Current research in chemical biology最新文献

Cucurbit[7]uril (CB[7]) is a supramolecular binding host for peptides and proteins with N-terminal Phe. However, the low occurrence of such peptides and proteins limits broader applications of this unique host-guest interaction. Here, we report a strategy to expand the scope of CB[7]-peptide interaction by site-specifically introducing N-terminal substitutions (e.g. benzyl groups) using reductive alkylation. N-terminal benzylated peptides have similar affinity to CB[7] as native peptides with N-terminal Phe and even stronger interactions can be achieved using better ligands. We further expanded this host-guest interaction to be stimuli responsive. By introducing benzyl carboxylate substituents, the CB[7]-peptide interaction shows pH-dependent binding. Furthermore, benzyl boronate substituents led to saccharide-dependent CB[7]-peptide interactions. We demonstrated that using this strategy to introduce stronger CB[7] binders to the N-terminus of human calcitonin (hCT) results in increased aggregation stability in the presence of CB[7]. This strategy to expand CB[7]-peptide interaction scope opens opportunities for future applications in peptides and proteins.

Cysteines, as one of the most intrinsically nucleophilic amino acids, play important roles in proteins involved in diverse biological processes. They are also targets of covalent drugs for treating cancers and other diseases. Understanding the cysteine reactivity towards different types of electrophilic reactive groups will contribute to design of cysteine-reactive probes and facilitate the development of cysteine-based covalent drugs. In this study, we systematically evaluated the cysteinome reactivity toward two common electrophilic probes that are based on nucleophilic substitution and Michael addition, respectively, using chemical proteomic strategies. Our profiling results showed that each probe had its own preferential reactivity towards different cysteines and the engagement of the ligand fragments could only be distinguished by the probe with the matching reactive group. Our study highlighted the importance of choosing proper cysteine-reactive probes for screening covalent ligands and provided informative guidance for covalent drug development.

Phagocytosis is an evolutionary conserved innate immunological response, critical for fighting off pathogens and/or infections in higher organisms, including humans. During this process, any detrimental foreign particles (e.g. bacteria, virus, dead cells) are engulfed by immune cells called phagocytes (e.g. macrophages, monocytes), and packaged in an intracellular entity (or organelle) called the phagosome. The phagosome then undergoes a well-choreographed sequence of changes in protein and lipid composition termed “phagosomal maturation”, eventually fuses with the lysosome to form the phagolysosome, and thus marks the end of phagocytosis. While a lot is known of the proteomic changes during phagosomal maturation, in comparison, till recently, little remained known of the lipidomic changes during this process. Here, we review the current knowledge of the lipid changes on purified phagosomes, namely early and late phagosomes, during phagosomal maturation, with a special focus on sphingolipid metabolism during this important immune response.

Insulin like growth factor receptor (IGF-1R) and Insulin receptor (IR) are widely accepted to play a prominent role in cancer drug discovery due to their well-established involvement in various stages of tumorigenesis. Previously, neutralization of IGF-1R via monoclonal antibodies was in focus, which failed because of compensatory activation of IR-A upon inhibition of IGF-1R. Recent studies have demonstrated high homology between IGF-IR and IR particularly in tyrosine kinase domain and targeting both receptors have produced efficient therapeutic approaches such as inhibition of cancer cell cycle proliferation. Herein, we have made an attempt to analyze the unique data set from different chemical classes, containing potent ATP competitors against tyrosine kinase domain. We performed the 2D, 3D quantitative structure–activity relationship (QSAR) studies on inhibitors of these receptors to predict useful pharmacophoric features. We have optimized virtual screening of structurally diverse data set of dual inhibitors of IGF-1R and IR. Based on QSAR studies, we predict potential novel clinical candidates with a demonstrated absorption, distribution, metabolism, elimination, and toxicology (ADMETox) track. We also demonstrated comprehensive analysis of co–crystal complexes along with their inhibitors and built 3D- GRid INdependent Descriptors (GRIND) model to obtain insightful features such as H-bond donors and acceptors, overall topology and Vander Waal volume (vdw_vol) which are found to be responsible for dual inhibition of receptors. These findings lead to further description that Tirofiban, Practolol, Edoxaban, Novobiocin have potential to perform dual inhibition of both targets.

