Hoffman, C. S. | Search bioRxiv

bioRxiv2024

Age-related increases in PDE11A4 protein expression trigger liquid:liquid phase separation (LLPS) of the enzyme that can be reversed by PDE11A4 small molecules inhibitors

PDE11A is a little-studied phosphodiesterase sub-family that breaks down cAMP/cGMP, with the PDE11A4 isoform being enriched in the memory-related brain region called the hippocampus. Age-related increases in PDE11A expression occur in human and rodent hippocampus and cause age-related cognitive decline of social memories. Interestingly, the age-related increase in PDE11A4 protein ectopically accumulates in spherical clusters that group together in the brain to form linear filamentous patterns termed "ghost axons." The biophysical/physiochemical mechanisms underlying this age-related clustering of PDE11A4 are not yet known. As such, we determine here if age-related clustering of PDE11A4 may reflect liquid:liquid phase separation (LLPS), and if PDE11A inhibitors being developed for age-related cognitive decline can reverse this biomolecular condensation. We found that human and mouse PDE11A4 exhibit several LLPS-promoting sequence features including intrinsically disordered regions, non-covalent pi-pi interactions, and prion-like domains, with multiple bioinformatic tools predicting PDE11A4 undergoes LLPS. Consistent with these predictions, age-related PDE11A4 clusters were non-membrane bound spherical droplets that progressively fuse over time in a concentration-dependent manner. 5 different PDE11 inhibitors (tadalafil, BC11-38, SMQ-02-57, SMQ-03-30 and SMQ-03-20) across 3 scaffolds reversed PDE11A4 LLPS (a.k.a. remixing) in hippocampal HT22 cells, with PDE11A4 droplets reforming (a.k.a. de-mixing) following a 5-hour washout of low but not high concentrations of these compounds. Strikingly, a single oral administration of 30 mg/kg SMQ-03-20 substantially reduced the presence of PDE11A4 ghost axon in the aged mouse brain. Thus, PDE11A4 exhibits 4 defining criteria of LLPS, and PDE11A small molecule inhibitors reverse this age-related phenotype both in vitro and in vivo.

neuroscience↗

bioRxiv2023

Evaluation of Known Human PDE Inhibitors Against Nematode PDE4s

Parasitic nematodes are responsible for more than one and a half billion infections world-wide. The drugs developed against these infections only target a few different proteins. As drug resistance is becoming more common, there is a need to develop new drugs against new targets. Cyclic Nucleotide Phosphodiesterases (PDEs), are enzymes that hydrolyze the cyclic molecules of cyclic AMP and cyclic GMP. Physical properties of mammalian PDEs have led them to become well-established as drug targets. Mammals possess 11 families of PDEs, many of which are the target of selective and potent drugs. Nematodes have 6 PDE genes representing 6 families, which have not been well-studied; C. elegans, is a model organism nematode that would allow people to assess the therapeutic benefit of targeting PDEs. The Hoffman Lab has developed a platform for discovering PDE inhibitors and has carried out high-throughput screens (HTS) to help identify inhibitors of mammalian PDE4, PDE7, PDE8, and PDE11 families. The PDE4 family in C. elegans is of particular interest as work in C. elegans suggests that it may be involved in neuronal function. However, research has shown that two compounds developed against mammalian PDE4s generally do not work on C. elegans PDE4. Therefore, the goal of this project is to screen a collection of compounds discovered by the Hoffman Lab to identify the compounds that will affect C. elegans or parasitic nematode PDE4s to find compounds that could then be tested for their effect on C. elegans and parasitic nematodes. This research could then identify an effective new target for drug development to treat infections by parasitic nematodes. SummaryParasitic nematodes are the soil worms responsible for more than one and a half billion infections around the world. While drugs are being developed against them, these drugs are designed against relatively few proteins, which is a problem as drug resistance becomes more common. Therefore, there is a need for new drugs. PDEs are enzymes that hydrolyze the signaling molecules cAMP and cGMP. Mammalian PDEs have been well-established as drug targets. In nematodes, there are 6 PDE genes representing 6 families of the 11 families found in mammals. Additionally, a free-living model organism nematode, Caenorhabditis elegans (C. elegans) can be used to assess the impact of PDE inhibition on nematode biology. In the Hoffman Lab, they have developed a platform for discovering PDE inhibitors and have used these in high throughput screens to identify inhibitors of mammalian PDE4, PDE7, PDE8, and PDE11 families. The PDE4 family in C. elegans is of particular interest as work in C. elegans suggests that it may be involved in neuronal function. However, research has shown that compounds developed against mammalian PDE4s generally do not work on C. elegans PDE4. Therefore, by the end of this project we hope to identify the compounds that do work on nematode PDE4s that could be used to test whether they have the potential to treat these infections.

microbiology↗