Gut Microbial ß-Glucuronidase Inhibition via Catalytic Cycle Interception.

Microbial ß-glucuronidases (GUSs) cause severe gut toxicities that limit the efficacy of cancer drugs and other therapeutics. Selective inhibitors of bacterial GUS have been shown to alleviate these side effects. Using structural and chemical biology, mass spectrometry, and cell-based assays, we establish that piperazine-containing GUS inhibitors intercept the glycosyl-enzyme catalytic intermediate of these retaining glycosyl hydrolases. We demonstrate that piperazine-based compounds are substrate-dependent GUS inhibitors that bind to the GUS-GlcA catalytic intermediate as a piperazine-linked glucuronide (GlcA, glucuronic acid). We confirm the GUS-dependent formation of inhibitor-glucuronide conjugates by LC-MS and show that methylated piperazine analogs display significantly reduced potencies. We further demonstrate that a range of approved piperazine- and piperidine-containing drugs from many classes, including those for the treatment of depression, infection, and cancer, function by the same mechanism, and we confirm through gene editing that these compounds selectively inhibit GUS in living bacterial cells. Together, these data reveal a unique mechanism of GUS inhibition and show that a range of therapeutics may impact GUS activities in the human gut.

Structure-activity relationships and cellular mechanism of action of small molecules that enhance the delivery of oligonucleotides.

The pharmacological effects of antisense and siRNA oligonucleotides are hindered by the tendency of these molecules to become entrapped in endomembrane compartments thus failing to reach their targets in the cytosol or nucleus. We have previously used high throughput screening to identify small molecules that enhance the escape of oligonucleotides from intracellular membrane compartments and have termed such molecules OECs (oligonucleotide enhancing compounds). Here, we report on the structure-activity relationships of a family of OECs that are analogs of a hit that emerged from our original screen. These studies demonstrate key roles for the lipophilic aromatic groups, the tertiary nitrogen, and the carbamate moiety of the parent compound. We have also investigated the intracellular site of action of the OECs and have shown that activity is due to the release of oligonucleotides from intermediate endosomal compartments rather than from early endosomes or from highly acidic downstream compartments. At high concentrations of OECs toxicity occurs in a manner that is independent of caspases or of lysosomal cathepsins but instead involves increased plasma membrane permeability. Thus, in addition to describing specific characteristics of this family of OECs, the current study provides insights into basic mechanisms of oligonucleotide trafficking and their implications for oligonucleotide delivery.

A Novel Family of Small Molecules that Enhance the Intracellular Delivery and Pharmacological Effectiveness of Antisense and Splice Switching Oligonucleotides.

The pharmacological effectiveness of oligonucleotides has been hampered by their tendency to remain entrapped in endosomes, thus limiting their access to cytosolic or nuclear targets. We have previously reported a group of small molecules that enhance the effects of oligonucleotides by causing their release from endosomes. Here, we describe a second novel family of oligonucleotide enhancing compounds (OECs) that is chemically distinct from the compounds reported previously. We demonstrate that these molecules substantially augment the actions of splice switching oligonucleotides (SSOs) and antisense oligonucleotides (ASOs) in cell culture. We also find enhancement of SSO effects in a murine model. These new compounds act by increasing endosome permeability and causing partial release of entrapped oligonucleotides. While they also affect the permeability of lysosomes, they are clearly different from typical lysosomotropic agents. Current members of this compound family display a relatively narrow window between effective dose and toxic dose. Thus, further improvements are necessary before these agents can become suitable for therapeutic use.

Multicomponent decarboxylative allylations.

The reaction of Meldrum's acid, pyrrolide, and allyl carbonates allows a multicomponent decarboxylative coupling to form allylated acyl pyrroles. This strategy is made possible by the in situ formation of ß-oxo carboxylates from Meldrum's acid. Subsequent decarboxylative enolate formation and electrophilic allylation complete the reaction. Addition of benzylidene malononitriles as good Michael acceptors allow a 4-component interceptive decarboxylative allylation.

Decarboxylative allylations of ester enolate equivalents.

A variety of ester enolate equivalents are generated in situ and undergo α-allylation in high yields via palladium-catalyzed decarboxylative allylation. The transformations are complete within very short reaction times under ambient conditions. Synthesis of α-allylated acyl derivatives provides access to other carboxylic acid and alcohol derivatives via acyl group substitution or reduction.

Decarboxylative benzylations of alkynes and ketones.

Benzyl esters of propiolic and beta-keto acids undergo catalytic decarboxylative coupling when treated with appropriate palladium catalysts. Such decarboxylative couplings allow the benzylation of alkynes without the use of strong bases and/or organometallics. This allows the synthesis of sensitive benzylic alkynes that are prone to undergo isomerizations under basic conditions. Additionally, decarboxylation facilitates the site-specific benzylation of diketones and ketoesters under mild, base-free conditions. Ultimately, the methodology described expands our ability to cross-couple medicinally relevant heterocycles.

Total synthesis of the putative structure of lucentamycin A.

A rapid and stereoselective enolate-Claisen rearrangement provides access to the 4-ethylidene-3-methylproline (Emp) subunit of lucentamycin A. Synthesis of the putative structure of the cytotoxic natural product suggests the need for structural revision.