The most popular PDEs are PDE5. Since cGMP produced by activation of this cell signalling pathway is central to a lot of physiological processes, PDE5 inhibition has been shown to exert a multitude of therapeutic roles, from erectile dysfunction to pulmonary hypertension. These inhibitors are designed to inhibit PDE5, but they are not as selective or affine as each isoform of PDE. They also induce allosteric protein structure changes. They are mainly due to their chemical arrangement and hence the binding activity with the PDE catalytic domain. This is why, in order to develop new, very selective PDE5 inhibitors, it’s important to know how these inhibitors affect PDE5 and the structural basis of their selectivity.
Phylogenetic and Regulatory Structures of PDE5
PDE5 is a complex protein with two different domains: regulatory and catalytic. The N-terminal regulatory domain has two tandem GAF (GAFa and GAFb) domains, which assist in the catalytic activity as well as in the dimerisation of the protein. PDE5’s regulatory GAF domain belongs to a family of regulatory domains that are shared by a variety of proteins including some PDEs, adenylate cyclases and transcription factors. PDE5’s unliganded GAFa domain is highly porous, and indeed can go through major conformational changes under cGMP. Not only does PDE5 contain a GAF domain, but its N-terminal regulatory region also includes a cGMP-regulated protein kinase (PKG) phosphorylation site conserved between all three PDE5 isoforms (PDE5A1, PDE5A2 and PDE5A3). This is the main characteristic of the PDE5 catalytic field: metal ions, which PDE must be able to carry out, are bound.
PDE5 Inhibitors
These competing PDE5 inhibitors that we have seen so far only bind to the catalytic domain and prevent cGMP (substrate) binding and catalysis. This inhibition results in cGMP buildup in cells across multiple tissues and has multiple therapeutic effects. The shape of the inhibitor, too, adjusts to match the active site and therefore becomes more bound to it.
Sildenafil
Sildenafil works on the catalytic domain by means of the Q pocket, H pocket, and L region. It doesn’t work directly with the M subsite. The amide chain of the pyrazolopyrimidinone moiety of sildenafil bonds to the side chain amide sequence of the conserved Gln817 via bidentate hydrogen bonds. Sildenafil methylpiperazine atom is linked to the L part of the active site and exposed on the protein surface. It hydrophobes with unprotected non-polar residues here, another reason sildenafil is not as PDE5-selective as it could be.
Vardenafil
Vardenafil is a stronger and more selective PDE5 inhibitor than sildenafil. It is at least 20 times more favorable to the enzyme than sildenafil. Given the heterocyclic ring arrangement difference, one can hypothesize that vardenafil has more and/or stronger binding (i.e., hydrogen bonding and stacking) with residues in the Q pocket through its heterocyclic rings. The Q pocket part of the inhibitor might be used as a scaffold for the construction of selective and effective inhibitors.
Tadalafil
Tadalafil is 200-600 times more bound to PDE5 than to PDE6, so it’s more selective than sildenafil or vardenafil. The methylenedioxyphenyl group of tadalafil fits into the H pocket and has vast hydrophobic contacts with its residues (which is why tadalafil is very selective even though it does not have any contact with the L region). PDE5 phosphorylation makes tadalafil more easily bindable, independent of cGMP allosteric binding, and more powerful.
Avanafil
PDE isoform selectivity and side effects for Avanafil are better. Avanafil acts as a competitive inhibitor of PDE5 by binding to residues that are not conserved between PDE isoforms, hence why it is selective for PDE5.
PDE5 Can Be a Target for Multiple Drug Inhibitors
PDE5 is involved in many of the cGMP-mediated physiological functions and there are many different regulatory mechanisms, from allosteric structural modifications to post-translational changes such as phosphorylation. PDE5 has been used as a target for several drug inhibitors in a number of diseases from erectile dysfunction to pulmonary hypertension. PDE5 inhibitors could be used to treat various cancers, by altering the NO-cGMP-PDE5 axis, and so they could be used as side effects for COVID-19 infection. However clinical trials are still needed to expand the therapeutic spectrum of these inhibitors to include more diseases. Furthermore, there is still a lot of ground to be filled on allosteric regulation of PDE5, specifically with drugs that might be able to adjust its activities tissue- and disease-specifically.
References
- Ahmed, Wesam S., et al. Phosphodiesterase 5 (PDE5): Structure-function regulation and therapeutic applications of inhibitors. Biomedicine & Pharmacotherapy. 2021, 134: 111128.
- Samidurai, A., et al. Beyond erectile dysfunction: cGMP-specific phosphodiesterase 5 inhibitors for other clinical disorders. Annual review of pharmacology and toxicology. 2023, 63(1): 585-615.
