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.

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.

The Development of DNA-Compatible S-Glycosyl Transformations.

In this study, we revealed two distinct S-glycosyl transformations in a DNA-encoded library (DEL)-compatible environment. The first approach involves 2-chloro-1,3-dimethylimidazolidinium chloride (DMC)-mediated S-glycosylation, which is facilitated by the coupling of unprotected sugar units with the thiol residue of the DNA-linked compounds. However, this methodology falls short of the requirement for DEL construction due to its limited substrate scope. We further investigated a photoinduced DNA-compatible S-glycosyl transformation through a radical process. In this alternative approach, allyl sugar sulfones serve as sugar donors and are conjugated to DNA-linked compounds upon irradiation with green light. Encouragingly, this on-DNA glycosyl chemistry demonstrated excellent compatibility with functional groups presented in both sugar units and peptides, affording the desired DNA-linked glycosyl derivatives with good to excellent conversions. This pioneering DNA-compatible S-glycosyl transformation represents a valuable tool, facilitating the preparation of glycosyl DELs and offering avenues for the exploration of sugar-incorporated delivery systems.

[Herbal cake-partitioned moxibustion regulates M1 and M2 macrophage polarization of colonic mucosa in rats with Crohn's disease].

OBJECTIVE: To observe the effect of herbal cake-partitioned moxibustion (Moxi) on the expressions of inflammatory factors and M1/M2 polarization in colonic mucosal macrophages in Crohn's disease (CD) rats, so as to explore its underlying mechanisms in the treatment of CD. METHODS: Forty male SD rats were randomly divided into normal, model, Moxi and medication groups (n=10). The CD model was established by enema of 2, 4, 6-trinitrobenzene sulfonic acid (TNBS) solution (5%TNBS∶50% alcohol=2∶1, 3 mL/kg), once every 7 days, 4 times altogether. For rats of the Moxi group, cake-partitioned moxibustion was given to "Tianshu" (ST25) and "Qihai" (CV6), two moxa-cones for each acupoint every time, once daily for 10 days. For rats of the medication group, intragastric perfusion of mesalazine solution was given twice daily for 10 days. After the treatment, the colonic mucosa tissue was sampled, and the macrophages were isolated, purified and cultured. The pathological changes of colon tissues were observed by H.E. staining. The ultrastructure of colon tissue was observed by transmission electron microscopy. The expression levels of α7nAChR, NF-κB p65 and TNF-α in colon mucosal macrophages were detected by Western blot. The number of M1 and M2 macrophages in colon mucosa was detected by flow cytometry and immunofluorescence assay. RESULTS: Compared with the normal group, the colon tissue of rats presented huge ulceration and inflammatory manifestations, the junction of colon epithelial cells was loose, the structure of organelles was damaged; the expression level of α7nAChR in macrophages of colon mucosa was significantly decreased (P<0.01), while the expression levels of NF-κB p65 and TNF-α, and the number of M1 and M2 macrophages were increased (P<0.01, P<0.05) in the model group. In comparison with the model group, the morphology and structure of colon mucosa tissues of rats in Moxi and medication groups were improved; the expression level of α7nAChR, the number of M2 macrophage in colon mucosa were significantly increased (P<0.01, P<0.05), while the expression levels of NF-κB p65 and TNF-α, and the number of M1 macrophage were significantly decreased (P<0.01, P<0.05) in both the Moxi and medication groups. CONCLUSION: Herbal cake-partitioned moxibustion may inhibit NF-κB activation by up-regulating the expression level of α7nAChR to promote the polarization of macrophages from M1 to M2 type, and reduce the proportion of M1 macrophages, inhibit the expression of TNF-α in colonic mucosa of CD rats, so as to relieve the intestinal inflammation.

Electroacupuncture improves follicular development and metabolism and regulates the expression of adiponectin, AMPK and ACC in an obese rat model of polycystic ovary syndrome.

