolic processing, and washout kinetics in vivo. This perspective/review highlights recent advances in the development of photoactive reagents for protein labelling. We also discuss the experimental conditions and critical requirements to implement light-induced synthesis of functionalised protein-conjugates in aqueous media effectively.

DNA-compatible one-pot synthesis of multi-substituted dihydrofuran via pyridinium ylide-mediated cyclization

Synthesis of chemically diverse heterocyclic scaffolds in DNA-encoded libraries is highly demanded. We herein reported a convenient one-pot multi-component on-DNA synthetic strategy to afford multi-substituted 2,3-dihydrofuran scaffolds via pyridinium ylide-mediated cyclization. This reaction exhibited modest to excellent conversions for a broad range of DNA-conjugated aldehydes, β-ketonitriles and pyridinium salts under mild reaction conditions. Furthermore, the compatibility of this strategy with DEL construction was verified by enzymatic DNA ligation, PCR amplification and mock library synthesis.

The Furan-Thiol-Amine Reaction Facilitates DNA-Compatible Thiopyrrole-Grafted Macrocyclization and Late-Stage Amine Transformation

We here report an efficient DNA-compatible furan-thiol-amine reaction for macrocyclization and late-stage amine transformation. This reaction, conducted under mild conditions, enables the facile cyclization of DNA-conjugated linear peptides into thiopyrrole-grafted macrocycles regardless of ring size or side-chain modification with good to excellent conversion yields. Additionally, this strategy was employed for the late-stage transformation of terminal amines, serving as critical intermediates in the construction of DNA-encoded peptide libraries. Diverse amines were successfully converted into their corresponding thiopyrrole scaffolds, thereby expanding the structural diversity that can be achieved within DNA-encoded libraries.

Photochemical and Collision-Induced Cross-Linking of Asp, Glu, Asn, and Gln Residues in Peptide-Nitrile Imine Conjugate Ions in the Gas Phase

Peptide conjugates furnished with a 2,5-diaryltetrazolecarbonyl tag at the C-terminal lysine, which we call peptide-tet-K, were found to undergo efficient cross-linking of Asp, Glu, Asn, and Gln residues to transient nitrile-imine intermediates produced by photodissociation and collision-induced dissociation (CID) of the tetrazole ring in gas-phase ions. UV photodissociation (UVPD) at 213 nm achieved cross-linking conversion yields of 37 and 61% for DAAAK-tet-K and EAAAK-tet-K, respectively. The yields for NAAAK-tet-K and QAAAK-tet-K were 29 and 57%, respectively. Even higher cross-link yields were found for CID-MS3 of stable denitrogenated ions, (peptide-tet-K-N2 + H)+, that were in the 69-83% range. Different types of cross-links were distinguished by CID-MSn that showed a distinct series of backbone fragment ions, loss of N-terminal groups, and loss of phenylhydrazine from the modified nitrile imines. The Asp and Glu side-chain carboxyl groups were major participants in cross-linking that resulted in proton and oxygen transfer to the nitrile imine group. Other types of cross-linking involved Asn and Gln CONH2 groups and backbone amides. Cyclic ion mobility-mass spectrometry was used to separate NAAAK-tet-K and QAAAK-tet-K conformers and products of their collision-induced denitrogenation. Linear nitrile-imine and cross-linked ion structures were identified by comparing the experimental collision cross sections (CCSexp) to those for structures obtained by combined Born-Oppenheimer molecular dynamics and density functional theory (DFT) calculations. The formation of cross-links was found to be energetically favorable and involved proton-facilitated nucleophilic attack at the nitrile-imine carbon atom.

