Targeting Mycobacterium tuberculosis Persistence through Inhibition of the Trehalose Catalytic Shift

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is the leading cause of death worldwide by infectious disease. Treatment of Mtb infection requires a six-month course of multiple antibiotics, an extremely challenging regimen necessitated by Mtb's ability to form drug-tolerant persister cells. Mtb persister formation is dependent on the trehalose catalytic shift, a stress-responsive metabolic remodeling mechanism in which the disaccharide trehalose is liberated from cell surface glycolipids and repurposed as an internal carbon source to meet energy and redox demands. Here, using a biofilm-persister model, metabolomics, and cryo-electron microscopy (EM), we found that azidodeoxy- and aminodeoxy-d-trehalose analogues block the Mtb trehalose catalytic shift through inhibition of trehalose synthase TreS (Rv0126), which catalyzes the isomerization of trehalose to maltose. Out of a focused eight-member compound panel constructed by chemoenzymatic synthesis, the natural product 2-trehalosamine exhibited the highest potency and significantly potentiated first- and second-line TB drugs in broth culture and macrophage infection assays. We also report the first structure of TreS bound to a substrate analogue inhibitor, obtained via cryo-EM, which revealed conformational changes likely essential for catalysis and inhibitor binding that can potentially be exploited for future therapeutic development. Our results demonstrate that inhibition of the trehalose catalytic shift is a viable strategy to target Mtb persisters and advance trehalose analogues as tools and potential adjunctive therapeutics for investigating and targeting mycobacterial persistence.

Azido Inositol Probes Enable Metabolic Labeling of Inositol-Containing Glycans and Reveal an Inositol Importer in Mycobacteria

Bacteria from the genus Mycobacterium include pathogens that cause serious diseases in humans and remain as difficult infectious agents to treat. Central to these challenges are the composition and organization of the mycobacterial cell envelope, which includes unique and complex glycans. Inositol is an essential metabolite for mycobacteria due to its presence in the structural core of the immunomodulatory cell envelope glycolipids phosphatidylinositol mannoside (PIM) and PIM-anchored lipomannan (LM) and lipoarabinomannan (LAM). Despite their importance to mycobacterial physiology and pathogenesis, many aspects of PIM, LM, and LAM construction and dynamics remain poorly understood. Recently, probes that allow metabolic labeling and detection of specific mycobacterial glycans have been developed to investigate cell envelope assembly and dynamics. However, these tools have been limited to peptidoglycan, arabinogalactan, and mycolic acid-containing glycolipids. Herein, we report the development of synthetic azido inositol (InoAz) analogues as probes that can metabolically label PIMs, LM, and LAM in intact mycobacteria. Additionally, we leverage an InoAz probe to discover an inositol importer and catabolic pathway in Mycobacterium smegmatis. We anticipate that in the future, InoAz probes, in combination with bioorthogonal chemistry, will provide a valuable tool for investigating PIM, LM, and LAM biosynthesis, transport, and dynamics in diverse mycobacterial organisms.

The role of chemoenzymatic synthesis in advancing trehalose analogues as tools for combatting bacterial pathogens

Trehalose, a disaccharide of glucose, is increasingly recognized as an important contributor to virulence in major bacterial pathogens, such as Mycobacterium tuberculosis, Clostridioides difficile, and Burkholderia pseudomallei. Accordingly, bacterial trehalose metabolic pathways that are not present in humans have gained traction as targets for antibiotic and diagnostic development. Toward this goal, trehalose can be modified through a combination of rational design and synthesis to produce functionalized trehalose analogues, which can be deployed to probe or inhibit bacterial trehalose metabolism. However, the unique α,α-1,1-glycosidic bond and C2 symmetry of trehalose make analogue synthesis via traditional chemical methods very challenging. We and others have turned to the creation of chemoenzymatic synthesis methods, which in principle allow the use of nature's trehalose-synthesizing enzymes to stereo- and regioselectively couple simple, unprotected substrates to efficiently and conveniently generate trehalose analogues. Here, we provide a contextual account of our team's development of a trehalose analogue synthesis method that employs a highly substrate-tolerant, thermostable trehalose synthase enzyme, TreT from Thermoproteus tenax. Then, in three vignettes, we highlight how chemoenzymatic synthesis has accelerated the development of trehalose-based imaging probes and inhibitors that target trehalose-utilizing bacterial pathogens. We describe the role of TreT catalysis and related methods in the development of (i) tools for in vitro and in vivo imaging of mycobacteria, (ii) anti-biofilm compounds that sensitize drug-tolerant mycobacteria to clinical anti-tubercular compounds, and (iii) degradation-resistant trehalose analogues that block trehalose metabolism in C. difficile and potentially other trehalose-utilizing bacteria. We conclude by recapping progress and discussing priorities for future research in this area, including improving the scope and scale of chemoenzymatic synthesis methods to support translational research and expanding the functionality and applicability of trehalose analogues to study and target diverse bacterial pathogens.

Validamycin A Delays Development and Prevents Flight in Aedes aegypti (Diptera: Culicidae)

Trehalose is a disaccharide that is the major sugar found in insect hemolymph fluid. Trehalose provides energy, and promotes growth, metamorphosis, stress recovery, chitin synthesis, and insect flight. The hydrolysis of trehalose is under the enzymatic control of the enzyme trehalase. Trehalase is critical to the role of trehalose in insect physiology, and is required for the regulation of metabolism and glucose generation. Trehalase inhibitors represent a novel class of insecticides that have not been fully developed. Here, we tested the ability of trehalose analogues to function as larvacides or adulticides in an important disease vector-Aedes aegypti. We show that validamycin A, but not 5-thiotrehalose, delays larval and pupal development and prevents flight of adult mosquitoes. Larval mosquitoes treated with validamycin A were hypoglycemic and pupae had increased levels of trehalose. Treatment also skewed the sex ratio toward male mosquitoes. These data reveal that validamycin A is a mosquito adulticide that can impair normal development of an important disease vector.

Degradation-resistant trehalose analogues block utilization of trehalose by hypervirulent Clostridioides difficile

Trehalose is used as an additive in thousands of foods, cosmetics, and pharmaceutical products, and it is being investigated as a therapeutic for multiple human diseases. However, its ability to be used as a carbon source by microbes is a concern, as highlighted by the recent finding that trehalose can be metabolized by and potentially enhance the virulence of epidemic Clostridioides difficile. Here, we show that trehalose analogues designed to resist enzymatic degradation are incapable of being used as carbon sources by C. difficile. Furthermore, we demonstrate that trehalose analogues, but not the known trehalase inhibitor validamycin A, inhibit native trehalose utilization by hypervirulent C. difficile. Thus, degradation-resistant trehalose analogues are valuable as trehalase inhibitors and as surrogates for or co-additives with trehalose in applications where enzymatic breakdown is a concern.