Chemical Space Profiling of SARS-CoV-2 PLpro Using DNA-Encoded Focused Libraries.

DNA-encoded library (DEL) technology is gaining attention for its rapid construction and deconvolution capabilities. Our study explored a novel strategy using rational DELs tailored for the SARS-CoV-2 papain-like protease, which revealed new fragments. Structural changes post-DEL screening mimic traditional medicinal chemistry lead optimization. We unveiled unique aromatic structures offering an alternative optimization path. Notably, we identified superior binding fragments targeting the BL2 groove. Derivative 16 emerged as the most promising by exhibiting IC50 values of 0.25 µM. Derivative 6, which features an aromatic fragment capped with a naphthalene moiety, showed IC50 values of 2.91 µM. Molecular modeling revealed hydrogen bond interactions with Lys157 residue and potential covalent interactions with nearby amino acid residues. This research underscored DEL's potential for fragment-based drug discovery against SARS-CoV-2 protease.

Leonurus japonicus Houtt. modulates neuronal apoptosis in intracerebral hemorrhage: Insights from network pharmacology and molecular docking.

ETHNOPHARMACOLOGICAL RELEVANCE: Leonurus japonicus Houtt. (Labiatae), commonly known as Chinese motherwort, is a herbaceous flowering plant that is native to Asia. It is widely acknowledged in traditional medicine for its diuretic, hypoglycemic, antiepileptic properties and neuroprotection. Currently, Leonurus japonicus (Leo) is included in the Pharmacopoeia of the People's Republic of China. Traditional Chinese Medicine (TCM) recognizes Leo for its myriad pharmacological attributes, but its efficacy against ICH-induced neuronal apoptosis is unclear. AIMS OF THE STUDY: This study aimed to identify the potential targets and regulatory mechanisms of Leo in alleviating neuronal apoptosis after ICH. MATERIALS AND METHODS: The study employed network pharmacology, UPLC-Q-TOF-MS technique, molecular docking, pharmacodynamic studies, western blotting, and immunofluorescence techniques to explore its potential mechanisms. RESULTS: Leo was found to assist hematoma absorption, thus improving the neurological outlook in an ICH mouse model. Importantly, molecular docking highlighted JAK as Leo's potential therapeutic target in ICH scenarios. Further experimental evidence demonstrated that Leo adjusts JAK1 and STAT1 phosphorylation, curbing Bax while augmenting Bcl-2 expression. CONCLUSION: Leo showcases potential in mitigating neuronal apoptosis post-ICH, predominantly via the JAK/STAT mechanism.

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.

Molecular insight into T cell exhaustion in hepatocellular carcinoma.

Hepatocellular carcinoma is one of the leading causes of cancer-related mortality globally. The emergence of immunotherapy has been shown to be a promising therapeutic approach for hepatocellular carcinoma in recent years. It has been well known that T cell plays a key role in current immunotherapy. However, sustained exposure to antigenic stimulation within the tumor microenvironment may lead to T cell exhaustion, which may cause treatment ineffectiveness. Therefore, reversing T cell exhaustion has been an important issue for the clinical application of immunotherapy, and a comprehensive understanding of the intricacies surrounding T cell exhaustion and its underlying mechanisms is imperative for devising strategies to overcome the T cell exhaustion during treatment. In this review, we summarized the reported drivers of T cell exhaustion in hepatocellular carcinoma and delineate potential ways to reverse it. Additionally, we discussed the interplay among metabolic plasticity, epigenetic regulation, and transcriptional factors in exhausted T cells in hepatocellular carcinoma, and their implication for future clinical applications.

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.

Endoscopic endonasal surgery of Rathke's cleft cysts-- preoperative imaging evaluation, personalized removal and multilevel sellar floor reconstruction.

OBJECTIVES: The purpose of this study was to evaluate the effectiveness of endoscopic endonasal surgery (EES) for Rathke's cleft cysts (RCCs) and the advantages of detailed preoperative imaging evaluation, intraoperative personalized removal and multilevel sellar floor reconstruction. METHODS: The clinical data of 43 patients with RCCs who were treated by EES in the neurosurgery department of affiliated hospital of Jiangnan University and Wuxi No.2 People's Hospital from January 2018 to January 2023 were retrospectively analyzed. The effectiveness of EES for RCCs was analyzed by imaging information, surgical procedures, symptom improvement and complications. RESULTS: All 43 RCCs were completely removed by EES, and all clinical symptoms improved to varying degrees. Postoperative relief of headache was achieved in 23 out of 26 patients (88.5 %); there was improvement in 10 out of 13 patients with visual field disorders (76.9 %) and in 8 out of 10 patients with endocrine abnormalities (80 %). New hormonal deficiency was discovered in 7 of all the patients postoperatively. There were 8 patients with postoperative diabetes insipidus and 1 patient with cerebrospinal fluid leakage. The incidence of new hormonal dysfunction and postoperative DI in expanded EES (33.3 %, 33.3 %) was higher than it in conventional EES (4 %, 8 %) (P < 0.05). The average follow-up time was 29.1 ± 14.8 months, and there were no deaths or infections. Three patients presented with cyst recurrence on MRI. CONCLUSIONS: The clinical manifestations and imaging characteristics of RCCs are variable, and a detailed preoperative review of the imaging is helpful for the development of surgical plans. RCCs can be treated more safely and thoroughly with less trauma and complications by intraoperative personalized removal and multilevel sellar floor reconstruction. The high incidence of new hormonal dysfunction and postoperative DI may be related to the disturbance of the pituitary stalk. EES has unique advantages and high clinical application value for the treatment of RCCs.