Photochemical and Collision-Induced Cross-Linking of Lys, Arg, and His to Nitrile Imines in Peptide Conjugate Ions in the Gas Phase

We report a study of internal covalent cross-linking with photolytically generated diarylnitrile imines of N-terminal arginine, lysine, and histidine residues in peptide conjugates. Conjugates in which a 4-(2-phenyltetrazol-5-yl)benzoyl group was attached to C-terminal lysine, that we call RAAA-tet-K, KAAA-tet-K, and HAAA-tet-K, were ionized by electrospray and subjected to UV photodissociation (UVPD) at 213 nm. UVPD triggered loss of N2 and proceeded by covalent cross-linking to nitrile imine intermediates that involved the side chains of N-terminal arginine, lysine, and histidine, as well as the peptide amide groups. Cross-linking yields were determined from UVPD-MS2 measurements as 67%, 66%, and 84% for RAAA-tet-K, KAAA-tet-K, and HAAA-tet-K ions, respectively. CID-MS3 of the denitrogenated ion intermediates from RAAA-tet-K, KAAA-tet-K, and HAAA-tet-K indicated overall cross-linking yields of 80%, 89%, and 80%, respectively. The nature of the cross-linking reactions and cross-link structures were investigated for RAAA-tet-K by high-resolution cyclic ion mobility mass spectrometry that identified precursor ion conformers and multiple dissociation products. All sequences were subjected to conformational analysis by Born-Oppenheimer molecular dynamics, and energy analysis by density functional theory calculations with M06-2X/def2qzvpp that provided relative and dissociation energies for several cross-link structural types. The cross-linking reactions were substantially exothermic, driving the efficient conversion of nitrile-imine intermediates to cyclic products. The principal steps in covalent cross-linking involved proton transfer onto the nitrile imine group accompanied by nucleophilic attack by the peptide side-chain and amide groups. Blocking the proton transfer and nucleophile resulted in a loss of cross-linking abilities.

Catalytic Biomaterials-Activated In Situ Chemical Reactions: Strategic Modulation and Enhanced Disease Treatment

Chemical reactions underpin biological processes, and imbalances in critical biochemical pathways within organisms can lead to the onset of severe diseases. Within this context, the emerging field of "Nanocatalytic Medicine" leverages nanomaterials as catalysts to modulate fundamental chemical reactions specific to the microenvironments of diseases. This approach is designed to facilitate the targeted synthesis and localized accumulation of therapeutic agents, thus enhancing treatment efficacy and precision while simultaneously reducing systemic side effects. The effectiveness of these nanocatalytic strategies critically hinges on a profound understanding of chemical kinetics and the intricate interplay of reactions within particular pathological microenvironments to ensure targeted and effective catalytic actions. This review methodically explores in situ catalytic reactions and their associated biomaterials, emphasizing regulatory strategies that control therapeutic responses. Furthermore, the discussion encapsulates the crucial elements-reactants, catalysts, and reaction conditions/environments-necessary for optimizing the thermodynamics and kinetics of these reactions, while rigorously addressing both the biochemical and biophysical dimensions of the disease microenvironments to enhance therapeutic outcomes. It seeks to clarify the mechanisms underpinning catalytic biomaterials and evaluate their potential to revolutionize treatment strategies across various pathological conditions.

Selenium(II)-Nitrogen Exchange (SeNEx) Chemistry: A Good Chemistry Suitable for Nanomole-Scale Parallel Synthesis, DNA-encoded Library Synthesis and Bioconjugation

The continuous development of click reactions with new connecting linkage is crucial for advancing the frontiers of click chemistry. Selenium-nitrogen exchange (SeNEx) chemistry, a versatile chemistry in click chemistry, represents an all-encompassing term for nucleophilic substitution events that replace nitrogen at an electrophilic selenium(II) center, enabling the flexible and efficient assembly of linkages around a Se(II) core. Several SeNEx chemistries have been developed inspired by the biochemical reaction between Ebselen and cysteine residue, and demonstrated significant potential in on-plate nanomole-scale parallel synthesis, selenium-containing DNA-encoded library (SeDEL) synthesis, as well as peptide and protein bioconjugation. This concept aims to present the origins, advancements, and applications of selenium(II)-nitrogen exchange (SeNEx) chemistry while also outlining the potential directions for future research in this field.