BACKGROUND: Polycystic ovary syndrome (PCOS) is a common endocrine disorder characterized by hyperandrogenism and follicular arrest. Electroacupuncture (EA) has been shown to be effective at improving hyperandrogenism and follicular arrest in PCOS; however, its mechanism of action remains to be deciphered. OBJECTIVE: In this study, we investigated whether EA improved follicular development in an obese rat model of PCOS and regulated the expression of adiponectin, AMP-activated protein kinase (AMPK) and acetyl-CoA carboxylase (ACC). METHODS: EA was administered at CV3, CV4 and ST40. Changes in body weight, paraovarian fat, estrus cycle, ovarian morphology, levels of related hormones, and glucose and lipid metabolism were evaluated. In addition, protein and mRNA expression of adiponectin, AMPK and ACC was measured. RESULTS: The body weight and paraovarian fat of rats in the EA group were reduced, while estrus cyclicity and ovarian morphology improved. Levels of free fatty acids, triglycerides, total cholesterol and low-density lipoprotein cholesterol were significantly reduced in the EA group, as well as blood glucose levels. Furthermore, levels of testosterone and luteinizing hormone were reduced in the EA group, while estradiol levels were increased. Protein and mRNA expression of adiponectin, AMPKα1 and liver kinase B1 (LKB1) was found to be increased in the EA group, while protein and mRNA expression of ACC were significantly reduced.Conclusion: Our findings suggest that EA improved follicular development and metabolism and regulated expression levels of adiponectin, AMPKα1, LKB1 and ACC in our obese rat model of PCOS.

High-Yield Preparation of American Oyster Defensin (AOD) via a Small and Acidic Fusion Tag and Its Functional Characterization.

The marine peptide, American oyster defensin (AOD), is derived from Crassostrea virginica and exhibits a potent bactericidal effect. However, recombinant preparation has not been achieved due to the high charge and hydrophobicity. Although the traditional fusion tags such as Trx and SUMO shield the effects of target peptides on the host, their large molecular weight (12-20 kDa) leads to the yields lower than 20% of the fusion protein. In this study, a short and acidic fusion tag was employed with a compact structure of only 1 kDa. Following 72 h of induction in a 5 L fermenter, the supernatant exhibited a total protein concentration of 587 mg/L. The recombinant AOD was subsequently purified through affinity chromatography and enterokinase cleavage, resulting in the final yield of 216 mg/L and a purity exceeding 93%. The minimum inhibitory concentrations (MICs) of AOD against Staphylococcus aureus, Staphylococcus epidermidis, and Streptococcus galactis ranged from 4 to 8 µg/mL. Moreover, time-killing curves indicated that AOD achieved a bactericidal rate of 99.9% against the clinical strain S. epidermidis G-81 within 0.5 h at concentrations of 2× and 4× MIC. Additionally, the activity of AOD was unchanged after treatment with artificial gastric fluid and intestinal fluid for 4 h. Biocompatibility testing demonstrated that AOD, at a concentration of 128 µg/mL, exhibited a hemolysis rate of less than 0.5% and a cell survival rate of over 83%. Furthermore, AOD's in vivo therapeutic efficacy against mouse subcutaneous abscess revealed its capability to restrain bacterial proliferation and reduce bacterial load, surpassing that of antibiotic lincomycin. These findings indicate AOD's potential for clinical usage.

Lactobacillus spp. in the reproductive system of female moths and mating induced changes and possible transmission.

BACKGROUND: The microbiome in the insect reproductive tract is poorly understood. Our previous study demonstrated the presence of Lactobacillus spp. in female moths, but their distribution and function remain unclear. Lactobacillus spp. are known as the 'healthy' vaginal microbiome in humans. RESULTS: Here, we studied the microbiome in the reproductive system (RS) and gut of Spodoptera frugiperda using 16S rDNA sequences. The obtained 4315 bacterial OTUs were classified into 61 phyla and 642 genera, with Proteobacteria, Firmicutes and Bacteroidota being the top three dominant phyla and Enterococcus and Asaia being dominant genera in most samples. Mating dramatically increased the abundance of pathogens or pathogenic functions in the gut, while in the RS, the change range was trivial. Taxonomy assignment identified thirteen Lactobacillus spp. in S. frugiperda, with Lactobacillus crustorum and Lactobacillus murinus showing high abundance. Three species found in S. frugiperda, namely L. reuteri, L. plantarum and L. brevis, have also been identified as human 'healthy' vaginal bacterial species. Lactobacillus spp. showed higher abundance in the RS of virgin females and lower abundance in the RS of virgin males and the gut of virgin females. Mating reduced their abundance in the RS of females but increased their abundance in the RS of males, especially in males mated with multiple females. The RS of virgin females and of multiple mated males were very similar in terms of composition and abundance of Lactobacillus species, with Lactobacillus crustorum showing much higher abundance in both tissues, potentially due to sexual transmission. CONCLUSIONS: Lactobacillus spp. showed high abundance and diversity in the RS of female moths. The higher abundance of Lactobacillus spp. in the RS of female moths and the similarity of Lactobacillus species in female moths with human 'healthy' vaginal Lactobacillus spp. suggest that these bacterial strains are also an important microbiome in the RS of female moths.

