Cross-coupling reactions are powerful synthetic tools for the formation of remarkable building blocks of many naturally occurring molecules, polymers and biologically active compounds. These reactions have brought potent transformations in chemical and pharmaceutical disciplines. In this review, we have focused on the use of cross-coupling reactions such as Suzuki, Negishi, Heck, Sonogashira and Stille in the total synthesis of some natural products of recent years (2016–2020). A short introduction of mentioned cross-coupling reactions along with highlighted aspects of natural products has been stated in separate sections. Additionally, few examples of natural products via incorporation of more than one type of cross-coupling reaction have also been added to demonstrate the importance of these reactions in organic synthesis.

Cross-coupling reactions towards the synthesis of natural products

Interplay between tumor-derived factors and tumor-associated neutrophils: opportunities for therapeutic interventions in cancer

Bovine mastitis caused by multi-drug resistant (MDR) Klebsiella pneumoniae is difficult to treat with antibiotics, whereas bacteriophages may be a viable alternative. Our objective was to use 2 K. pneumoniae strains, 1 MDR and the other non-MDR, to isolate phages from sewage samples and compare their biological and genomic characteristics. Additionally, phage infected mouse mammary gland was also analyzed by H&E staining and ELISA kits to compare morphology and inflammatory factors, respectively. Based on assessments with double agar plates and transmission electron microscopy, phage CM_Kpn_HB132952 had clear plaques surrounded by translucent halos on the bacterial lawn of K. pneumoniae KPHB132952 and belonged to Siphoviridae, whereas phage CM_Kpn_HB143742 formed a clear plaque on the bacterial lawn of K. pneumoniae KPHB143742 and belonged to Podoviridae. In 1-step growth curves, CM_Kpn_HB132952 and CM_Kpn_HB143742 had burst sizes of 0.34 and 0.73 log10 PFU/mL, respectively. The former had a latent period of 50 min and an optimal multiplicity of infection (MOI) of 0.01, whereas for the latter, the latent period was 30 min (MOI = 1). Phage CM_Kpn_HB132952 had better thermal and acid–base stability than phage CM_Kpn_HB143742. Additionally, both phages had the same host range rate but different host ranges. Based on Illumina NovaSeq, phages CM_Kpn_HB132952 and CM_Kpn_HB143742 had 140 and 145 predicted genes, respectively. Genomic sequencing and phylogenetic tree analysis indicated that both phages were novel phages belonging to the Klebsiella family. Additionally, the histopathological structure and inflammatory factors TNF-α and IL-1β were not significantly different among phage groups and the control group. In conclusion, using 1 MDR and 1 non-MDR strain of K. pneumoniae, we successfully isolated two phages from the same sewage sample, and demonstrated that they had distinct biological and genomic characteristics.

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Biological and genomic characteristics of two bacteriophages isolated from sewage, using one multidrug-resistant and one non-multidrug-resistant strain of Klebsiella pneumoniae

http://sioc-journal.cn/Jwk_yjhx/EN/article/downloadArticleFile.do?attachType=PDF&id=349255

Direct Synthesis of 3-Sulfonylquinolines from N-Propargylanilines with Sulfonyl Chlorides

Genetic engineering of bacteriophages: Key concepts, strategies, and applications.