Macrocyclizing DNA-Linked Peptides via Three-Component Cyclization and Photoinduced Chemistry.

While DNA-encoded macrocyclic libraries have gained substantial attention and several hit compounds have been identified from DNA-encoded library technology, efficient on-DNA macrocyclic methods are also required to construct DNA-linked libraries with a high degree of cyclization and DNA integrity. In this paper, we reported a set of on-DNA methodologies, including the use of an OPA-mediated three-component cyclization with native handles of amino acids and photoredox chemistries. These chemistries proceed smoothly under mild conditions in good to excellent conversions, successfully generating novel isoindole, isoindoline, indazolone, and bicyclic scaffolds.

Ferroptosis in cancer immunity and immunotherapy: Multifaceted interplay and clinical implications.

Ferroptosis is a type of cell death characterized by iron-dependent phospholipid peroxidation and reactive oxygen species overproduction. Ferroptosis induces immunogenic cell death and elicits anti-tumor immune responses, playing an important role in cancer immunotherapy. Ferroptosis suppression in cancer cells impairs its immunotherapeutic efficacy. To overcome this issue, ferroptosis inducers (FINs) have been combined with other cancer therapies to create an anti-tumor immune microenvironment. However, the ferroptosis-based crosstalk between immune and tumor cells is complex because oxidative products released by ferroptotic tumor cells impair the functions of anti-tumor immune cells, resulting in immunotherapeutic resistance. In the present article, we have reviewed ferroptosis in tumor and immune cells and summarized the crosstalk between ferroptotic tumor cells and the immune microenvironment. Based on the existing literature, we have further discussed future perspectives on opportunities for combining ferroptosis-targeted therapies with cancer immunotherapies.

Intracellular self-aggregation of biomimetic Fe3O4 nanoparticles for enhanced ferroptosis-inducing therapy of breast cancer.

Nanomedicines based on ferroptosis may be effective strategies for cancer therapy due to their unique inducing mechanism. However, the challenges, including non-target distribution, poor accumulation and retention of nanomedicine, have a profound impact on the effectiveness of drug delivery. Here, we developed cancer cell membrane (CCM)-coated Fe3O4 nanoparticles (NPs) modified with supramolecular precursors and loaded with sulfasalazine (SAS) for breast cancer therapy. Benefiting from the coating of the CCM, these NPs can be specifically recognized and internalized by tumor cells rapidly after being administered and form aggregates via the host-guest interaction between adamantane (ADA) and cyclodextrins (CD), which in turn effectively reduces the exocytosis of tumor cells and prolongs the retention time. In vitro and in vivo studies showed that Fe3O4 NPs possessed effective cellular uptake and precise specific accumulation in tumor cells and tissues through CCM-targeted supramolecular in situ aggregation, demonstrating enhanced ferroptosis-inducing therapy of breast cancer. Overall, this work provided a supramolecular biomimetic platform to achieve targeted delivery of Fe3O4 NPs with high efficiency and precise self-assembly for improved cancer therapy.

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.

Structure-Activity Relationship Study of 1H-Pyrrole-3-carbonitrile Derivatives as STING Receptor Agonists.

The use of small agonists to target stimulators of interferon genes (STING) has been demonstrated to be a promising strategy for the treatment of various cancers and infectious diseases. Herein, we discovered a series of 1H-pyrrole-3-carbonitrile derivatives as potential STING agonists. On this basis, the structure-activity relationship of this scaffold was studied by introducing various substituents on the aniline ring system. Representative compounds 7F, 7P, and 7R all displayed comparable activities to the reported STING agonist SR-717 in binding various hSTING alleles and induced reporter signal in human THP1 cell lines. Model compound 7F induced phosphorylation of TBK1, IRF3, p65, and STAT3 in a STING-dependent fashion and stimulated the expression of target genes IFNB1, CXCL10, and IL6 in a time-dependent manner in human THP1 cells. Our findings afforded a series of novel STING agonists with promising potential.

Design, Construction, and Screening of Diversified Pyrimidine-Focused DNA-Encoded Libraries.

Pyrimidine is a ubiquitous component in natural products and approved drugs, providing an ideal modular scaffold for generating libraries with drug-like properties. DNA-encoded library technology introduces a novel library modality where each small molecule is covalently linked to a unique oligo tag. This technology offers the advantages of rapidly generating and interrogating large-scale libraries containing billions of members, substantially reducing the entry barrier to their use in both academia and the pharmaceutical industry. In this Letter, we describe the synthesis of three DNA-encoded libraries based on different functionalized pyrimidine cores featuring diversified chemoselectivity and regioselectivity. Preliminary screening of these DNA-encoded libraries against BRD4 identified compounds with nanomolar inhibition activities.