On-DNA Three-Component Cycloaddition of Diazo Compounds, Nitrosoarenes, and Alkenes: Syntheses of Isoxazolidines for DNA-Encoded Chemical Libraries

A DNA-compatible three-component reaction is disclosed for the synthesis of on-DNA polysubstituted isoxazolidines that serve as privileged core scaffolds in numerous natural products and bioactive molecules. This one-pot approach involves the 1,3-dipolar cycloaddition of DNA-tagged styrenes with diazo compounds and nitrosoarenes in an aqueous solution of KOAc. The reaction demonstrates excellent functional group compatibility, providing a conventional protocol for the construction of a DNA-labeled isoxazolidine library.

Identification of protein partners for small molecules reshapes the understanding of nonalcoholic steatohepatitis and drug discovery

AIMS

Nonalcoholic steatohepatitis (NASH) is the severe subtype of nonalcoholic fatty diseases (NAFLD) with few options for treatment. Patients with NASH exhibit partial responses to the current therapeutics and adverse effects. Identification of the binding proteins for the drugs is essential to understanding the mechanism and adverse effects of the drugs and fuels the discovery of potent and safe drugs. This paper aims to critically discuss recent advances in covalent and noncovalent approaches for identifying binding proteins that mediate NASH progression, along with an in-depth analysis of the mechanisms by which these targets regulate NASH.

MATERIALS AND METHODS

A literature search was conducted to identify the relevant studies in the database of PubMed and the American Chemical Society. The search covered articles published from January 1990 to July 2024, using the search terms with keywords such as NASH, benzophenone, diazirine, photo-affinity labeling, thermal protein profiling, CETSA, target identification.

KEY FINDINGS

The covalent approaches utilize drugs modified with diazirine and benzophenone to covalently crosslink with the target proteins, which facilitates the purification and identification of target proteins. In addition, they map the binding sites in the target proteins. By contrast, noncovalent approaches identify the binding targets of unmodified drugs in the intact cell proteome. The advantages and limitations of both approaches have been compared, along with a comprehensive analysis of recent innovations that further enhance the efficiency and specificity.

SIGNIFICANCE

The analyses of the applicability of these approaches provide novel tools to delineate NASH pathogenesis and promote drug discovery.

Synthesis of Thiohydantoin Scaffolds on DNA for Focused DNA-Encoded Library Construction

Thiohydantoin represents a significant class of biologically active privileged heterocyclic scaffolds. Herein, we present a convenient and robust DNA-compatible method for constructing a thiohydantoin-focused DNA-encoded library. This reaction can be applied to a wide variety of isothiocyanate partners, arylamine feedstocks, and diverse α-amine acid derivatives, exhibiting excellent conversions, high functional group tolerance, and preservation of DNA tag integrity. Our method allows for easy access to a valuable three-cycle thiohydantoin-focused DNA-encoded library.

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.

Structural phase transition and potential superconductivity initiated by pressure-driven in 1T-CrSe2

The exploration of the superconducting properties of antiferromagnetic parent compounds containing transition metals under pressure provides a unique idea for finding and designing superconducting materials with better performance. In this paper, the close relationship between the possible superconductivity and structure phase transition of the typical van der Waals layered material 1T-CrSe2induced by pressure is studied by means of electrical transport and x-ray diffraction for the first time. We introduce the possibility of pressure-induced superconductivity at 20 GPa, with a criticalTcof approximately at 4 K. The superconductivity persists up to the highest measured pressure of 70 GPa, with a maximumTc∼ 5 K at 24 GPa. We observed a structure phase transition fromP-3m1 toC2/mspace group in the range of 9.4-11.7 GPa. The results show that the structural phase transition leads to the metallization of 1T-CrSe2and the further pressure effect makes the superconductivity appear in the new structure. The material undergoes a transition from a two-dimensional layered structure to a three-dimensional structure under pressure. This is the first time that possible superconductivity has been observed in 1T-CrSe2.