We read with interest the study by Kartal et al showing that the gutmicrobiotaderived biomarkers for disease stratification are often shared by subjects across disease cohorts. Here, we confirmed their observations with findings from a newly diagnosed natural killer/Tcell lymphoma (NKTCL) cohort, in which the gut biomarkers were significantly overlapped with those of multiple disease cohorts and consistently enriched/depleted in subjects with those diseases. Importantly, many of the shared biomarkers were remarkably associated with patient outcomes in our cohort, implying that they may have broad prognostic values in multiple diseases. ‘Microbiotagutlymphoma axis’ represents a fascinating avenue of microbiotamediated lymphomagenesis and intervention opportunity, but the implications of gut microbiota in NKTCL remain enigmatic. To identify gut microbiotaderived diagnostic biomarkers for NKTCL, we recruited a discovery cohort consisting of 30 treatmentnaïve patients and 20 healthy controls (HCs), and a validation cohort, including 12 patients and 13 HCs, respectively (online supplemental materials and methods). We applied shotgun metagenomic sequencing to their faecal samples, profiled their gut metagenomes using mOTUs2 V.2.5, and trained a patientstratification classifier with all specieslevel taxonomic features using the LASSO algorithm implemented in SIAMCAT. Our classifier achieved an accuracy of 0.868 area under the receiver operating characteristic curve (AUROC) on the discovery cohort, and 0.910 AUROC on the validation cohort (figure 1A). To increase the sample size for model training, we retrained a LASSO classifier for the NKTCL using all the samples from both cohorts, and achieved an accuracy of 0.813 AUROC in crossvalidation, which strongly support the role of gut microbiota as diagnostic biomarkers for NKTCL. To examine the specificity of the NKTCL gutmicrobiotaderived signature, we applied the allsample NKTCL classifier to 29 public gut microbiota cohorts (online supplemental table S1). We observed an overall false positive rate (FPR) of 3.1% in the HCs, but higher FPRs in patients of several cohorts (figure 1B), especially those of the pancreatic cancer (Kartal_ DE_2022_PC, Kartal_ES_2022_PC, Nagata_JP_2022_PC), Crohn’s Disease (He_2017_CD, Franzosa_2018_CD, Forslund_2015_CD) and liver disease (Qin_2014_LD). These results imply significant overlaps in the biomarkers between these diseases and NKTCL, which was confirmed using LEfSe analysis (figure 1C). Importantly, these biomarkers were consistently enriched/ depleted in most cohorts, including the enrichment of oralderived taxa of Veillonella and Streptococcus in the patients, and known beneficial species in HCs such as Faecalibacterium prausnitzii, Eubacterium rectale and Bifidobacterium adolescentis 6 7 (figure 1C). These findings indicate that our classifier can accurately distinguish NKTCL patients from HCs; nevertheless, due to the shared biomarkers with other diseases, combination of selected clinical indicators with microbial biomarkers would be salutary for a distinctive diagnostic model. Survival data were available for the NKTCL patients in the discovery cohort. Notably, many identified microbiome biomarkers, especially those shared by multiple diseases, could significantly predict the overall survival (OS) and progressionfree survival (PFS) of the patients, including Streptococcus parasanguinis, Romboutsia timonensis and Veillonella atypica (online supplemental figure 1A–D). Finally, we created a Streptococcus parasanguinis– Romboutsia timonensis index (SRI) as the relative abundance ratio of the two species, and obtained the best prognostic prediction power than other individual species and combinations. Namely, NKTCL patients with higher SRI scores showed significantly worse OS and PFS than those with lower SRI scores (figure 1D–E). Furthermore, we observed remarkable correlations between high SRI score and multiple adverse prognostic factors of NKTCL, including PINKE, stage, lymph node involvement and responses to firstline treatment (all p<0.05; figure 1F). Overall, our results lend support for gut microbiota as a potent assistive diagnostic tool for NKTCL. Moreover, the SRI score, based on the shared biomarkers, may have extensive prognostic utility in multiple diseases and deserves further scrutiny (online supplemental discussion). Zhuangzhuang Shi, Guoru Hu, Min W Li, Lei Zhang, Xin Li, Ling Li, Xinhua Wang, Xiaorui Fu, Zhenchang Sun, Xudong Zhang, Li Tian, Zhaoming Li, WeiHua Chen , Mingzhi Zhang Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China Department of Bioinformatics and Systems Biology, Huazhong University of Science and Technology College of Life Sciences and Technology, Wuhan, Hubei, China Lymphoma Diagnosis and Treatment Centre of Henan Province, Zhengzhou, Henan, China State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key Laboratory for Esophageal Cancer Research, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, Shandong, China College of Life Science, Henan Normal University, Xinxiang, Henan, China

https://gut.bmj.com/content/gutjnl/early/2022/11/08/gutjnl-2022-328256.full.pdf

Gut microbiota as non-invasive diagnostic and prognostic biomarkers for natural killer/T-cell lymphoma

Pathogenic strains of Escherichia coli are responsible for 0.8 million deaths per year and together ranked the first among all pathogenic species. Here, we obtained, for the first time, an engineered phage, Eλ, that could specifically and efficiently eliminate EHEC, one of the most common and often lethal pathogens that can spread from person to person. ABSTRACT Bacteriophages (phages) are ideal alternatives to traditional antimicrobial agents in a world where antimicrobial resistance (AMR) is emerging and spreading at an unprecedented speed. In addition, due to their narrow host ranges, phages are also ideal tools to modulate the gut microbiota in which alterations of specific bacterial strains underlie human diseases, while dysbiosis caused by broad-spectrum antibiotics can be harmful. Here, we engineered a lambda phage (Eλ) to target enterohemorrhagic Escherichia coli (EHEC) that causes a severe, sometimes lethal intestinal infection in humans. We enhanced the killing ability of the Eλ phage by incorporating a CRISPR-Cas3 system into the wild-type λ (wtλ) and the specificity by introducing multiple EHEC-targeting CRISPR spacers while knocking out the lytic gene cro. In vitro experiments showed that the Eλ suppressed the growth of EHEC up to 18 h compared with only 6 h with the wtλ; at the multiplicity of infection (MOI) of 10, the Eλ killed the EHEC cells with ~100% efficiency and did not affect the growth of other laboratory- and human-gut isolated E. coli strains. In addition, the EHEC cells did not develop resistance to the Eλ. Mouse experiments further confirmed the enhanced and strain-specific killing of the Eλ to EHEC, while the overall mouse gut microbiota was not disturbed. Our methods can be used to target other genes that are responsible for antibiotic resistance genes and/or human toxins, engineer other phages, and support in vivo application of the engineered phages. IMPORTANCE Pathogenic strains of Escherichia coli are responsible for 0.8 million deaths per year and together ranked the first among all pathogenic species. Here, we obtained, for the first time, an engineered phage, Eλ, that could specifically and efficiently eliminate EHEC, one of the most common and often lethal pathogens that can spread from person to person. We verified the superior performance of the Eλ over the wild-type phage with in vitro and in vivo experiments and showed that the Eλ could suppress EHEC growth to nondetectable levels, fully rescue the EHEC-infected mice, and rescore disturbed mouse gut microbiota. Our results also indicated that the EHEC did not develop resistance to the Eλ, which has been the biggest challenge in phage therapy. We believe our methods can be used to target other pathogenic strains of E. coli and support in vivo application of the engineered phages.

Guoru Hu

Papers

Gut microbiota as non-invasive diagnostic and prognostic biomarkers for natural killer/T-cell lymphoma

An Engineered λ Phage Enables Enhanced and Strain-Specific Killing of Enterohemorrhagic Escherichia coli

Total synthesis of bysspectin A