Spotlight pubs.acs.org/acschemicalbiology
■
GUT MICROBIOTA-MEDIATED METABOLISM REVIEWED
toxicology risk assessment, and improve drug discovery and development. Heidi A. Dahlmann
■
VANCOMYCIN ANALOGS RESIST BACTERIAL RESISTANCE
Adapted from Koppel et al., Science 2017, 356, eaag2770, doi: 10.1126/science.aag2770. Reprinted with permission from AAAS.
The study of gut microbiota-mediated metabolism of xenobiotics, which are molecules not produced in the human body, is one of today’s hottest research topics, spanning disciplines ranging from analytical chemistry to microbiology to toxicology. As early as the 1950s, scientists were aware that gut microbes were involved in the chemical transformation of ingested compounds. In the decades that followed, researchers gleaned information about the contributions of whole microbiomes as well as individual strains on metabolism of specific dietary compounds, environmental contaminants, and pharmaceuticals. However, piecing together the individual puzzle pieces to reveal the bigger picture of how the gut microbiome influences nutrition, disease risk, and drug efficacy remains a daunting task. A new review by Emily P. Balskus and coauthors provides an overview of the major “knowns” and “unknowns” in the field of gut microbiome-mediated xenobiotic metabolism (Science 2017, 356, eaag2770, DOI: 10.1126/science.aag2770). The authors discuss the main pathways of gut microbiota-mediated biotransformation, namely hydrolysis, nonhydrolytic or radicalbased bond cleavage, reduction, and functional group transfers; they also describe the common xenobiotic targets of these pathways, including industrial compounds such as azo dyes, melamine, and heavy metals and pharmaceuticals such as antiinflammatory agents, anticancer chemotherapeutics, and CNStargeting drugs. Microbe-mediated transformations of dietary components associated with human health are discussed, with questions raised about the specific enzymes involved in gluten, cholesterol, polyphenol, artificial sweetener, and heterocylic amine biotransformation and their potential role in influencing disease treatment. Finally, the authors elaborate on recent studies on the microbe-mediated biotransformation of the congestive heart medicine digoxin, the dietary compound choline, and the cancer chemotherapeutic irinotecan. The review ultimately informs the broader scientific community about how understanding gut microbiome-mediated xenobiotic metabolism can guide personalized medicine and nutrition, inform © 2017 American Chemical Society
Okano, A., et al., Proc. Natl. Acad. Sci., U.S.A., 114, E5052−E5061, DOI: 10.1073/pnas.1704125114. Copyright 2017 National Academy of Sciences, U.S.A.
Vancomycin is a powerful antibiotic that has been clinically administered for nearly 60 years. The peptidoglycan natural product binds to bacterial cell wall precursors containing D-AlaD-Ala, preventing a late-stage enzyme-mediated cross-linking reaction that helps form the cell wall. Because vancomycin targets a substrate rather than an enzyme and does not need to cross the cell wall to be active, bacteria are unable to develop resistance by common mechanisms such as enzyme mutation, upregulated efflux, or metabolic inactivation. In contrast, resistant bacteria utilize cell wall precursors containing D-Ala-D-Lac instead of D-Ala-D-Ala, which significantly reduces vancomycin’s substrate affinity and, consequently, potency against resistant strains. Researchers led by Dale L. Boger previously reported vancomycin analogs in which a carbonyl residue in the target binding pocket was switched to a methylene group, a swap that bestowed binding affinity for D-Ala-D-Lac without diminishing binding affinity for D-Ala-D-Ala. Subsequent studies indicated that the addition of a (4-chlorobiphenyl)methyl (CBP) group to vancomycin’s pendant disaccharide enhanced antimicrobial potency via a mechanism distinct from improved D-Ala-D-Ala and D-Ala-D-Ala binding. In a new study, Boger and co-workers investigated the effect of additional peripheral modifications to the methylene-containing vancomycin derivative on antimicrobial activity against vancomycin-resistant bacteria (Proc. Natl. Acad. Sci., U.S.A. 2017, 114, E5052−E5061; DOI: 10.1073/pnas.1704125114). They found that inclusion of a pendant quaternary ammonium Published: July 21, 2017 1716
DOI: 10.1021/acschembio.7b00574 ACS Chem. Biol. 2017, 12, 1716−1718
ACS Chemical Biology
■
salt improved activity by inducing membrane permeability, and that the enhancements provided by the pocket modification, the CBP group, and the quaternary ammonium salt were synergistic, resulting in a vancomycin analog that was greater than 10 000-fold more potent than vancomycin against vancomycin-resistant Enterococci. The research team also demonstrated that as the number of modifications with different modes of evading antibacterial resistance increased, the amount of time it took for sensitive strains to develop resistance also increased, prompting the authors to suggest that their multimode approach may provide antibiotics with extended clinical lifetimes that could match or exceed that of vancomycin itself. Heidi A. Dahlmann
■
Spotlight
MEASURING SENESCENCE TWO PHOTONS AT A TIME
Reprinted with permission from Lazano-Torres, et al., J. Am. Chem. Soc., 139, 8808−8811, DOI: 10.1021/jacs.7b04985. Copyright 2017 American Chemical Society.
