Antibacterial Strategy against H. pylori: Inhibition of the Radical SAM Enzyme MqnE in Menaquinone Biosynthesis

Resolving the Multidecade-Long Mystery in MoaA Radical SAM Enzyme Reveals New Opportunities to Tackle Human Health Problems

MoaA is one of the most conserved radical S-adenosyl-l-methionine (SAM) enzymes, and is found in most organisms in all three kingdoms of life. MoaA contributes to the biosynthesis of molybdenum cofactor (Moco), a redox enzyme cofactor used in various enzymes such as purine and sulfur catabolism in humans and anaerobic respiration in bacteria. Unlike many other cofactors, in most organisms, Moco cannot be taken up as a nutrient and requires de novo biosynthesis. Consequently, Moco biosynthesis has been linked to several human health problems, such as human Moco deficiency disease and bacterial infections. Despite the medical and biological significance, the biosynthetic mechanism of Moco’s characteristic pyranopterin structure remained elusive for more than two decades. This transformation requires the actions of the MoaA radical SAM enzyme and another protein, MoaC. Recently, MoaA and MoaC functions were elucidated as a radical SAM GTP 3′,8-cyclase and cyclic pyranopterin monophosphate (cPMP) synthase, respectively. This finding resolved the key mystery in the field and revealed new opportunities in studying the enzymology and chemical biology of MoaA and MoaC to elucidate novel mechanisms in enzyme catalysis or to address unsolved questions in Moco-related human health problems. Here, we summarize the recent progress in the functional and mechanistic studies of MoaA and MoaC and discuss the field’s future directions.

Selective Transformations of Carbohydrates Inspired by Radical-Based Enzymatic Mechanisms

Enzymes are a longstanding source of inspiration for synthetic reaction development. However, enzymatic reactivity and selectivity are frequently untenable in a synthetic context, as the principles that govern control in an enzymatic setting often do not translate to small molecule catalysis. Recent synthetic methods have revealed the viability of using small molecule catalysts to promote highly selective radical-mediated transformations of minimally protected sugar substrates. These transformations share conceptual similarities with radical SAM enzymes found in microbial carbohydrate biosynthesis and present opportunities for synthetic chemists to access microbial and unnatural carbohydrate building blocks without the need for protecting groups or lengthy synthetic sequences. Here, we highlight strategies through which radical reaction pathways can enable the site-, regio-, and diastereoselective transformation of minimally protected carbohydrates in both synthetic and enzymatic systems.

A review on the structures and biological activities of anti-Helicobacter pylori agents

Helicobacter pylori is one of the main causal risk factor in the generation of chronic gastritis, gastroduodenal ulcers and gastric carcinoma. Thus, the eradication of H. pylori infection is an important way for preventing and managing the gastric diseases. Multiple-therapy with several antibacterial agents is used for the eradication of H. pylori infections; however the increase of resistance to H. pylori strains has resulted in unsatisfactory eradication and unsuccessful treatment. Furthermore, the combination therapy with high dosing leads to the disruption of intestinal microbial flora and undesired side effects. Therefore, the search for new therapeutic agents with high selectivity against H. pylori is a field of current interest. In recent years, diverse compounds originating from natural sources or synthetic drug design programs were evaluated and tried to optimize for applying against H. pylori. In this review, we have described various classes of anti-H. pylori compounds, their structure-activity relationship studies, and mechanism of actions, which could be useful for the development of new drugs for the treatment of H. pylori infections.

Menaquinone Biosynthesis: The Mechanism of 5,8-Dihydroxy-2-naphthoate Synthase (MqnD)

MqnD catalyzes the conversion of cyclic dehypoxanthine futalosine (6) to 5,8-dihydroxy-2-naphthoic acid (7) and an uncharacterized product. This study describes a chemoenzymatic synthesis of 6. This synthesis achieved a 2-fold yield enhancement by using titanium(III) citrate as the reducing agent and another 5-fold yield enhancement using a fluorinated analogue of dehypoxanthine futalosine (5) that was converted to 6 by an ipso substitution mechanism. This synthetic route enabled the synthesis of 6 in sufficient quantity to identify the second reaction product and to determine that the MqnD-catalyzed reaction proceeds by a hemiacetal ring opening-tautomerization-retroaldol sequence.