The Role and Therapeutic Perspectives of Sirtuin 3 in Cancer Metabolism Reprogramming, Metastasis, and Chemoresistance.

Sirtuin 3 (SIRT3), the nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase, acts as a metabolic modulator mainly located in mitochondria via regulating the process of the relevant biochemical processes by targeting crucial mediators. Recently, owing to its dual role in cancer, SIRT3 has attracted extensive attention. Cancer cells have different metabolic patterns from normal cells, and SIRT3-mediated metabolism reprogramming could be critical in the cancer context, which is closely related to the mechanism of metabolism reprogramming, metastasis, and chemoresistance in tumor cells. Therefore, it is crucial to elucidate the relevant pathological mechanisms and take appropriate countermeasures for the progression of clinical strategies to inhibit the development of cancer. In this review, existing available data on the regulation of cancer metabolism reprogramming, metastasis, and chemoresistance progression of SIRT3 are detailed, as well as the status quo of SIRT3 small molecule modulators is updated in the application of cancer therapy, aiming to highlight strategies directly targeting SIRT3-mediated tumor-suppressing and tumor-promoting, and provide new approaches for therapy application. Furthermore, we offer an effective evidence-based basis for the evolvement of potential personalized therapy management strategies for SIRT3 in cancer settings.

Effectiveness of herb-partitioned moxibustion combined with electroacupuncture on polycystic ovary syndrome in patients with symptom pattern of kidney deficiency and phlegm-dampne.

OBJECTIVE: To observe the effect of herb-partitioned moxibustion combined with electroacupuncture on polycystic ovary syndrome (PCOS) in patients with symptom pattern of kidney deficiency and phlegm-dampness. METHODS: Totally 62 PCOS patients who met the inclusion criteria were randomly divided into intervention group and control group. In the intervention group, acupoints were subjected to (43 ± 1) ℃ herb-partitioned moxibustion and electroacupuncture treatment. In the control group, acupoints were subjected to (37 ± 1) ℃ herb-partitioned moxibustion and sham electroacupuncture treatment. Treatment was provided 3 times per week for 12 weeks, and the treatment was stopped during menstruation. After the treatment, the clinical efficacy, the Traditional Chinese Medicine (TCM) symptom pattern score, basal body temperature (BBT) levels, menstrual cycle, and related sex hormone levels of the two groups were evaluated. RESULTS: Sixty patients were eventually included in the study (30 in the intervention group and 30 in the control group). There were not obvious between-group differences in the baseline efficacy parameters (all P > 0.05). (a) After treatment, the two groups have improved in terms of clinical efficacy, TCM symptom pattern score, menstrual cycle and, BBT (P < 0.01, < 0.05), and the intervention group was better than the control group (P < 0.01, < 0.05). (b) In the intervention group, the estradiol (E2) and P450 aromatase (P450arom) levels were increased (all P < 0.05), the testosterone (T) level was decreased (P < 0.05), and the luteotropic hormone (LH) and anti-Müllerian hormone (AMH) levels were significantly decreased (P < 0.01). In the control group, E2 level was increased (P < 0.05), and LH level was decreased (P < 0.05). After treatment, the T, LH, and AMH levels of the intervention group were decreased compared with those of the control group (all P < 0.05), and the P450arom level was increased (P < 0.05). CONCLUSIONS: Herb-partitioned moxibustion combined with electroacupuncture can effectively improve the related clinical symptoms of PCOS patients with kidney deficiency and phlegm-dampness. Herb-partitioned moxibustion combined with electroacupuncture may inhibit the overexpression of AMH to increase the expression level of P450arom in ovarian granulosa cells, thereby reconstructing the dependence of follicular development on FSH, and finally improving abnormal follicular development and hyperandrogenism in PCOS patients with kidney deficiency and phlegmdampness. TRIAL REGISTRATION NUMBER: ChiCTR1900024182.

Exenatide regulates inflammation and the production of reactive oxygen species via inhibition of S1PR2 synthesis.