The tumour-promoting role of protein homeostasis: Implications for cancer immunotherapy.

Protein homeostasis, an important aspect of cellular fitness that encompasses the balance of production, folding and degradation of proteins, has been linked to several diseases of the human body. Multiple interconnected pathways coordinate to maintain protein homeostasis within the cell. Recently, the role of the protein homeostasis network in tumorigenesis and tumour progression has gradually come to light. Here, we summarize the involvement of the most prominent components of the protein quality control mechanisms (HSR, UPS, autophagy, UPR and ERAD) in tumour development and cancer immunity. In addition, evidence for protein quality control mechanisms and targeted drugs is outlined, and attempts to combine these drugs with cancer immunotherapy are discussed. Altogether, combination therapy represents a promising direction for future investigations, and this exciting insight will be further illuminated by the development of drugs that can reach a balance between the benefits and hazards associated with protein homeostasis interference.

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.

A multifunctional polydopamine/genipin/alendronate nanoparticle licences fibrin hydrogels osteoinductive and immunomodulatory potencies for repairing bone defects.

Here, we fabricated a hybrid nanoparticle composed of polydopamine nanoparticles (pNPs), alendronate (Al) and genipin (GP) for cranial bone defect repair. Al was crosslinked into pNPs via GP (Al@pNPs), after which hybrid nanoparticles were obtained. By embedding these Al@pNPs into the fibrin hydrogels, a multifunctional bone repair scaffold was fabricated (Al@pNPs/Fg). The Al@pNPs/Fg exhibited three synergistic effects on the bone microenvironment: i) enhanced ectomesenchymal stem cell (EMSC) osteogenic differentiation by activating the piezo 1 channel; ii) inhibited the formation and function of osteoclasts related to the NF-κB signaling pathways; and iii) promoted M2 polarization and anti-inflammatory factor expression under normal and simulated inflammatory conditions. Al@pNPs/Fg ultimately promoted cranial bone defect regeneration in an SD rat model. This simple and low-cost technology provides a new approach to constructing an efficient delivery system and has desirable biological properties, providing a tissue-committed niche for the repair of bone defects.

Human nasal mucosa ectomesenchymal stem cells derived extracellular vesicles loaded omentum/chitosan composite scaffolds enhance skull defects regeneration.

Engineered bone tissue that can promote osteogenic differentiation is considered an ideal substitute for materials to heal bone defects. Extracellular vesicle (EV)-based cell-free regenerative therapies represent an emerging promising alternative for bone tissue engineering. We hypothesized that EVs derived from human nasal mucosa-derived ectomesenchymal stem cells (hEMSCs) can promote bone tissue regeneration. Herein, hEMSCs were cultured with osteogenic induction medium or normal medium to generate two types of EVs. We first demonstrated that the two EVs exhibited strong potential to promote rat suture mesenchymal stem cell (SMSC) osteogenesis by transferring TG2 to SMSCs and regulating extracellular matrix (ECM) synthesis. Next, we developed a composite hydrogel made of porcine omentum and chitosan into which EVs were adsorbed to enable the effective delivery of EVs with sustained release kinetics. Implantation of the EV-loaded hydrogels in a critical-size rat cranial defect model significantly promoted bone regeneration. Therefore, we suggest that our hEMSC-derived EV-loading system can serve as a new therapeutic paradigm for promoting bone tissue regeneration in the clinic.

Endoscopic Lateral and Superior Cerebellar Keyhole Approach to the Anterior and Middle Incisural Space and Meckel Cave: An Anatomic Study.

OBJECTIVE: We sought to assess the feasibility of endoscopic lateral and superior cerebellar keyhole approach for exposure of the anterior and middle incisural space and Meckel cave. METHODS: The endoscopic lateral and superior cerebellar keyhole approach was performed in 6 cadaveric heads (12 sides) using 0- and 30-degree endoscopes, respectively. The anatomic structures for this approach to the anterior and middle incisural space and Meckel cave were observed. RESULTS: By grinding out the suprameatal tubercle and petrous apex and incising the tentorium, the anatomic structures in the anterior incisural space were visualized. The mean area exposed with a 0-degree endoscope in the anterior incisural space was 212.50 ± 6.04 mm2, significantly less than that exposed with a 30-degree endoscope (233.83 ± 8.72 mm2) (P < 0.05). The anatomic distance of the Meckel cave in the depth was the same between a 0-degree endoscope and a 30-degree endoscope; however, the distance in the width was 9.48 and 12.32 mm, respectively (P < 0.01). The area of petrous window grinded by a 30-degree endoscope was only increased by 5.83 mm2, compared with a 0-degree endoscope (P > 0.05). CONCLUSIONS: This approach provides access to the anterior and middle incisural space and Meckel cave, which is feasible to clearly expose the anatomic structures in those regions with minimal invasiveness. Additionally, better visualization and surgical space can be achieved under a 30-degree endoscope.