Menaquinone Biosynthesis: New Strategies to Trap Radical Intermediates in the MqnE-Catalyzed Reaction

Aminofutalosine synthase (MqnE) is a radical SAM enzyme that catalyzes the conversion of 3-((1-carboxyvinyl)oxy)benzoic acid to aminofutalosine during the futalosine-dependent menaquinone biosynthesis. In this Communication, we report the trapping of a radical intermediate in the MqnE-catalyzed reaction using sodium dithionite, molecular oxygen, or 5,5-dimethyl-1-pyrroline-N-oxide. These radical trapping strategies are potentially of general utility in the study of other radical SAM enzymes.

Characterization and Mechanistic Study of the Radical SAM Enzyme ArsS Involved in Arsenosugar Biosynthesis

Arsenosugars are a group of arsenic-containing ribosides that are found predominantly in marine algae but also in terrestrial organisms. It has been proposed that arsenosugar biosynthesis involves a key intermediate 5'-deoxy-5'-dimethylarsinoyl-adenosine (DDMAA), but how DDMAA is produced remains elusive. Now, we report characterization of ArsS as a DDMAA synthase, which catalyzes a radical S-adenosylmethionine (SAM)-mediated alkylation (adenosylation) of dimethylarsenite (DMAs^III ) to produce DDMAA. This radical-mediated reaction is redox neutral, and multiple turnover can be achieved without external reductant. Phylogenomic and biochemical analyses revealed that DDMAA synthases are widespread in distinct bacterial phyla with similar catalytic efficiencies; these enzymes likely originated from cyanobacteria. This study reveals a key step in arsenosugar biosynthesis and also a new paradigm in radical SAM chemistry, highlighting the catalytic diversity of this superfamily of enzymes.

Helicobacter pylori treatment in the post-antibiotics era-searching for new drug targets

Abstract

Helicobacter pylori, a member of Epsilonproteobacteria, is a Gram-negative microaerophilic bacterium that colonizes gastric mucosa of about 50% of the human population. Although most infections caused by H. pylori are asymptomatic, the microorganism is strongly associated with serious diseases of the upper gastrointestinal tract such as chronic gastritis, peptic ulcer, duodenal ulcer, and gastric cancer, and it is classified as a group I carcinogen. The prevalence of H. pylori infections varies worldwide. The H. pylori genotype, host gene polymorphisms, and environmental factors determine the type of induced disease. Currently, the most common therapy to treat H. pylori is the first line clarithromycin–based triple therapy or a quadruple therapy replacing clarithromycin with new antibiotics. Despite the enormous recent effort to introduce new therapeutic regimens to combat this pathogen, treatment for H. pylori still fails in more than 20% of patients, mainly due to the increased prevalence of antibiotic resistant strains. In this review we present recent progress aimed at designing new anti-H. pylori strategies to combat this pathogen. Some novel therapeutic regimens will potentially be used as an extra constituent of antibiotic therapy, and others may replace current antibiotic treatments.

Key points

• Attempts to improve eradication rate of H. pylori infection.

• Searching for new drug targets in anti-Helicobacter therapies.

Study on the Effect of Capsaicin on the Intestinal Flora through High-Throughput Sequencing

As a common kind of food, pepper is well known for its special effects on the physiological state of human individuals. Capsaicin, the main component of pepper, is speculated to be linked with intestinal microorganisms on account of their direct contact. Herein, we first utilized mouse models and 16S rRNA high-throughput sequencing to compare the differences in intestinal flora between mouse groups with and without capsaicin treatment by gavage. The mice in the two groups showed significantly distinct performance in terms of body weight, leukocyte count, fecal humidity, and constituent ratios of intestinal bacteria, such as Faecalibacterium, Akkermansia, Roseburia, Helicobacter, and Bacteroides species. In particular, the Faecalibacterium abundance was the most highly variable among the 5 bacterial genera. Based on statistical analysis and comparison, the variation tendency of body weight, leukocyte count, and fecal humidity was closely related to the bacteria. In conclusion, capsaicin could affect the physiological state of mice by changing the constitution of the intestinal flora.