BACKGROUND: Microvascular dysfunction is one of the most serious complications of diabetic retinopathy (DR). As a novel treatment drug for type 2 diabetes, exenatide possesses protective properties against retinal neurodegeneration. Sphingosine-1-phosphate receptor 2 (S1PR2) could regulate blood glucose in diabetes, and inhibition of S1PR2 is involved in the treatment of diabetes. However, the mechanism of exenatide in human retinal vascular endothelial cells (hRVECs) has not been fully defined. OBJECTIVES: We tested the hypothesis that S1PR2 plays a vital role in high glucose (HG)-induced hRVECs, and that exenatide could ameliorate HG-induced hRVEC injury by regulating S1PR2 production. MATERIAL AND METHODS: The hRVECs underwent HG-stimulation. Quantitative real-time polymerase chain reaction (RT-qPCR) and western blot were performed to examine the expression of S1PR2. Oxidative stress levels, inflammatory markers and cell apoptosis were detected using reactive oxygen species (ROS) staining, enzyme-linked immunosorbent assay (ELISA) kits and TUNEL staining. RESULTS: High glucose increased the level of S1PR2 in hRVECs and reduced the expression of glucagon-like peptide-1 receptor (GLP1R) compared to the control group. Exenatide decreased the level of S1PR2 induced by HG. Sphingosine-1 blocked the effects of exenatide, alleviating the ROS and cell apoptosis induced by HG. JTE-013 treatment protected hRVECs from injury by HG. The inhibitory effects of exenatide on S1PR2 expression lessened HG-induced hRVEC injury. CONCLUSIONS: The results demonstrate a possible mechanism of exenatide mediated inhibition of S1PR2 synthesis, and support S1PR2 as a novel target for treating DR.

The Role and Therapeutic Value of Syndecan-1 in Cancer Metastasis and Drug Resistance.

Metastasis and relapse are major causes of cancer-related fatalities. The elucidation of relevant pathomechanisms and adoption of appropriate countermeasures are thus crucial for the development of clinical strategies that inhibit malignancy progression as well as metastasis. An integral component of the extracellular matrix, the type 1 transmembrane glycoprotein syndecan-1 (SDC-1) binds cytokines and growth factors involved in tumor microenvironment modulation. Alterations in its localization have been implicated in both cancer metastasis and drug resistance. In this review, available data regarding the structural characteristics, shedding process, and nuclear translocation of SDC-1 are detailed with the aim of highlighting strategies directly targeting SDC-1 as well as SDC-1-mediated carcinogenesis.

Acupuncture in a Rat Model of Asthma.

A high platform can fix rats without restriction and completely expose the acupoints on the back during acupuncture manipulation. This article describes methods for the fabrication of the high platform, establishes a rat model of asthma and measures changes in respiratory function using a noninvasive and real-time whole-body plethysmography (WBP) system.

Improved production of recombinant Rhizomucor miehei lipase by coexpressing protein folding chaperones in Pichia pastoris, which triggered ER stress.

Rhizomucor miehei lipase (RML) is a biocatalyst that widely used in laboratory and industrial. Previously, RML with a 70-amino acid propeptide (pRML) was cloned and expressed in P. pastoris. Recombinant strains with (strain containing 4-copy prml) and without ER stress (strain containing 2-copy prml) were obtained. However, the effective expression of pRML in P. pastoris by coexpressing ER-related elements in pRML-produced strain with or without ER stress has not been reported to date. In this study, an efficient way to produce functional pRML was explored in P. pastoris. The coexpression of protein folding chaperones, including PDI and ERO1, in different strains with or without ER stress, was investigated. PDI overexpression only increased pRML production in 4-copy strain from 705 U/mL to 1430 U/mL because it alleviated the protein folded stress, increased the protein concentration from 0.56  mg/mL to 0.65 mg/mL, and improved enzyme-specific activity from 1238 U/mg to 2186 U/mg. However, PDI coexpression could not improve pRML production in the 2-copy strain because it increased protein folded stress, while ERO1 coexpression in the two strains all had a negative effect on pRML expression. We also investigated the effect of the propeptide on the substrate specificity and the condition for pRML enzyme powder preparation. Results showed that the relative activity exceeded 80% when the substrates C8-C10 were detected at 35°C and pH 6, and C8-C12 at 45°C and pH 8. The optimal enzyme powder preparation pH was 7, and the maximum recovery rate for pRML was 73.19%.

Ultrasound-assisted hydrolysis of lard for free fatty acids catalyzed by combined two lipases in aqueous medium.