The proteases TMPRSS2 (transmembrane protease serine 2) and furin are known to play important roles in viral infectivity including systematic COVID-19 infection through priming of the spike protein of SARS-CoV-2 and related viruses. To discover small-molecules capable of inhibiting these host proteases, we established convenient and cost-effective cell-based assays employing Vero cells overexpressing TMPRSS2 and furin. A cell-based proteolytic assay for broad-spectrum protease inhibitors was also established using human prostate cancer cell line LNCaP. Evaluation of camostat, nafamostat, and gabexate in these cell-based assays confirmed their known TMPRSS2 inhibitory activities. Diminazene, a veterinary medicinal agent and a known furin inhibitor was found to inhibit both TMPRSS2 and furin with IC₅₀s of 1.35 and 13.2 μM, respectively. Establishment and the use of cell-based assays for evaluation TMPRSS2 and furin inhibitory activity and implications of dual activity of diminazene vs TMPRSS2 and furin are presented.

Targeted protein degradation (TPD) is a rapidly developing field in chemical biology and drug discovery. Various TPD modalities have emerged, with proteolysis-targeting chimeras (PROTACs) being the most well-developed at present. In PROTACs, a heterobifunctional molecule is used to recruit an E3 ligase to degrade a protein of therapeutic interest. Most of the PROTAC candidates that have been developed thus far use either CRBN or VHL as the hijacked E3 ligase, which poses several limitations. In order to overcome these limitations and furthermore realize the full potential of TPD as a therapeutic modality, the field will need to unlock additional E3 ligases. This review will therefore present 11 alternative E3 ligases for TPD. It will also describe some of the ongoing platform development that is facilitating the discovery of additional E3 ligases for TPD.

The natural product baicalein derivative baicalein-8-sulfonic acid (BaSO₃H) showed significant inhibitory effects on hepatocarcinoma cells viabilities and colony formation, but its molecular target(s) and mechanism were still not clearly elucidated. Using a DNA-programmed photoaffinity labeling method, we identified 12 targets that specifically bound with BaSO₃H. Among these, BaSO₃H bound with c-Jun N-terminal kinase 2 (JNK2) at an affinity of 33.1 nM (K_d) to induce apoptosis and autophagy in hepatocarcinoma cells.

Chirality is an inherent aspect of biology, and interactions between biomolecules are often influenced by stereochemistry and topographic complexity. This has implications for how small-molecule libraries are assembled for screening campaigns in chemical biology and drug discovery. Here we review the state of the field in the context of harnessing chirality as a source of chemical information at the chemistry-biology interface. We further highlight the emergence of screening libraries containing stereoisomeric sets of compounds and the concept of using stereoselectivity of phenotype and/or target engagement as a way to prioritize actionable targets and streamline the identification of selective and potent modulators of disease-relevant biomolecules. The chemical information density of FDA-approved drugs and the effect of stereochemistry on molecular complexity are reported. Finally, axial chirality and atroposelectivity are discussed as potential expansions of the aforementioned concepts.

Anilines are valuable synthons in pharmaceuticals and agrochemicals. These compounds are generally produced by chemocatalytic reduction of the corresponding nitrobenzene precursors. However, known synthetic methods often lack sufficient activity or selectivity, which results in low yields or the formation of a variety of undesired side products. We envisaged a biocatalytic approach as a promising general platform for selective and mild nitroarene reduction. Herein, we report using nitroreductases in combination with vanadium salts for the quantitative reduction of nitroaromatics to their corresponding anilines. Substrate scope studies were performed with fourteen nitrobenzene and four nitropyridine compounds. In one example, the reaction was intensified to 27 ​g/L substrate loading at 25 ​mL scale, where chemoselective reduction of the nitro group was obtained with full conversion and more than 93% selectivity toward aniline product (isolated in 82% yield). These conditions demonstrate the first general enzymatic method for the reduction of nitroaromatics to anilines.

PARP inhibitor development is on the rise as more PARP family members emerge as novel drug targets in diseases such as cancer, inflammation, and viral infection. Understanding a drug's mechanism of action and potential risks for toxicity requires proteome-wide characterization of both on- and off-target engagement. This review will highlight different methods to map out the protein interaction profile of a small molecule, using the clinically approved PARP inhibitors as a case study. The approaches discussed here will mainly focus on chemoproteomic workflows, using inhibitor bead-conjugates and photoaffinity labeling probes, but will also touch on the utility of biochemical assays. Collectively, these strategies have revealed new targets for PARP inhibitors beyond the expected PARP1/2, providing valuable insights for understanding mechanism of action, toxicity, and polypharmacology.