REPEAT SEQUENCES INDUCE RNA FOCI FORMATION
The term “senescence” is derived from the Latin word that means “to grow old,” but cellular senescence is an irreversible arrest in growth that can occur from aging or other cellular stresses. A number of drug and genetic studies in mice have shown that selective destruction of senescent cells can reduce degenerative processes in the body and increase lifespan. These findings have led to increased interest in senolytics, pharmaceuticals to induce apoptosis in senescent cells. As this hunt for the proverbial fountain of youth in a pill continues, an additional challenge arises: how can you selectively visualize the senescent cells in living organisms? Lazano-Torres et al. (J. Am. Chem. Soc. 2017, DOI: 10.1021/ jacs.7b04985) recently presented a solution to this question by employing the ultrasensitive imaging properties of two-photon excitation microscopy. The researchers synthesized a novel probe compound, AHGa, with a feature inspired by the high levels of lysosomal β-galactosidase (β-Gal) found in senescent cells. They engineered AHGa to carry an N-glycosidic bond connecting galactose to the naphthalimide fluorophore. Upon hydrolysis of this bond by β-Gal, the fluorescence emission intensity was dramatically higher. They went on to use the new compound to visualize senescent cells in tissue culture and in mice carrying tumor xenografts. While cancer cells that were dividing normally were not readily visualized by AHGa, treatment with a drug that induces cell cycle arrest resulted in a bright signal from the cells. This study introduces yet another powerful use of two-photon fluorescence probes for in vivo monitoring of a biological phenomenon that is normally difficult to track and quantify. Jason G. Underwood
Reprinted by permission from Macmillan Publishers Ltd.: Nature Jain, A., and Vale, R. D., 546, 243−247, copyright 2017.
Many serious neurological and neuromuscular disorders, including Huntington’s disease, amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD), are characterized by the synthesis of repeated nucleotide triplets of high G/C content during transcription. Disease-causing repeats occur in both the coding or noncoding regions of RNA transcripts, and disease phenotypes typically emerge only when the repeats exceed a certain number of copies. One hypothesis to explain this phenomenon is that repeat-containing RNA form aberrant foci that sequester various RNA binding proteins in the nucleus. Recently, Howard Hughes Medical Institute researchers Ankur Jain and Ronald D. Vale experimentally explored the possibility that sequence-specific physicochemical properties of repeat-containing RNAs induce foci formation (Nature 2017, 546, 243−247). The research duo synthesized fluorescently labeled RNAs containing varying copies of repeats such as CAG and GGGGCC, which are associated with Huntington’s and ALS/FTD diseases, respectively. They found that intermolecular base pairing in G/C-rich repeat regions of RNA led to RNA gelation even in the absence of RNA-binding proteins. Foci formation also occurred in cells induced to transcribe the repeat sequences, while foci formation could be disrupted both in vitro and in cells with agents that interfere with nucleic acid base-pairing. The authors suggest that foci formed by repeat expansions in seemingly unrelated genes may be responsible for the development of similar physiological effects across different clinical syndromes, and they note that disruption of RNA− RNA base-pairing may work for treating repeat expansion diseases. Heidi A. Dahlmann
■
PROGRAMMING RIPPS TO PRODUCE NON-NATURAL PRODUCTS
Reprinted with permission from Burkhart, B. J., et al., ACS Cent. Sci., DOI: 10.1021/acscentsci.7b00141. Copyright 2017 American Chemical Society. 1717
DOI: 10.1021/acschembio.7b00574 ACS Chem. Biol. 2017, 12, 1716−1718
ACS Chemical Biology
Spotlight
One strategy for overcoming the obstacles in organic synthesis is to modify biosynthetic pathways to produce molecules of interest. In the latest twist on this idea, Burkhart et al. have developed novel, chimeric ribosomally synthesized and posttranslationally modified peptides (RiPPs) to produce new nonnatural products (ACS. Cent. Sci., 2017, DOI: 10.1021/ acscentsci.7b00141). Biology provides a range of valuable molecular templates and enzymatic tools for producing natural products and related compounds in high yields, but it is often hard to program in the desired chemistries. In recent decades, researchers have explored biosynthetic pathways such as modified polyketide synthesis and nonribosomal peptide synthesis to produce complex organic products, with limited success. Another potential biosynthetic platform is RiPPs, which are genetically encoded with a leader sequence and a core peptide sequence. After translation, the leader sequence is bound by enzymes, which then modify the core sequence of the peptides in a variety of ways. In nature, RiPPs generate complex chemical functionalities including azoline heterocycles, many types of macrocycles, D-amino acids, as well as a variety of other modifications. In this study, the team rationally engineered hybrid RiPPs to allow for modifications by enzymes from different pathways on the same core peptide. Initially, they modified the peptide leader sequence so that it was recognized by enzymes from two different pathways and optimized the spacing between the recognition and substrate components. The initial combination of enzymes was designed to install a thiazoline, a heterocyclic modification, with other RiPP modifications such as thioether cross-links to create hybrid peptide structures that have not been reported in natural RiPP products. They tested their system by expressing the precursor peptide and the modifying enzymes in E. coli. The team also designed various core peptides that could be modified by the same combinations of enzymes to produce different products. Finally, they demonstrated that they could also use secondary tailoring enzymes that install bioactive groups such as D-alanine subsequent to the primary RiPP modifications. Their overall strategy produces hybrid RiPPs in moderate yields (1 mg/L of culture) and points to the potential of combinatorial biosynthesis with RiPPs. Sarah A. Webb
1718
DOI: 10.1021/acschembio.7b00574 ACS Chem. Biol. 2017, 12, 1716−1718