Isothiocyanate intermediates facilitate divergent synthesis of N-heterocycles for DNA-encoded libraries

The versatile reactivity of isothiocyanate intermediates enabled the diversity-oriented synthesis (DOS) of N-heterocycles in a DNA-compatible manner. We first reported a mild in situ conversion of DNA-conjugated amines to isothiocyanates. Subsequently, a set of diverse transformations was successfully developed to construct 2-thioxo-quinazolinones, 1,2,4-thiadiazoles, and 2-imino thiazolines. Finally, the feasibility of these approaches in constructing DELs was further demonstrated through enzymatic ligation and mock pool preparation. This study demonstrated the advantages of combining in situ conversion strategies with DOS, which effectively broadened the chemical and structural diversity of DELs.

Intermolecular Aza-Wacker Coupling of Alkenes with Azoles by Photo-Aerobic Selenium-π-Acid Multicatalysis

Herein, the intermolecular, photoaerobic aza-Wacker coupling of azoles with alkenes by means of dual and ternary selenium-π-acid multicatalysis is presented. The title method permits an expedited avenue toward a broad scope of N-allylated azoles and representative azinones under mild conditions with broad functional group tolerance, as is showcased in more than 60 examples including late-stage drug derivatizations. From a regiochemical perspective, the protocol is complementary to cognate photoredox catalytic olefin aminations, as they typically proceed through either allylic hydrogen atom abstraction or single electron oxidation of the alkene substrate. These methods predominantly result in C-N bond formations at the allylic periphery of the alkene or the less substituted position of the former π-bond (i.e., anti-Markovnikov selectivity). The current process, however, operates through a radical-polar crossover mechanism, which solely affects the selenium catalyst, thus allowing the alkene to be converted strictly through an ionic two-electron transfer regime under Markovnikov control. In addition, it is shown that the corresponding N-vinyl azoles can also be accessed by sequential or one-pot treatment of the allylic azoles with base, thus emphasizing the exquisite utility of this method.

Rhodium-Promoted C-H Activation/Annulation between DNA-Linked Terminal Alkyne and Aromatic Acid: A Finding from the Selection Outcomes

Inspired by previous selection outcomes, we investigated and developed a rhodium-promoted C-H activation/annulation reaction of DNA-linked terminal alkynes and aromatic acids. This reaction exhibits excellent efficiency with high conversions and a broad substrate scope. Most importantly, the unique DEL-compatible conditions provide a better scenario for yielding an isocoumarin scaffold compared to conventional organic reaction conditions, and this newly developed on-DNA method has confirmed its feasibility in preparing DNA-encoded libraries.

Using DNA-encoded libraries of fragments for hit discovery of challenging therapeutic targets

INTRODUCTION

The effectiveness of Fragment-based drug design (FBDD) for targeting challenging therapeutic targets has been hindered by two factors: the small library size and the complexity of the fragment-to-hit optimization process. The DNA-encoded library (DEL) technology offers a compelling and robust high-throughput selection approach to potentially address these limitations.

AREA COVERED

In this review, the authors propose the viewpoint that the DEL technology matches perfectly with the concept of FBDD to facilitate hit discovery. They begin by analyzing the technical limitations of FBDD from a medicinal chemistry perspective and explain why DEL may offer potential solutions to these limitations. Subsequently, they elaborate in detail on how the integration of DEL with FBDD works. In addition, they present case studies involving both de novo hit discovery and full ligand discovery, especially for challenging therapeutic targets harboring broad drug-target interfaces.

EXPERT OPINION

The future of DEL-based fragment discovery may be promoted by both technical advances and application scopes. From the technical aspect, expanding the chemical diversity of DEL will be essential to achieve success in fragment-based drug discovery. From the application scope side, DEL-based fragment discovery holds promise for tackling a series of challenging targets.

Synthesis of Diacylhydrazine Derivatives Based on Tetrazole-Focused DNA-Encoded Library

Utilizing already existing DNA-encoded libraries (DELs) for the generation of a distinct DEL represents an expedited strategy for expanding the chemical space. Herein, we leverage the unique photoreactivity of tetrazoles to synthesize diacylhydrazines on DNA. Widely available carboxylic acids serving as building blocks were employed under the mild photomediated reaction conditions, affording diverse DNA-conjugated diacylhydrazines. This methodology also demonstrates robustness in DEL-compatible synthesis and facilitates the preparation of oligonucleotide-based chemical probes.