Lard is a by-product of animal processing. It is inexpensive compared with vegetable oils; however, its use is limited due to the high calorific value and high-saturated fatty acid content. While using lard as the source of free fatty acids (FFA) can significantly increase its utilization value. This study aimed to research the method on efficient hydrolysis of lard catalyzed by combi-lipases and assisted with ultrasound pretreatment. A 1,3-specific lipase from Rhizomucor miehei (termed pRML, 1540 U/mL) and a nonspecific mono- and diacylglycerol lipase from Penicillium cyclopium (termed MDL, 2000 U/mL) were used as biocatalysts. Results showed that the maximum hydrolysis rate of lard after 6 h at 45°C by using pRML and MDL alone was, respectively, 39.9% and 8.5%. When pRML combined with MDL (combi-lipases), hydrolysis rate can reach to 78.1%. While combi-lipases were assisted with 5 min ultrasound pretreatment before the reaction, the hydrolysis rate can further increase to 97%. The combi-lipases with different specificity and assisted with ultrasound pretreatment may be a useful technology for the enzyme production of FFA from complex lipid substrates, such as lard.

Metallothionein-2 is associated with the amelioration of asthmatic pulmonary function by acupuncture through protein phosphorylation.

BACKGROUND: Acupuncture has long been used for asthma treatment but the underlying mechanism remains unclear. Previous study showed that metallothionein-2 (MT-2) was significantly decreased in asthmatic lung tissue. However, the relationship between acupuncture treatment and MT-2 expression during asthma is still unknown, and the detailed effect analysis of MT-2 on phosphorylation in airway smooth muscle cells (ASMCs) is also unclear. METHODS: The acupuncture effect on pulmonary resistance (RL) was investigated in a rat model of asthma, and the mRNA and protein levels of MT-2 in lung tissue were detected. Primary ASMCs were isolated and treated with MT-2 recombinant protein to study the MT-2 effects on ASMC relaxation. A Phospho Explorer antibody microarray was applied to detect protein phosphorylation changes associated with MT-2-induced ASMC relaxation. Bioinformatic analysis were performed with PANTHER database, DAVID and STRING. Phosphorylation changes in key proteins were confirmed by Western blot. RESULTS: Acupuncture significantly reduced RL at 2-5 min (P < 0.05 vs asthma) in asthmatic rats. Acupuncture continued to increase MT-2 mRNA expression in lung tissue for up to 14 days (P < 0.05 vs asthma). The MT-2 protein expression was significantly decreased in the asthmatic rats (P < 0.05 vs control), while MT-2 protein expression was significantly increased in the asthmatic model group treated with acupuncture (P < 0.05 vs asthma). Primary ASMCs were successfully isolated and recombinant MT-2 protein (100, 200, 400 ng/ml) significantly relaxed ASMCs (P < 0.05 vs control). MT-2 induced phosphorylation changes in 51 proteins. Phosphorylation of 14 proteins were upregulated while 37 proteins were downregulated. PANTHER classification revealed eleven functional groups, and the phosphorylated proteins were identified as transferases (27.8 %), calcium-binding proteins (11.1 %), etc. DAVID functional classification showed that the phosphorylated proteins could be attributed to eight functions, including protein phosphorylation and regulation of GTPase activity. STRING protein-protein interaction network analysis showed that Akt1 was one of the most important hubs for the phosphorylated proteins. The phosphorylation changes of Akt1 and CaMK2ß were consistent in both the Phospho Explorer antibody microarray and Western blot. CONCLUSION: Acupuncture can significantly ameliorate RL, and the MT-2 mRNA and protein levels in lung tissue are increased during treatment. MT-2 significantly relaxes ASMCs and induces a series of protein phosphorylation. These phosphorylation changes, including Akt1 and CaMK2ß, may play important roles in the therapeutic effects of acupuncture on asthma.

[A review of deep learning methods for the detection and classification of pulmonary nodules].

Lung cancer has the highest mortality rate among all malignant tumors. The key to reducing lung cancer mortality is the accurate diagnosis of pulmonary nodules in early-stage lung cancer. Computer-aided diagnostic techniques are considered to have potential beyond human experts for accurate diagnosis of early pulmonary nodules. The detection and classification of pulmonary nodules based on deep learning technology can continuously improve the accuracy of diagnosis through self-learning, and is an important means to achieve computer-aided diagnosis. First, we systematically introduced the application of two dimension convolutional neural network (2D-CNN), three dimension convolutional neural network (3D-CNN) and faster regions convolutional neural network (Faster R-CNN) techniques in the detection of pulmonary nodules. Then we introduced the application of 2D-CNN, 3D-CNN, multi-stream multi-scale convolutional neural network (MMCNN), deep convolutional generative adversarial networks (DCGAN) and transfer learning technology in classification of pulmonary nodules. Finally, we conducted a comprehensive comparative analysis of different deep learning methods in the detection and classification of pulmonary nodules.